記述言語：英語   掲載種別：研究論文（学術雑誌）  

Reduced-representation sequencing (RRS) provides cost-effective and time-saving genotyping platforms. Despite the outstanding advantage of RRS in throughput, the obtained genotype data usually contain a large number of errors. Several error correction methods employing the hidden Markov model (HMM) have been developed to overcome these issues. These methods assume that markers have a uniform error rate with no bias in the allele read ratio. However, bias does occur because of uneven amplification of genomic fragments and read mismapping. In this paper, we introduce an error correction tool, GBScleanR, which enables robust and precise error correction for noisy RRS-based genotype data by incorporating marker-specific error rates into the HMM. The results indicate that GBScleanR improves the accuracy by more than 25 percentage points at maximum compared to the existing tools in simulation data sets and achieves the most reliable genotype estimation in real data even with error-prone markers.

DOI： 10.1093/genetics/iyad055

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1016/j.fcr.2022.108725

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担当区分：最終著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

Phenotypic differences among breeding lines that introduce the same superior gene allele can be a barrier to effective development of cultivars with desirable traits in some crop species. For example, a deficient mutation of the Protein Disulfide Isomerase Like 1-1 (PDIL1-1) gene can cause accumulation of glutelin seed storage protein precursors in rice endosperm, and improves rice flour characteristics and food processing properties. However, the gene must be expressed to be useful. A deficient mutant allele of PDIL1-1 was introduced into two rice cultivars with different genetic backgrounds (Koshihikari and Oonari). The grain components, agronomic traits, and rice flour and food processing properties of the resulting lines were evaluated. The two breeding lines had similar seed storage protein accumulation, amylose content, and low-molecular-weight metabolites. However, only the Koshihikari breeding line had high flour quality and was highly suitable for rice bread, noodles, and sponge cake, evidence of the formation of high-molecular-weight protein complexes in the endosperm. Transcriptome analysis revealed that mRNA levels of fourteen PDI, Ero1, and BiP genes were increased in the Koshihikari breeding line, whereas this change was not observed in the Oonari breeding line. We elucidated part of the molecular basis of the phenotypic differences between two breeding lines possessing the same mutant allele in different genetic backgrounds. The results suggest that certain genetic backgrounds can negate the beneficial effect of the PDIL1-1 mutant allele. Better understanding of the molecular basis for such interactions may accelerate future breeding of novel rice cultivars to meet the strong demand for gluten-free foods.

DOI： 10.1186/s12284-022-00560-w

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1016/j.rsci.2021.05.009

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記述言語：日本語   掲載種別：研究論文（学術雑誌）   出版者・発行元：日本育種学会  

<p>イネでは，毎年多くの収量関連遺伝子単離の論文が公表されるが，実際の育種に応用されているものは必ずしも多くない．そこで，日本のイネ品種を遺伝的背景とした収量に関連する9の対立遺伝子について，準同質遺伝子系統を収集・作出し，背景品種との比較試験を実施した．粗玄米重の増加が確認されたものは「コシヒカリ」の遺伝的背景にqCTd11^Takanari，SD1^DGWG，TGW6^KasalathとSD1^DGWGの2つの対立遺伝子を導入した系統および「あきだわら」の遺伝的背景にDEP1^Ballilaを導入した系統であった．これらの対立遺伝子やQTLは，遺伝的背景が日本の品種の場合でも収量を向上させるポテンシャルが期待できる．一方で，「コシヒカリ」の遺伝的背景にqLIA3^Takanari，GPS^Takanari，GS3^Oochikara，GW2^BG1およびGN1A^Takanariを導入した系統では粗玄米重の増加が確認できなかった．これらの対立遺伝子やQTLは，単独ではその効果が小さかったり，シンク容量が大きくなりすぎてソース能が不十分である等の可能性が示唆された．また，「コシヒカリ」を遺伝的背景とした複数の準同質遺伝子系統を用いた試験では，穂重と穂数の負の相関が検出された．これは，シンク容量の増加が期待されたGW2^BG1およびGS3^Oochikara（粒大の増加）やGN1A^Takanari（粒数の増加）の多収化の効果が確認できなかった主要な要因と推察された．シンク容量の増加だけでは多収化は達成できず，qCTd11^Takanariのように単位葉面積あたりの光合成能力の向上に繋がる対立遺伝子や，sd1^DGWGやDEP1^Ballilaなどのような群落構造を大きく変化させる対立遺伝子を組合せて利用するなど，ソース能の向上と並行して取組む必要があると考察された．</p>

DOI： 10.1270/jsbbr.20j21

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1016/j.fcr.2021.108128

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.3389/fpls.2020.579305

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1016/j.fcr.2019.107694

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担当区分：最終著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1007/s11032-020-1101-5

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1016/j.molp.2019.01.019

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1093/jxb/erz303

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1371/journal.pone.0221424

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1007/s10725-019-00517-y

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1007/s10725-018-0468-3

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担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1270/jsbbs.19003

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1371/journal.pone.0224386

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担当区分：責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Springer Nature  

DOI： 10.1186/s12284-018-0207-4

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担当区分：責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1270/jsbbs.17129

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier B.V.  

Manipulating plant architecture is a promising strategy for further improving rice production. The canopy extinction coefficient (k), the most important parameter of canopy architecture, represents the characteristics of light penetration into the canopy, and is determined mainly by the leaf inclination angle. With its erect leaves, the high-yielding indica cultivar ‘Takanari’ has a smaller k during ripening than the elite japonica cultivar ‘Koshihikari’. Using chromosome segment substitution lines derived from a cross between ‘Takanari’ and ‘Koshihikari’ we previously detected a quantitative trait locus (QTL) for leaf inclination angle on a chromosome 3. Here, we tested a near-isogenic line (NIL-3) carrying the ‘Takanari’ allele of a QTL for larger leaf inclination angle on chromosome 3, qLIA3, in the ‘Koshihikari’ genetic background for the effects of qLIA3 on k, dry matter production, and grain yield. NIL-3 had leaves with a larger inclination angle from the full heading through ripening stages and a smaller k at the ripening stage than ‘Koshihikari’. There were no differences in plant height, panicle size, heading date, leaf area index, or individual leaf photosynthesis between NIL-3 and ‘Koshihikari’. Biomass at harvest was significantly greater in NIL-3 than in ‘Koshihikari’ owing to a higher net assimilation rate during ripening, resulting in a higher grain yield. qLIA3 might incorporate a promising gene for improving rice production.

DOI： 10.1016/j.fcr.2018.01.025

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGEROPEN  

Background: In cereal crops, stem lodging can be classified into two types: stem-breaking type and stem-bending type. To improve stem-lodging resistance, the strong culm traits of superior lodging-resistant varieties must be characterized. The identification of quantitative trait loci (QTLs) and the corresponding genes associated with the parameters for bending moment at breaking (M) and flexural rigidity (FR) is expected to enable the efficient development of lodging-resistant varieties. A set of Chromosome Segment Substitution Lines (CSSLs) derived from the cross between Takanari and Koshihikari were used in this study to identify QTLs associated with lodging resistance.Results: The indica variety Takanari possesses large M due to its large section modulus (SM) despite its small bending stress (BS), whereas Takanari also has large FR due to its large secondary moment of inertia (SMI) and Young's modulus (YM). The QTLs for BS were assigned to chromosomes 3, 5, 6, 8, 9, 10, 11, and 12. Koshihikari alleles increased BS in these QTLs. The YM was increased by substitution of the Koshihikari chromosomal segments on chromosomes 2, 10, and 11. Other QTLs mapped to chromosomes 7 and 12, such that the Koshihikari alleles contributed to the decrease of YM. QTLs for cellulose density were assigned to chromosomes 1, 3, and 5, which were replaced by substitutions of Koshihikari segments. The QTLs for hemicellulose, cellulose, and holocellulose densities identified on chromosome 5 overlapped with those for BS, indicating the positive effect of the Koshihikari segment on increasing BS.Conclusions: These results suggested that the QTLs for the densities of cell wall materials in japonica varieties contributed to increased BS and might be utilized for improving lodging resistance in indica varieties of rice.

DOI： 10.1186/s12284-018-0216-3

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担当区分：責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

Multi-parent advanced generation inter-cross (MAGIC) lines have broader genetic variation than bi-parental recombinant inbred lines. Genome-wide association study (GWAS) using high number of DNA polymorphisms such as single-nucleotide polymorphisms (SNPs) is a popular tool for allele mining in MAGIC populations, in which the associations of phenotypes with SNPs are investigated; however, the effects of haplotypes from multiple founders on phenotypes are not considered. Here, we describe an improved method of allele mining using the newly developed Japan-MAGIC (JAM) population, which is derived from eight high-yielding rice cultivars in Japan. To obtain information on the haplotypes in the JAM lines, we predicted the haplotype blocks in the whole chromosomes using 16,345 SNPs identified via genotyping-by-sequencing analysis. Using haplotype-based GWAS, we clearly detected the loci controlling the glutinous endosperm and culm length traits. Information on the alleles of the eight founders, which was based on the effects of mutations revealed by the analysis of next-generation sequencing data, was used to narrow down the candidate genes and reveal the associations between alleles and phenotypes. The haplotype-based allele mining (HAM) proposed in this study is a promising approach to the detection of allelic variation in genes controlling agronomic traits in MAGIC populations.

DOI： 10.1038/s41598-018-22657-3

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

The biomass yield (plant weight) of rice fluctuates from year to year. In a previous study, we demonstrated that six quantitative trait loci (QTLs) contribute to the variation in the plant weight of recombinant inbred lines (RILs) of high-yielding Japanese rice cultivars. However, it remains unclear whether the effects of those QTLs are stable over multiple years. Therefore, we evaluated the effect of the alleles on the plant weight of RILs over multiple years, including a change of fertilization level (i.e., in different environments). Even though the biomass yields of all RILs fluctuated among environments, RILs that were selected on the basis of the genotypes of the detected QTLs had a stable rank order of plant weight that corresponded to their genotypes. This multiple-environment experiment reveals the highly significant contribution of both genotypic and environmental variances to the observed variance in plant weight. A marginally significant QTL-environment interaction was detected at only one of the six QTLs, with a subtle contribution. These results support the idea that the biomass yield of rice can be improved through QTL-based allele selection.

DOI： 10.1371/journal.pone.0206054

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掲載種別：研究論文（学術雑誌）  

DOI： 10.1038/s41598-017-01690-8

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担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

The high-yielding indica x japonica rice (Oryza sativa L) cultivar Akenohoshi tends to maintain a higher photosynthetic rate during ripening owing to its higher nitrogen accumulation and nitrogen partitioning to leaves than the commercial japonica cultivar Koshihikari. By using recombinant inbred lines derived from a cross between Akenohoshi and Koshihikari, we detected at least 6 quantitative trait loci (QTLs) for maintaining higher leaf chlorophyll content, 4 QTLs for nitrogen content, and 5 QTLs for the rate of nitrogen transport to shoots during ripening in the paddy field. Then we developed two chromosome segment substitution lines carrying Akenohoshi segments on the short arm of chromosome 3, where the QTLs for chlorophyll content reduction were clustered, in the Koshihikari genetic background. The lines showed higher rate of nitrogen transport to shoots, leaf chlorophyll and nitrogen contents, and therefore a higher rate of leaf photosynthesis, than Koshihikari. We concluded that a 7.7-Mb region present in both two lines, named qCHR1, is important for maintaining chlorophyll and nitrogen contents during senescence. The Akenohoshi allele at qCHR1 increased nitrogen accumulation and nitrogen partitioning to leaves during ripening, but did not change yield. (C) 2017 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.fcr.2017.03.001

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：FRONTIERS MEDIA SA  

Increasing the rate of leaf photosynthesis is one important approach for increasing grain yield in rice (Ora sativa). Exploiting the natural variation in CO2 assimilation rate (A) between rice cultivars using quantitative genetics is one promising means to identify genes contributing to higher photosynthesis. In this study, we determined precise location of Carbon Assimilation Rate 8 (CAR8) by crossing a high-yielding indica cultivar with a Japanese commercial cultivar, Fine mapping suggested that CAR8 encodes a putative Heme Activator Protein 3 (OsHAP3) subunit of a CCAAT box binding transcription factor called OsHAP3H. Sequencing analysis revealed that the indica allele of CAR8 has a 1-bp deletion at 322 bp from the start codon, resulting in a truncated protein of 125 amino acids. In addition, CAR8 is identical to DTH8/Ghd8/LHD1, which was reported to control rice flowering date. The increase of A is largely due to an increase of RuBP regeneration rate via increased leaf nitrogen content, and partially explained by reduced stomatal limitation via increased stomatal conductance relative to A. This allele also increases hydraulic conductivity, which would promote higher stomatal conductance. This indicates that CAR8 affects multiple physiological aspects relating to photosynthesis. The detailed analysis of molecular functions of CAR8 would help to understand the association between photosynthesis and flowering and demonstrate specific genetic mechanisms that can be exploited to improve photosynthesis in rice and potentially other crops.

DOI： 10.3389/fpls.2017.00060

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記述言語：英語   出版者・発行元：Japanese Society of Breeding  

Many quantitative trait loci (QTLs) for agronomically important traits such as grain yield, disease resistance, and stress tolerance of rice (Oryza sativa L.) have been detected by using segregating populations derived from crosses between indica and japonica subspecies or with wild relatives. However, the QTLs involved in the control of natural variation in agronomic traits among closely related cultivars are still unclear. Decoding the whole genome sequences of Nipponbare and other temperate japonica rice cultivars has accelerated the collection of a huge number of single nucleotide polymorphisms (SNPs). These SNPs are good resource for developing polymorphic DNA markers and for detecting QTLs distributed across all rice chromosomes. The temperate japonica rice cultivar Koshihikari has remained the top cultivar for about 40 years since 1979 in Japan. Unraveling the genetic factors in Koshihikari will provide important insights into improving agronomic traits in temperate japonica rice cultivars. Here we describe recent progress in our studies as an example of genetic analysis in closely related cultivars.

DOI： 10.1270/jsbbs.17053

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：NATURE PUBLISHING GROUP  

Severe lodging has occurred in many improved rice varieties after the recent strong typhoons in East and Southeast Asian countries. The indica variety Takanari possesses strong culm characteristics due to its large section modulus, which indicates culm thickness, whereas the japonica variety Koshihikari is subject to substantial bending stress due to its thick cortical fibre tissue. To detect quantitative trait loci (QTLs) for lodging resistance and to eliminate the effects of genetic background, we used reciprocal chromosome segment substitution lines (CSSLs) derived from a cross between Koshihikari and Takanari. The oppositional effects of QTLs for section modulus were confirmed in both genetic backgrounds on chromosomes 1, 5 and 6, suggesting that these QTLs are not affected by the genetic background and are controlled independently by a single factor. The candidate region of a QTL for section modulus included SD1. The section modulus of NIL-sd1 was lower than that of Koshihikari, whereas the section modulus of NIL-SD1 was higher than that of Takanari. This result indicated that those regions regulate the culm thickness. The reciprocal effects of the QTLs for cortical fibre tissue thickness were confirmed in both genetic backgrounds on chromosome 9 using CSSLs.

DOI： 10.1038/srep30572

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：PUBLIC LIBRARY SCIENCE  

Biomass yield of rice (Oryza sativa L.) is an important breeding target, yet it is not easy to improve because the trait is complex and phenotyping is laborious. Using progeny derived from a cross between two high-yielding Japanese cultivars, we evaluated whether quantitative trait locus (QTL)-based selection can improve biomass yield. As a measure of biomass yield, we used plant weight (aboveground parts only), which included grain weight and stem and leaf weight. We measured these and related traits in recombinant inbred lines. Phenotypic values for these traits showed a continuous distribution with transgressive segregation, suggesting that selection can affect plant weight in the progeny. Four significant QTLs were mapped for plant weight, three for grain weight, and five for stem and leaf weight (at alpha = 0.05); some of them overlapped. Multiple regression analysis showed that about 43% of the phenotypic variance of plant weight was significantly explained (P &lt; 0.0001) by six of the QTLs. From F-2 plants derived from the same parental cross as the recombinant inbred lines, we divergently selected lines that carried alleles with positive or negative additive effects at these QTLs, and performed successive selfing. In the resulting F-6 lines and parents, plant weight significantly differed among the genotypes (at alpha = 0.05). These results demonstrate that QTL-based selection is effective in improving rice biomass yield.

DOI： 10.1371/journal.pone.0151830

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

Key message A QTL for cold tolerance at the booting stage of rice cultivar 'Kuchum' was detected and delimited into a 1.36 Mb region, and a cold-tolerant line was developed by QTL pyramiding.Low temperature in summer causes pollen sterility in rice, resulting in a serious loss of yield. The second most widely grown rice cultivar in Japan, 'Hitomebore', has been developed as a cultivar highly tolerant to low temperature at the booting stage. However, even 'Hitomebore' exhibits sterility at a temperature lower than 18.5 degrees C. Further improvement of cold tolerance of rice is required. In the present study, QTLs for cold tolerance in a Bhutanese rice variety, 'Kuchum', were analyzed using backcrossed progenies and a major QTL, named qCT-4, was detected on chromosome 4. Evaluating cold tolerance of seven types of near isogenic lines having 'Kuchum' alleles around qCT-4 with a 'Hitomebore' genetic background, qCT-4 was delimited to a region of ca. 1.36 Mb between DNA markers 9_1 and 10_13. Homozygous 'Kuchum' alleles at qCT-4 showed an effect of increasing seed fertility by ca. 10 % under cold-water treatment. Near isogenic lines of 'Hitomebore' having 'Silewah' alleles of Ctb1 and Ctb2 and a 'Hokkai PL9' allele of qCTB8 did not exhibit higher cold tolerance than that of 'Hitomebore'. On the other hand, a qLTB3 allele derived from a Chinese cultivar 'Lijiangxintuanheigu' increased cold tolerance of 'Hitomebore', and pyramiding of the qCT-4 allele and the qLTB3 allele further increased seed fertility under cold-water treatment. Since NILs of 'Hitomebore' with the 'Kuchum' allele of qCT-4 were highly similar to 'Hitomebore' in other agronomic traits, the qCT-4 allele is considered to be useful for developing a cold-tolerant cultivar.

DOI： 10.1007/s00122-015-2654-2

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

The yield of Koshihikari, a Japanese premium rice variety, is relatively lower than that of modern high yielding varieties. IR64 carries several well-known genes such as GS3, an important gene for grain size, sd-1, a semi-dwarf gene, and NARROW LEAF1 (NAL1), a gene for small, narrow flag leaves. In this study, we used two sets of chromosome segment substitution lines (CSSLs), from Koshihikari and IR64, and attempted to evaluate the genetic factors that cause differences between parents by analyzing the function of chromosome regions affecting a trait (CRATs). For 28 traits, we identified 312 CRATs in the Koshihikari background and 275 in the IR64 background. In these, donor alleles had positive effects in 84 and 103 CRATs, respectively. Among these, the CRAT related to GS3 and those for grain number expanded the potential sink size in Koshihikari, although this did not affect final yield. The combination of CRATs that enhances source ability may increase grain yield. Although the sd-1 gene might improve resistance to lodging, the yield of CSSLs with sd-1 decreased by 28.7 %. These results suggest that the smaller biomass conferred by sd-1 might reduce canopy photosynthesis. In the Koshihikari background, the CRAT related to NAL1 and those located on chr. 6 increased SPAD value but had the opposite effect on leaf size. Two CRATs that were detected on chr. 6 and 7 increased leaf area without any effect on the SPAD value. The combination of these CRATs for area and SPAD value might improve source ability.

DOI： 10.1007/s10722-015-0237-3

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担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER IRELAND LTD  

Dry matter production of crops is determined by how much light they intercept and how efficiently they use it for carbon fixation; i.e., photosynthesis. The high-yielding rice cultivar, Akenohoshi, maintains a high photosynthetic rate in the middle of the day owing to its high hydraulic conductance in comparison with the elite commercial rice cultivar, Koshihikari. We developed 94 recombinant inbred lines derived from Akenohoshi and Koshihikari and measured their exudation rate to calculate hydraulic conductance to osmotic water transport in a paddy field. A quantitative trait locus (QTL) for exudation rate was detected on the long arm of chromosome 2 at the heading and ripening stages. We developed chromosome segment substitution lines which carried Akenohoshi segments in the Koshihikari genetic background, and measured hydraulic conductance to both osmotic and passive water transport. The QTL was confirmed to be located within a region of about 4.2 Mbp on the distal end of long arm of chromosome 2. The Akenohoshi allele increased root surface area and hydraulic conductance, but didn't increase hydraulic conductivity of a plant. (C) 2015 The Authors. Published by Elsevier Ireland Ltd.

DOI： 10.1016/j.plantsci.2015.08.014

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：JAPANESE SOC BREEDING  

Plant breeding programs aim to develop cultivars with high adaptability to the specific conditions in a local region. As a result, unique genes and gene combinations have been accumulated in local elite breeding populations during the long history of plant breeding. Genetic analyses on such genes and combinations may be useful for developing new cultivars with more-desirable agronomic traits. Here, we attempted to detect quantitative trait loci (QTL) for rice blast resistance (BR) using a local breeding rice population from Hokkaido, Japan. Using genotyping data on single nucleotide polymorphisms and simple sequence repeat markers distributed throughout the whole genomic region, we detected genetic regions associated with phenotypic variation in BR by a genome-wide association mapping study (GWAS). An additional association analysis using other breeding cultivars verified the effect and inheritance of the associated region. Furthermore, the existence of a gene for BR in the associated region was confirmed by QTL mapping. The results from these studies enabled us to estimate potential of the Hokkaido rice population as a gene pool for improving BR. The results of this study could be useful for developing novel cultivars with vigorous BR in rice breeding programs.

DOI： 10.1270/jsbbs.65.388

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：GENETICS SOCIETY AMERICA  

We investigated the natural variations in the flag leaf morphology of rice. We conducted a principal component analysis based on nine flag leaf morphology traits using 103 accessions from the National Institute of Agrobiological Sciences Core Collection. The first component explained 39% of total variance, and the variable with highest loading was the width of the flag leaf (WFL). A genome-wide association analysis of 102 diverse Japanese accessions revealed that marker RM6992 on chromosome 4 was highly associated with WFL. In analyses of progenies derived from a cross between Takanari and Akenohoshi, the most significant quantitative trait locus (QTL) for WFL was in a 10.3-kb region containing the NARROW LEAF 1 (NAL1) gene, located 0.4 Mb downstream of RM6992. Analyses of chromosomal segment substitution lines indicated that a mutation (G1509A single-nucleotide mutation, causing an R233H amino acid substitution in NAL1) was present at the QTL. This explained 13 and 20% of total variability in WFL and the distance between small vascular bundles, respectively. The mutation apparently occurred during rice domestication and spread into japonica, tropical japonica, and indica subgroups. Notably, one accession, Phulba, had a NAL1 allele encoding only the N-terminal, or one-fourth, of the wild-type peptide. Given that the Phulba allele and the histidine-type allele showed essentially the same phenotype, the histidine-type allele was regarded as malfunctional. The phenotypes of transgenic plants varied depending on the ratio of histidine-type alleles to arginine-type alleles, raising the possibility that H-233-type products function differently from and compete with R-233-type products.

DOI： 10.1534/genetics.115.181040

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER HEIDELBERG  

Brown spots on mature leaves from the heading to ripening stages in rice are considered to be lesions induced by heat stress. However, there are few studies of lesions that are induced by heat stress rather than by pathogen infections. To understand the genetic background underlying such lesions, we used the chromosome segment substitution line (CSSL) SL518, derived from a distant cross between rice cultivars Koshihikari (japonica) and Nona Bokra (indica). We observed brown spots on mature leaf blades of the CSSL, although the parents barely showed any spots. Spot formation in SL518 was accelerated by high temperature, suggesting that the candidate gene for spot formation is related to heat stress response. Using progeny derived from a cross between SL518 and Koshihikari, we mapped the causative gene, BROWN-SPOTTED LEAF 1 (BSPL1), on chromosome 5. We speculated that one or more Nona Bokra genes suppress spot formation caused by BSPL1 and identified candidate genomic regions on chromosomes 2 and 9 using a cross between a near-isogenic line for BSPL1 and other CSSLs possessing Nona Bokra segments in the Koshihikari genetic background. In conclusion, our data support the concept that multiple genes are complementarily involved in brown spot formation induced by heat stress and will be useful for cloning of the novel gene(s) related to the spot formation.

DOI： 10.1007/s00438-014-0975-5

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：JAPANESE SOC BREEDING  

Improving the eating quality of cooked rice has been one of the most important objectives in rice breeding programs. Eating quality of cooked rice is a complex trait including several components, such as external appearance, taste, aroma, and texture. Therefore, dissection of these components followed by marker-assisted selection of detected QTL(s) may be a useful approach for achieving desirable eating quality in rice breeding. Whiteness of cooked rice (WCR) is an important factor related to the external appearance of cooked rice. WCR is known to be associated with the amylose and protein contents of the endosperm. However, the genetic basis of WCR remains unclear. In this study, we evaluated phenotypic variation in WCR among recently developed rice cultivars from Hokkaido, Japan. Then, we developed doubled haploid lines (DHLs) derived from a cross between two cultivars from Hokkaido, Joiku No. 462 (high WCR) and Jokei06214 (low WCR). Using the DHLs, we detected two QTLs for WCR, qWCR3 and qWCR11, on chromosomes 3 and 11, respectively. We also examined the dosage effect of the two QTLs based on both the categorized segregants in the DHLs and the relationship between the WCR phenotype and inheritance around the QTL regions in cultivars from Hokkaido.

DOI： 10.1270/jsbbs.65.201

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：JAPANESE SOC BREEDING  

There is increasing evidence that global warming affects the development of rice. High temperatures during ripening increase the ratio of undesirable chalky grains followed by deteriorating grain appearance quality. In order to detect quantitative trait loci (QTLs) controlling the occurrence of white-back and basal-white chalky grains of brown rice, QTL analysis was performed using recombinant inbred lines derived from a cross between two strains, 'Tsukushiroman' (sensitive to heat stress) and Chikushi 52' (tolerant of heat stress). The F-7 and F-8 lines were exposed to heat stress during the ripening period in two locations, Fukuoka and Kagoshima, in Japan. QTLs for white-back grains and basal-white grains were detected on chromosomes 1, 3, and 8, and those for basal-white grains were detected on chromosomes 2, 3, and 12. QTLs on chromosome 8 for white-back grains were shared in the plants grown in both locations. Near-isogenic lines (NILs), which harbored a segment from Chikushi 52' on chromosome 8 with the genetic background of 'Tsukushiroman', showed relatively lower ratios of white-back grains than `Tsukushiroman'. Therefore, insertion of the Chikushi 52' genomic region of the QTL on chromosome 8 can improve the quality of rice when it is grown under heat stress conditions.

DOI： 10.1270/jsbbs.65.216

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：BMC  

Background: Heading date, a crucial factor determining regional and seasonal adaptation in rice (Oryza sativa L.), has been a major selection target in breeding programs. Although considerable progress has been made in our understanding of the molecular regulation of heading date in rice during last two decades, the previously isolated genes and identified quantitative trait loci (QTLs) cannot fully explain the natural variation for heading date in diverse rice accessions.Results: To genetically dissect naturally occurring variation in rice heading date, we collected QTLs in advanced-backcross populations derived from multiple crosses of the japonica rice accession Koshihikari (as a common parental line) with 11 diverse rice accessions (5 indica, 3 aus, and 3 japonica) that originate from various regions of Asia. QTL analyses of over 14,000 backcrossed individuals revealed 255 QTLs distributed widely across the rice genome. Among the detected QTLs, 128 QTLs corresponded to genomic positions of heading date genes identified by previous studies, such as Hd1, Hd6, Hd3a, Ghd7, DTH8, and RFT1. The other 127 QTLs were detected in different chromosomal regions than heading date genes.Conclusions: Our results indicate that advanced-backcross progeny allowed us to detect and confirm QTLs with relatively small additive effects, and the natural variation in rice heading date could result from combinations of large- and small-effect QTLs. We also found differences in the genetic architecture of heading date (flowering time) among maize, Arabidopsis, and rice.

DOI： 10.1186/s12870-015-0501-x

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：CELL PRESS  

Lodging has been a major roadblock to attaining increased crop productivity. In an attempt to understand the mechanism for culm strength in rice, we isolated an effective quantitative trait locus (QTL), STRONG CULM3 (SCM3), the causal gene of which is identical to rice TEOS1NTE BRANCHED1 (OsTB1), a gene previously reported to positively control strigolactone (SL) signaling. A near-isogenic line (NIL) carrying SCM3 showed enhanced culm strength and increased spikelet number despite the expected decrease in tiller number, indicating that SL also has a positive role in enhancing culm strength and spikelet number. We produced a pyramiding line carrying SCM3 and SCM2, another QTL encoding AP01 involved in panicle development. The NIL-SCM2+SCM3 showed a much stronger culm than NIL-SCM2 and NIL-SCM3 and an increased spikelet number caused by the additive effect of these QTLs. We discuss the importance of utilizing suitable alleles of these STRONG CULM QTLs without inducing detrimental traits for breeding.

DOI： 10.1016/j.molp.2014.10.009

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：OXFORD UNIV PRESS INC  

Viability and fertility in organisms depend on epistatic interactions between loci maintained in lineages. Here, we describe reduced fitness of segregants (hybrid breakdown, HB) that emerged in an F-2 population derived from a cross between 2 rice (Oryza sativa L.) cultivars, "Tachisugata" (TS) and "Hokuriku 193" (H193), despite both parents and F(1)s showing normal fitness. Quantitative trait locus (QTL) analyses detected 13 QTLs for 4 morphological traits associated with the HB and 6 associated with principal component scores calculated from values of the morphological traits in the F-2 population. Two-way analysis of variance of the putative QTLs identified 4 QTL pairs showing significant epistasis; among them, a pair on chromosomes 1 and 12 made the greatest contribution to HB. The finding was supported by genetic experiments using F-3 progeny. HB emerged only when a plant was homozygous for the TS allele at the QTL on chromosome 1 and homozygous for the H193 allele at the QTL on chromosome 12, indicating that each allele behaves as recessive to the other. Our results support the idea that epistasis is an essential part of hybrid fitness.

DOI： 10.1093/jhered/esu065

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担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：BIOMED CENTRAL LTD  

Background: Increasing rice yield potential is a major objective in rice breeding programs, given the need for meeting the demands of population growth, especially in Asia. Genetic analysis using genomic information and high-yielding cultivars can facilitate understanding of the genetic mechanisms underlying rice yield potential. Chromosome segment substitution lines (CSSLs) are a powerful tool for the detection and precise mapping of quantitative trait loci (QTLs) that have both large and small effects. In addition, reciprocal CSSLs developed in both parental cultivar backgrounds may be appropriate for evaluating gene activity, as a single factor or in epistatic interactions.
Results: We developed reciprocal CSSLs derived from a cross between Takanari (one of the most productive indica cultivars) and a leading japonica cultivar, Koshihikari; both the cultivars were developed in Japan. Forty-one CSSLs covered most of the Takanari genome in the Koshihikari background and 39 CSSLs covered the Koshihikari genome in the Takanari background. Using the reciprocal CSSLs, we conducted yield trials under canopy conditions in paddy fields. While no CSSLs significantly exceeded the recurrent parent cultivar in yield, genetic analysis detected 48 and 47 QTLs for yield and its components in the Koshihikari and Takanari backgrounds, respectively. A number of QTLs showed a trade-off, in which the allele with increased sink-size traits (spikelet number per panicle or per square meter) was associated with decreased ripening percentage or 1000-grain weight. These results indicate that increased sink size is not sufficient to increase rice yield in both backgrounds. In addition, most QTLs were detected in either one of the two genetic backgrounds, suggesting that these loci may be under epistatic control with other gene(s).
Conclusions: We demonstrated that the reciprocal CSSLs are a useful tool for understanding the genetic mechanisms underlying yield potential in the high-yielding rice cultivar Takanari. Our results suggest that sink-size QTLs in combination with QTLs for source strength or translocation capacity, as well as careful attention to epistatic interactions, are necessary for increasing rice yield. Thus, our findings provide a foundation for developing rice cultivars with higher yield potential in future breeding programs.

DOI： 10.1186/s12870-014-0295-2

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1093/mp/ssu131

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：NATURE PUBLISHING GROUP  

Lignin modification has been a breeding target for the improvements of forage digestibility and energy yields in forage and bioenergy crops, but decreased lignin levels are often accompanied by reduced lodging resistance. The rice mutant gold hull and internode2 (gh2) has been identified to be lignin deficient. GH2 has been mapped to the short arm of chromosome 2 and encodes cinnamyl-alcohol dehydrogenase (CAD). We developed a long-culm variety, 'Leaf Star', with superior lodging resistance and a gh phenotype similar to one of its parents, 'Chugoku 117'. Thegh loci in Leaf Star and Chugoku 117 were localized to the same region of chromosome 2 as the gh2 mutant. Leaf Star had culms with low lignin concentrations due to a natural mutation in OsCAD2 that was not present in Chugoku 117. However, this variety had high culm strength due to its strong, thick culms. Additionally, this variety had a thick layer of cortical fiber tissue with well-developed secondary cell walls. Our results suggest that rice can be improved for forage and bioenergy production by combining superior lodging resistance, which can be obtained by introducing thick and stiff culm traits, with low lignin concentrations, which can be obtained using the gh2 variety.

DOI： 10.1038/srep06567

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：BIOMED CENTRAL LTD  

Background: High-yielding cultivars of rice (Oryza sativa L.) have been developed in Japan from crosses between overseas indica and domestic japonica cultivars. Recently, next-generation sequencing technology and high-throughput genotyping systems have shown many single-nucleotide polymorphisms (SNPs) that are proving useful for detailed analysis of genome composition. These SNPs can be used in genome-wide association studies to detect candidate genome regions associated with economically important traits. In this study, we used a custom SNP set to identify introgressed chromosomal regions in a set of high-yielding Japanese rice cultivars, and we performed an association study to identify genome regions associated with yield.
Results: An informative set of 1152 SNPs was established by screening 14 high-yielding or primary ancestral cultivars for 5760 validated SNPs. Analysis of the population structure of high-yielding cultivars showed three genome types: japonica-type, indica-type and a mixture of the two. SNP allele frequencies showed several regions derived predominantly from one of the two parental genome types. Distinct regions skewed for the presence of parental alleles were observed on chromosomes 1, 2, 7, 8, 11 and 12 (indica) and on chromosomes 1, 2 and 6 (japonica). A possible relationship between these introgressed regions and six yield traits (blast susceptibility, heading date, length of unhusked seeds, number of panicles, surface area of unhusked seeds and 1000-grain weight) was detected in eight genome regions dominated by alleles of one parental origin. Two of these regions were near Ghd7, a heading date locus, and Pi-ta, a blast resistance locus. The allele types (i.e., japonica or indica) of significant SNPs coincided with those previously reported for candidate genes Ghd7 and Pi-ta.
Conclusions: Introgression breeding is an established strategy for the accumulation of QTLs and genes controlling high yield. Our custom SNP set is an effective tool for the identification of introgressed genome regions from a particular genetic background. This study demonstrates that changes in genome structure occurred during artificial selection for high yield, and provides information on several genomic regions associated with yield performance.

DOI： 10.1186/1471-2164-15-346

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：OXFORD UNIV PRESS  

Increases in rates of individual leaf photosynthesis (P-n) are critical for future increases of rice yields. A previous study, using introgression lines derived from a cross between indica cultivar Habataki, with one of the highest recorded values of P-n, and the Japanese elite cultivar Koshihikari, identified four QTLs (qCAR4, qCAR5, qCAR8, and qCAR11) that affect P-n. The present study examined the combined effect of qCAR4 and qCAR8 on P-n in the genetic background of Koshihikari. The pyramided near-isogenic line NIL(qCAR4qCAR8) showed higher P-n than both NIL(qCAR4) and NIL(qCAR8), equivalent to that of Habataki despite being due to only two out of the four QTLs. The high P-n of NIL(qCAR4qCAR8) may be attributable to the high leaf nitrogen content, which may have been inherited from NIL(qCAR4), to the large hydraulic conductance due to the large root surface area from NIL(qCAR4), and to the high hydraulic conductivity from NIL(qCAR8). It might be also attributable to high mesophyll conductance, which may have been inherited from NIL(qCAR4). The induction of mesophyll conductance and the high leaf nitrogen content and high hydraulic conductivity could not be explained in isolation from the Koshihikari background. These results suggest that QTL pyramiding is a useful approach in rice breeding aimed at increasing P-n.

DOI： 10.1093/jxb/eru047

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

The rice local population was clearly differentiated into six groups over the 100-year history of rice breeding programs in the northern limit of rice cultivation over the world.
Genetic improvements in plant breeding programs in local regions have led to the development of new cultivars with specific agronomic traits under environmental conditions and generated the unique genetic structures of local populations. Understanding historical changes in genome structures and phenotypic characteristics within local populations may be useful for identifying profitable genes and/or genetic resources and the creation of new gene combinations in plant breeding programs. In the present study, historical changes were elucidated in genome structures and phenotypic characteristics during 100-year rice breeding programs in Hokkaido, the northern limit of rice cultivation in the world. We selected 63 rice cultivars to represent the historical diversity of this local population from landraces to the current breeding lines. The results of the phylogenetic analysis demonstrated that these cultivars clearly differentiated into six groups over the history of rice breeding programs. Significant differences among these groups were detected in five of the seven traits, indicating that the differentiation of the Hokkaido rice population into these groups was correlated with these phenotypic changes. These results demonstrated that breeding practices in Hokkaido have created new genetic structures for adaptability to specific environmental conditions and breeding objectives. They also provide a new strategy for rice breeding programs in which such unique genes in local populations in the world can explore the genetic potentials of the local populations.

DOI： 10.1007/s00122-014-2274-2

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担当区分：責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：BIOMED CENTRAL LTD  

Background: In genetic analysis of agronomic traits, quantitative trait loci (QTLs) that control the same phenotype are often closely linked. Furthermore, many QTLs are localized in specific genomic regions (QTL clusters) that include naturally occurring allelic variations in different genes. Therefore, linkage among QTLs may complicate the detection of each individual QTL. This problem can be resolved by using populations that include many potential recombination sites. Recently, multi-parent populations have been developed and used for QTL analysis. However, their efficiency for detection of linked QTLs has not received attention. By using information on rice, we simulated the construction of a multi-parent population followed by cycles of recurrent crossing and inbreeding, and we investigated the resulting genome structure and its usefulness for detecting linked QTLs as a function of the number of cycles of recurrent crossing.
Results: The number of non-recombinant genome segments increased linearly with an increasing number of cycles. The mean and median lengths of the non-recombinant genome segments decreased dramatically during the first five to six cycles, then decreased more slowly during subsequent cycles. Without recurrent crossing, we found that there is a risk of missing QTLs that are linked in a repulsion phase, and a risk of identifying linked QTLs in a coupling phase as a single QTL, even when the population was derived from eight parental lines. In our simulation results, using fewer than two cycles of recurrent crossing produced results that differed little from the results with zero cycles, whereas using more than six cycles dramatically improved the power under most of the conditions that we simulated.
Conclusion: Our results indicated that even with a population derived from eight parental lines, fewer than two cycles of crossing does not improve the power to detect linked QTLs. However, using six cycles dramatically improved the power, suggesting that advanced intercrossing can help to resolve the problems that result from linkage among QTLs.

DOI： 10.1186/1471-2156-15-50

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：JAPANESE SOC BREEDING  

To advance the identification of quantitative trait loci (QTLs) to reduce Cd content in rice (Oryza sativa L.) grains and breed low-Cd cultivars, we developed a novel population consisting of 46 chromosome segment substitution lines (CSSLs) in which donor segments of LAC23, a cultivar reported to have a low grain Cd content, were substituted into the Koshihikari genetic background. The parental cultivars and 32 CSSLs (the minimum set required for whole-genome coverage) were grown in two fields with different natural levels of soil Cd. QTL mapping by single-marker analysis using ANOVA indicated that eight chromosomal regions were associated with grain Cd content and detected a major QTL (qlGCd3) with a high F-test value in both fields (F=9.19 and 5.60) on the long arm of chromosome 3. The LAC23 allele at qlGCd3 was associated with reduced grain Cd levels and appeared to reduce Cd transport from the shoots to the grains. Fine substitution mapping delimited qlGCd3 to a 3.5-Mbp region. Our results suggest that the low-Cd trait of LAC23 is controlled by multiple QTLs, and qlGCd3 is a promising candidate QTL to reduce the Cd level of rice grain.

DOI： 10.1270/jsbbs.63.284

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担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：NATURE PUBLISHING GROUP  

Improvement of leaf photosynthesis is an important strategy for greater crop productivity. Here we show that the quantitative trait locus GPS (GREEN FOR PHOTOSYNTHESIS) in rice (Oryza sativa L.) controls photosynthesis rate by regulating carboxylation efficiency. Map-based cloning revealed that GPS is identical to NAL1 (NARROW LEAF1), a gene previously reported to control lateral leaf growth. The high-photosynthesis allele of GPS was found to be a partial loss-of-function allele of NAL1. This allele increased mesophyll cell number between vascular bundles, which led to thickened leaves, and it pleiotropically enhanced photosynthesis rate without the detrimental side effects observed in previously identified nal1 mutants, such as dwarf plant stature. Furthermore, pedigree analysis suggested that rice breeders have repeatedly selected the high-photosynthesis allele in high-yield breeding programs. The identification and utilization of NAL1 (GPS) can enhance future high-yield breeding and provides a new strategy for increasing rice productivity.

DOI： 10.1038/srep02149

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記述言語：英語   出版者・発行元：JAPAN INT RESEARCH CENTER AGRICULTURAL SCIENCES  

Recent progress in genomics has promoted understanding of genetic mechanisms controlling complex crop production traits. In rice, yield is one of the most complex traits and generally determined by relationship between sink and source ability. While several quantitative trait locus (QTL) genes have been identified for sink-size traits, there has been little progress in genetic analysis for source ability. One of the reasons is that the source ability such as photosynthesis is a dynamic trait, hampering efforts to make precise measurements due to the technical difficulty involved in handling so many plants simultaneously. To facilitate genetic studies for source ability, we developed rapid and precise methods to evaluate leaf photosynthesis, one of the important factors for source ability in rice. QTL analysis using such methods successfully detected several promising QTLs and verified the potential utility of the evaluation methods. Our work reflects the importance of steady observation of rice plants in paddy fields and includes the application of the latest technology used in various areas of science to develop improved criteria for each trait toward advanced genetic studies.

DOI： 10.6090/jarq.47.227

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記述言語：日本語   出版者・発行元：日本育種学会  

カドミウム(Cd)は環境中に広く存在する元素であり，ほとんどの農作物は低濃度のCdを含んでいる(Kikuchi et al.2002)。しかし，わが国には過去の産業活動の結果として土壌のCd汚染が生じた地域があり，そこで生産された農作物は比較的高いCd濃度を含む可能性がある。Cdは「イタイイタイ病」の原因物質と同定され，ヒトが食品を通じて一定量以上を長期間摂取し続けると，腎機能に悪影響を及ぼすことが知られている(食品安全委員会 2009)。2007年の日本人の平均的な食品由来のCd摂取量は，2.8同/kg体重/週であり，暫定耐容摂取量7μg/kg体重/週の4割である(食品安全委員会 2009)。その内訳の中で最も寄与率の高い食品はコメであり，総摂取量の37.2%を占めている(食品安全委員会 2009)我が国のコメのCd濃度の基準値は，Codexが定める国際基準値の0.4mg/kgに従い(Codex2006)，2010年に1.0mg/kgから0.4mg/kgへの食品衛生法の改正が告示され(厚生労働省 2010)，2011年2月に施行された。これまでに，この基準値を超えるコメを生産する可能性のある地域では，土壌汚染濃度に応じ，客土法やアルカリ資材施用法，湛水管理法などコメ中のCd濃度を低減さぜる対策が行われてきた(農林水産省 2011)。しかし，高濃度のCd汚染地を対象にした客土法には高い土壌浄化能力があるものの，環境負荷が大きくコストが高い(Ishikawa et al.2006)一方，低から中程度のCd汚染地で実施されているアルカリ資材施用や湛水管理によるCd低減対策は，効果の安定性(Murakami et al.2007)や濯瓶水の確保など問題点が多い(農林水産省 2011)。そこで我々は，資材施用や湛水管理等の対策が講じられてきた水田(Cd汚染が低から中程度)の浄化としてファイトレメディエーションに着目し，その浄化に適した植物としてCd高集積イネ品種が有望であることを示した(Ishikawa et al.2006，Murakami et al.2007)。またその有効性を圃場レベルにおいて確認した(Ibaraki et al.2009，Murakami et al.2008，2009，本間ら2009)。この技術の利点は，環境負荷が少なく低コストであり，またイネを用いるために新しい設備投資が少ないことが挙げられる。一方で，これまでにCd高集積品種として見出された「長香穀」，「Jarjan」，「AnjanaDhan」はいずれもインド型の在来種であり(Uraguchi et al.2009)，脱粒や倒伏といった機械収穫時に不利となる形質を併せ持つ。そのためCd高集積イネを用いたファイトレメディエーションの実用化および効率化には，これらの不良形質を改良した新規Cd高集積系統の育成が望まれる。特に脱粒性は栽培技術による難脱粒化が困難であり，脱粒によるCd収奪量低下や通常作復帰後の異株発生の直接的原因となる。そのためCd高集積品種への難脱粒性形質の付与は，実用的Cdファイトレメディエーション用イネ品種育成の第一歩として水回のCd除染の効率化に貢献することが期待される。そこで我々は，突然変異育種法を用いCd高集積品種「Jarjan」および「AnjanaDhan」の脱粒性を改善した「難脱粒性Jarjan」および「難脱粒性A吋anaDhan」を育成した。本稿では両系統の育成過程とその特性について紹介する。

DOI： 10.1270/jsbbr.15.17

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：OXFORD UNIV PRESS  

Increases in rates of individual leaf photosynthesis (P-n) are critical for future increases in yields of rice plants. Although many efforts have been made to improve rice P-n with transgenic technology, the desired increases in P-n have not yet been achieved. Two rice lines with extremely high values of P-n were identified among the backcrossed inbred lines derived from the indica variety Takanari, one of the most productive varieties in Japan, and the elite japonica variety Koshihikari (Koshihikari/Takanari//Takanari). The P-n values of the two lines at an ambient CO2 concentration of 370mol mol(1) as well as at a saturating concentration of CO2 were 2050% higher than those of the parental varieties. Compared with Takanari, these lines had neither a higher content nor a higher activity of ribulose 1,5-bisphosphate carboxylase/oxygenase when the leaf nitrogen contents were similar, but they did have high mesophyll conductance with respect to CO2 flux due to their higher density and more highly developed lobes of mesophyll cells. These lines also had higher electron transport rates. The plant growth rates of these lines were higher than that of Takanari. The findings show that it is possible to increase P-n significantly, both at the current atmospheric concentration of CO2 and at the increased concentration of CO2 expected in the future, using appropriate combinations of genetic resources that are available at present.

DOI： 10.1093/jxb/ers382

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：PUBLIC LIBRARY SCIENCE  

During the last 90 years, the breeding of rice has delivered cultivars with improved agronomic and economic characteristics. Crossing of different lines and successive artificial selection of progeny based on their phenotypes have changed the chromosomal constitution of the ancestors of modern rice; however, the nature of these changes is unclear. The recent accumulation of data for genome-wide single-nucleotide polymorphisms (SNPs) in rice has allowed us to investigate the change in haplotype structure and composition. To assess the impact of these changes during modern breeding, we studied 177 Japanese rice accessions, which were categorized into three groups: landraces, improved cultivars developed from 1931 to 1974 (the early breeding phase), and improved cultivars developed from 1975 to 2005 (the late breeding phase). Phylogenetic tree and structure analysis indicated genetic differentiation between non-irrigated (upland) and irrigated (lowland) rice groups as well as genetic structuring within the irrigated rice group that corresponded to the existence of three subgroups. Pedigree analysis revealed that a limited number of landraces and cultivars was used for breeding at the beginning of the period of systematic breeding and that 11 landraces accounted for 70% of the ancestors of the modern improved cultivars. The values for linkage disequilibrium estimated from SNP alleles and the haplotype diversity determined from consecutive alleles in five-SNP windows indicated that haplotype blocks became less diverse over time as a result of the breeding process. A decrease in haplotype diversity, caused by a reduced number of polymorphisms in the haplotype blocks, was observed in several chromosomal regions. However, our results also indicate that new haplotype polymorphisms have been generated across the genome during the breeding process. These findings will facilitate our understanding of the association between particular haplotypes and desirable phenotypes in modern Japanese rice cultivars.

DOI： 10.1371/journal.pone.0032982

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

Background: The high-quality sequence information and rich bioinformatics tools available for rice have contributed to remarkable advances in functional genomics. To facilitate the application of gene function information to the study of natural variation in rice, we comprehensively searched for articles related to rice functional genomics and extracted information on functionally characterized genes.
Results: As of 31 March 2012, 702 functionally characterized genes were annotated. This number represents about 1.6% of the predicted loci in the Rice Annotation Project Database. The compiled gene information is organized to facilitate direct comparisons with quantitative trait locus (QTL) information in the Q-TARO database. Comparison of genomic locations between functionally characterized genes and the QTLs revealed that QTL clusters were often co-localized with high-density gene regions, and that the genes associated with the QTLs in these clusters were different genes, suggesting that these QTL clusters are likely to be explained by tightly linked but distinct genes. Information on the functionally characterized genes compiled during this study is now available in the Overview of Functionally Characterized Genes in Rice Online database (OGRO) on the Q-TARO website (http://qtaro.abr.affrc.go.jp/ogro). The database has two interfaces: a table containing gene information, and a genome viewer that allows users to compare the locations of QTLs and functionally characterized genes.
Conclusions: OGRO on Q-TARO will facilitate a candidate-gene approach to identifying the genes responsible for QTLs. Because the QTL descriptions in Q-TARO contain information on agronomic traits, such comparisons will also facilitate the annotation of functionally characterized genes in terms of their effects on traits important for rice breeding. The increasing amount of information on rice gene function being generated from mutant panels and other types of studies will make the OGRO database even more valuable in the future.

DOI： 10.1186/1939-8433-5-26

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：NATL ACAD SCIENCES  

Nonphotochemical quenching (NPQ) regulates energy conversion in photosystem II and protects plants from photoinhibition. Here we analyze NPQ capacity in a number of rice cultivars. NPQ was strongly induced under medium and high light intensities in rice leaves. Japonica cultivars generally showed higher NPQ capacities than Indica cultivars when we measured a rice core collection. We mapped NPQ regulator and identified a locus (qNPQ1-2) that seems to be responsible for the difference in NPQ capacity between Indica and Japonica. One of the two rice PsbS homologues (OsPsbS1) was found within the qNPQ1-2 region. PsbS protein was not accumulated in the leaf blade of the mutant harboring transferred DNA insertion in OsPsbS1. NPQ capacity increased as OsPsbS1 expression increased in a series of transgenic lines ectopically expressing OsPsbS1 in an Indica cultivar. Indica cultivars lack a 2.7-kb region at the point 0.4 kb upstream of the OsPsbS1 gene, suggesting evolutionary discrimination of this gene.

DOI： 10.1073/pnas.1104809108

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記述言語：英語   出版者・発行元：JAPANESE SOC BREEDING  

DOI： 10.1270/jsbbs.61.221

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：CROP SCIENCE SOC JAPAN  

The whole-leaf photosynthetic rate in rice plants is controlled by various physiological processes. In a high-yielding indica rice variety, Habataki, the leaf photosynthetic rate (LPR) of the uppermost fully expanded leaves was approximately 130 to 140% of that in a japonica variety, Sasanishiki, from booting to the early ripening stage. We characterized the difference in the LPR between Habataki and Sasanishiki Leaves of Habataki contained higher levels of nitrogen and, as a consequence, of Rubisco, and had higher stomatal conductance that was associated with higher hydraulic conductance from roots to leaves than those of Sasanishiki. These features were responsible for the higher LPR of Habataki. An analysis of chromosome segment substitution lines (CSSLs) in which chromosome segments from Habataki were substituted into the genetic background of Sasanishiki showed that three genetic regions on chromosomes 4, 5 and 11 were responsible for the increase in the LPR. Each of these regions was estimated to increase the LPR by 15 to 30%, and we showed that they were associated with higher activity of mesophyll photosynthesis due to higher leaf nitrogen content and greater stomatal conductance. Leaf nitrogen content and stomatal conductance may be useful parameters for further quantitative trait locus analysis of efficient photosynthesis in leaves.

DOI： 10.1626/pps.14.118

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：OXFORD UNIV PRESS  

DNA marker-assisted selection appears to be a promising strategy for improving rates of leaf photosynthesis in rice. The rate of leaf photosynthesis was significantly higher in a high-yielding indica variety, Habataki, than in the most popular Japanese variety, Koshihikari, at the full heading stage as a result of the higher level of leaf nitrogen at the same rate of application of nitrogen and the higher stomatal conductance even when the respective levels of leaf nitrogen were the same. The higher leaf nitrogen content of Habataki was caused by the greater accumulation of nitrogen by plants. The higher stomatal conductance of Habataki was caused by the higher hydraulic conductance. Using progeny populations and selected lines derived from a cross between Koshihikari and Habataki, it was possible to identify the genomic regions responsible for the rate of photosynthesis within a 2.1 Mb region between RM17459 and RM17552 and within a 1.2 Mb region between RM6999 and RM22529 on the long arm of chromosome 4 and on the short arm of chromosome 8, respectively. The designated region on chromosome 4 of Habataki was responsible for both the increase in the nitrogen content of leaves and hydraulic conductance in the plant by increasing the root surface area. The designated region on chromosome 8 of Habataki was responsible for the increase in hydraulic conductance by increasing the root hydraulic conductivity. The results suggest that it may be possible to improve photosynthesis in rice leaves by marker-assisted selection that focuses on these regions of chromosomes 4 and 8.

DOI： 10.1093/jxb/erq387

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：JAPANESE SOC BREEDING  

Phytoextraction by high-cadmium (Cd)-accumulating rice (Oryza saliva L.) cultivars has been proposed as an attractive technique for cleaning up Cd-contaminated paddy field soil. To breed rice cultivars useful for Cd phytoextraction, it is necessary to understand the genetic basis of Cd accumulation in aerial parts. We developed backcross inbred lines (BILs) derived from a cross between a low-Cd-accumulating cultivar, Koshihikari (japonica), and a relatively high-Cd-accumulating cultivar, Jarjan (indica). The BILs were grown in fields containing two low levels of Cd and in pots of soil containing a moderate level of Cd. A quantitative trait locus (QTL) analysis revealed that a major QTL, qCdp7 (QTL potentially useful for Cd-phytoextraction on chromosome 7) contributed to accumulation of Cd in both brown rice and straw of plants grown in any of the three soils, and it accounted for 31% to 54% of the phenotypic variance. To confirm the phytoextraction-promotion ability of qCdp7, we grew BILs carrying the Jarjan allele of qCdp7 in Cd-contaminated soil, and confirmed the reduction of the Cd concentration in the shoots of Koshihikari subsequently grown in the phytoextracted soil. These results demonstrate that the Jarjan qCdp7 allele is effective at phytoextracting Cd from the soil.

DOI： 10.1270/jsbbs.61.43

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

Rice yield potential is determined by the balance between sink size and source capacity. To clarify the factors that limit yield in temperate japonica cultivars, we compared the yield performance of Sasanishiki, a temperate japonica cultivar, with those of three near-isogenic lines (NILs) of Sasanishiki with introgression of quantitative trait loci (QTL) derived from a high-yielding indica cultivar, Habataki: qSBN1, which increases the number of secondary rachis branches; qPBN6, which increases the number of primary rachis branches; and a pyramid line that combines these two QTLs. NIL (SBN1), NIL (PBN6), and NIL (SBN1 + PBN6) produced 28-37%, 9-16%, and 62-65% more spikelets per panicle than Sasanishiki, respectively. However, the NILs with increased spikelet number per panicle did not increase grain yield significantly, because compensation is taken place among different yield components. The pyramid line nevertheless had 4-12% higher yield than Sasanishiki due to greater translocation of carbohydrates from stem to panicle. There was no difference in carbohydrate accumulation before heading or in biomass production among Sasanishiki and the three NILs. The results indicate that increasing sink size does not substantially improve yield in Sasanishiki, which lacks sufficient substrate supply to fully satisfy the increased sink demand that results from the spikelet-number QTLs. (C) 2010 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.fcr.2010.08.013

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：OXFORD UNIV PRESS  

The rate of photosynthesis in paddy rice often decreases at noon on sunny days because of water stress, even under submerged conditions. Maintenance of higher rates of photosynthesis during the day might improve both yield and dry matter production in paddy rice. A high-yielding indica variety, &apos;Habataki&apos;, maintains a high rate of leaf photosynthesis during the daytime because of the higher hydraulic conductance from roots to leaves than in the standard japonica variety &apos;Sasanishiki&apos;. This research was conducted to characterize the trait responsible for the higher hydraulic conductance in &apos;Habataki&apos; and identified a chromosome region for the high hydraulic conductance.
Hydraulic conductance to passive water transport and to osmotic water transport was determined for plants under intense transpiration and for plants without transpiration, respectively. The varietal difference in hydraulic conductance was examined with respect to root surface area and hydraulic conductivity (hydraulic conductance per root surface area, L(p)). To identify the chromosome region responsible for higher hydraulic conductance, chromosome segment substitution lines (CSSLs) derived from a cross between &apos;Sasanishiki&apos; and &apos;Habataki&apos; were used.
The significantly higher hydraulic conductance resulted from the larger root surface area not from L(p) in &apos;Habataki&apos;. A chromosome region associated with the elevated hydraulic conductance was detected between RM3916 and RM2431 on the long arm of chromosome 4. The CSSL, in which this region was substituted with the &apos;Habataki&apos; chromosome segment in the &apos;Sasanishiki&apos; background, had a larger root mass than &apos;Sasanishiki&apos;.
The trait for increasing plant hydraulic conductance and, therefore, maintaining the higher rate of leaf photosynthesis under the conditions of intense transpiration in &apos;Habataki&apos; was identified, and it was estimated that there is at least one chromosome region for the trait located on chromosome 4.

DOI： 10.1093/aob/mcq175

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

Over the past two decades, genetic dissection of complex phenotypes of economic and biological interest has revealed the chromosomal locations of many quantitative trait loci (QTLs) in rice and their contributions to phenotypic variation. Mapping resolution has varied considerably among QTL studies owing to differences in population size and number of DNA markers used. Additionally, the same QTLs have often been reported with different locus designations. This situation has made it difficult to determine allelic relationships among QTLs and to compare their positions. To facilitate reliable comparisons of rice QTLs, we extracted QTL information from published research papers and constructed a database of 1,051 representative QTLs, which we classified into 21 trait categories. This database (QTL Annotation Rice Online database; Q-TARO, http://qtaro.abr.affrc.go.jp/) consists of two web interfaces. One interface is a table containing information on the mapping of each QTL and its genetic parameters. The other interface is a genome viewer for viewing genomic locations of the QTLs. Q-TARO clearly displays the co-localization of QTLs and distribution of QTL clusters on the rice genome.

DOI： 10.1007/s12284-010-9041-z

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

One of the major challenges in genetics has been to identify the nucleotide polymorphisms responsible for phenotypic variation. Through intensive analysis, several major quantitative trait loci (QTLs) for agronomic traits in rice have been identified and the underlying candidate genes have been delimited. Advanced mapping populations, including chromosome segment substitution lines, have enhanced the power of genetic analysis to detect QTL alleles, even those with minor effects. Recent examples of marker-assisted selection have proven the potential of this strategy for crop improvement. The genome-wide discovery of single nucleotide polymorphisms (SNPs), even among closely related cultivars, has enhanced the power of allele mining in a wide range of rice breeding materials. An array-based SNP genotyping system can be used to visualize pedigree haplotypes in breeding materials, including landraces and modern cultivars. All of these technologies are accelerating the genetic dissection of complex agronomic traits and further improvement of rice.

DOI： 10.1007/s12284-010-9044-9

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担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

Leaf photosynthesis, an important determinant of yield potential in rice, can be estimated from measurements of chlorophyll content. We searched for quantitative trait loci (QTLs) for Soil and Plant Analyzer Development (SPAD) value, an index of leaf chlorophyll content, and assessed their association with leaf photosynthesis. QTL analysis derived from a cross between japonica cultivar Sasanishiki and high-yielding indica cultivar Habataki detected a QTL for SPAD value on chromosome 4. This QTL explained 31% of the total phenotypic variance, and the Habataki allele increased the SPAD value. Chromosomal segment substitution line (CSSL) with the corresponding segment from Habataki had a higher leaf photosynthetic rate and SPAD value than Sasanishiki, suggesting an association between SPAD value and leaf photosynthesis. The CSSL also had a lower specific leaf area (SLA) than Sasanishiki, reflecting its thicker leaves. Substitution mapping under Sasanishiki genetic background demonstrated that QTLs for SPAD value and SLA were co-localized in the 1,798-kb interval. The results suggest that the phenotypes for SPAD value and SLA are controlled by a single locus or two tightly linked loci, and may play an important role in increasing leaf photosynthesis by increasing chlorophyll content or leaf thickness, or both.

DOI： 10.1007/s12284-010-9047-6

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：BIOMED CENTRAL LTD  

Background: To create useful gene combinations in crop breeding, it is necessary to clarify the dynamics of the genome composition created by breeding practices. A large quantity of single-nucleotide polymorphism (SNP) data is required to permit discrimination of chromosome segments among modern cultivars, which are genetically related. Here, we used a high-throughput sequencer to conduct whole-genome sequencing of an elite Japanese rice cultivar, Koshihikari, which is closely related to Nipponbare, whose genome sequencing has been completed. Then we designed a high-throughput typing array based on the SNP information by comparison of the two sequences. Finally, we applied this array to analyze historical representative rice cultivars to understand the dynamics of their genome composition.
Results: The total 5.89-Gb sequence for Koshihikari, equivalent to 15.7x the entire rice genome, was mapped using the Pseudomolecules 4.0 database for Nipponbare. The resultant Koshihikari genome sequence corresponded to 80.1% of the Nipponbare sequence and led to the identification of 67 051 SNPs. A high-throughput typing array consisting of 1917 SNP sites distributed throughout the genome was designed to genotype 151 representative Japanese cultivars that have been grown during the past 150 years. We could identify the ancestral origin of the pedigree haplotypes in 60.9% of the Koshihikari genome and 18 consensus haplotype blocks which are inherited from traditional landraces to current improved varieties. Moreover, it was predicted that modern breeding practices have generally decreased genetic diversity
Conclusions: Detection of genome-wide SNPs by both high-throughput sequencer and typing array made it possible to evaluate genomic composition of genetically related rice varieties. With the aid of their pedigree information, we clarified the dynamics of chromosome recombination during the historical rice breeding process. We also found several genomic regions decreasing genetic diversity which might be caused by a recent human selection in rice breeding. The definition of pedigree haplotypes by means of genome-wide SNPs will facilitate next-generation breeding of rice and other crops.

DOI： 10.1186/1471-2164-11-267

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記述言語：日本語   出版者・発行元：日本作物学会  

DOI： 10.14829/jcsproc.229.0.352.0

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記述言語：日本語   出版者・発行元：日本作物学会  

DOI： 10.14829/jcsproc.229.0.96.0

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記述言語：日本語   出版者・発行元：日本作物学会  

DOI： 10.14829/jcsproc.229.0.98.0

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：OXFORD UNIV PRESS  

Large phenotypic variations in the cadmium (Cd) concentration of rice grains and shoots have been observed. However, the genetic control of Cd accumulation remains poorly understood. Quantitative trait loci (QTLs) determining the grain Cd concentration of rice grown in a Cd-polluted paddy field were identified. Using a mapping population consisting of 85 backcross inbred lines derived from a cross between the low-Cd-accumulating cultivar Sasanishiki (japonica) and high-Cd-accumulating cultivar Habataki (indica), two QTLs for increasing grain Cd concentration were found on chromosomes 2 and 7. A major-effect QTL, qGCd7 (QTL for grain Cd on chromosome 7), was detected on the short arm of chromosome 7. It accounted for 35.5% of all phenotypic variance in backcross inbred lines. qGCd7 was not genetically related to any QTLs for concentrations of essential trace metals (Cu, Fe, Mn, and Zn) or those for agronomic traits such as heading date, suggesting that this QTL is specific to Cd. Furthermore, the existence of qGCd7 was confirmed using chromosome segment substitution lines (CSSLs) and an F(2) population from a cross between the target CSSL and Sasanishiki grown in a Cd-polluted paddy soil. To our knowledge, qGCd7 is a novel QTL with major effects for increasing grain Cd concentrations.

DOI： 10.1093/jxb/erp360

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担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

Leaf photosynthetic potential, a major determinant of yield potential in rice, is mostly explained by stomatal conductance (g(s)) as well as leaf N content (Rubisco protein content). Therefore, the rapid and precise evaluation of g(s) as well as leaf N content would be a valuable addition to rice breeding programs aimed at improved yield potential. We established a simple method based on infrared thermography to estimate varietal differences in g(s). Seven rice varieties were cultivated in two-row plots in 2007, and canopy temperatures in three varieties, including a control variety, Koshihikari, were simultaneously measured to determine canopy temperature difference (CTd) between Koshihikari and the other varieties on clear days. The varieties Takanari, Habataki, and TUAT1-5-6a displayed significantly (P &lt; 0.05) lower leaf temperature and higher g(s) and leaf photosynthetic rate (P(n)) than Koshihikari. CTd was closely correlated with g(s) and P(n). These results indicate that CTd may be useful as a relative index to estimate varietal differences in g(s). A significant CTd was still observed even under cloudy conditions in 2008. Takanari and TUAT1-5-6a had lower leaf temperature than Koshihikari on cloudy days as well as on clear days. Subsequent investigation of photosynthetic light response curves revealed that Takanari and TUAT1-5-6a had higher g(s) and P(n) than Koshihikari under lower irradiance. These results suggest that infrared thermography may be a simple method of evaluating varietal differences in g(s) through CTd, and that it may be practicable even under cloudy conditions. (C) 2009 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.fcr.2009.10.019

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：WILEY-BLACKWELL PUBLISHING, INC  

The stub-spreading trait, also designated as &apos;tiller angle&apos;, is one of the components that determine the plant type. In rice, the trait is quite important because of its close relationship to the yield performance. The Spk(t) gene is a major determinant of the trait in the cross of &apos;Kasalath&apos; (indica) and &apos;Nipponbare&apos; (japonica). In this study, the Spk(t) gene was isolated by a map-based cloning strategy. Sequence analysis of the cDNA clones from the locus revealed that the Spk(t) transcripts and the spk(t) transcripts encode identical 259-aa proteins of unknown function; however, the structure of the 3&apos;-untranslated region of each allele is quite different. Additional transgenic experiments in rice demonstrated that the difference is caused by a single-nucleotide polymorphism at the 3&apos;-splicing site specific to the Spk(t) allele which thereby plays a critical role in the phenotypic expression. In addition to revealing the molecular mechanism underlying the allele differentiation at the Spk(t) locus, the information presented here should be useful for breeding of this trait in rice.

DOI： 10.1111/j.1439-0523.2009.01639.x

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担当区分：責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：JAPANESE SOC BREEDING  

To identify quantitative trait loci (QTLs) associated with culm length in Japanese japonica rice varieties, we conducted QTL analyses using a set of reciprocal backcrossed inbred lines (BILs) from crosses between Nipponbare and Koshihikari. We detected five QTLs in the two BILs that are involved in the culm-length difference between Nipponbare and Koshihikari. A QTL located on the short arm of chromosome 1, qCL1, was commonly detected near the simple sequence repeat (SSR) marker RM8068 in both BILs in three growing seasons. The Nipponbare allele of qCL1 shortened from 1.9 to 3.0cm of culm length. Substitution lines (SLs) of Koshihikari in which the QTL was replaced with the Nipponbare allele exhibited decreased lengths of lower internodes. qCL1 was mapped within about 2.6 Mbp in the region distal from SSR marker RM10132, suggesting qCL1 differed from the dwarf or semi-dwarf genes that have been previously reported. Japanese japonica rice landraces with Nipponbare alleles of DNA markers around qCL1 had significantly shorter culm length than other landraces. The results suggest that the novel allele for short culm length was originally distributed in Japanese rice landraces and has been used for introducing the semi-dwarf phenotype and improving plant architecture during practical breeding.

DOI： 10.1270/jsbbs.59.285

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担当区分：筆頭著者   記述言語：英語   出版者・発行元：OXFORD UNIV PRESS  

Completion of the genome analysis followed by extensive comprehensive studies on a variety of genes and gene families of rice (Oryza sativa) resulted in rapid accumulation of information concerning the presence of many complex traits that are governed by a number of genes of distinct functions in this most important crop cultivated worldwide. The genetic and molecular biological dissection of many important rice phenotypes has contributed to our understanding of the complex nature of the genetic control with respect to these phenotypes. However, in spite of the considerable advances made in the field, details of genetic control remain largely unsolved, thereby hampering our exploitation of this useful information in the breeding of new rice cultivars. To further strengthen the field application of the genome science data of rice obtained so far, we need to develop more powerful genomics-assisted methods for rice breeding based on information derived from various quantitative trait loci (QTL) and related analyses. In this review, we describe recent progresses and outcomes in rice QTL analyses, problems associated with the application of the technology to rice breeding and their implications for the genetic study of other crops along with future perspectives of the relevant fields.

DOI： 10.1093/dnares/dsp006

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

Increasing leaf photosynthesis offers a possible way to improve yield potential in rice (Oryza sativa L.). Carbon isotope discrimination (Delta(13)C) has potential as an indirect selection criterion. In this study, we searched for quantitative trait loci (QTLs) controlling Delta(13)C, and assessed their association with leaf photosynthesis. Substitution mapping by using chromosome segment substitution lines (CSSLs), that carry segments from the indica cultivar Kasalath in the genetic background of the japonica cultivar Koshihikari, identified genomic regions affecting Delta(13)C on chromosomes (Chr.) 2, 3, 6, 7, and 12. One of the CSSLs, SL208, in which most regions on Chr. 3 were substituted with Kasalath segments, showed higher leaf stomatal conductance for CO(2) (g (s)) and Delta(13)C than Koshihikari during the vegetative stage although leaf photosynthetic rate did not differ between them. These results suggest an association between Delta(13)C and g (s). To test this association, we performed a QTL analysis for Delta(13)C at vegetative and heading stages in an F(2) population derived from a cross between SL208 and Koshihikari. The results confirmed a QTL controlling Delta(13)C on the long arm of Chr. 3. By using a near-isogenic line specific to Hd6, we ruled out the possibility that variation in Delta(13)C was generated through the pleiotropic effect of heading date.

DOI： 10.1007/s00122-009-0990-9

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

To understand the genetic basis of yield-related traits of rice, we developed 39 chromosome segment substitution lines (CSSLs) from a cross between an average-yielding japonica cultivar, Sasanishiki, as the recurrent parent and a high-yielding indica cultivar, Habataki, as the donor. Five morphological components of panicle architecture in the CSSLs were evaluated in 2 years, and 38 quantitative trait loci (QTLs) distributed on 11 chromosomes were detected. The additive effect of each QTL was relatively small, suggesting that none of the QTLs could explain much of the phenotypic difference in sink size between Sasanishiki and Habataki. We developed nearly isogenic lines for two major QTLs, qSBN1 (for secondary branch number on chromosome 1) and qPBN6 (for primary branch number on chromosome 6), and a line containing both. Phenotypic analysis of these lines revealed that qSBN1 and qPBN6 contributed independently to sink size and that the combined line produced more spikelets. This suggests that the cumulative effects of QTLs distributed throughout the genome form the major genetic basis of panicle architecture in rice.

DOI： 10.1007/s00122-008-0722-6

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担当区分：筆頭著者   記述言語：英語   掲載種別：論文集(書籍)内論文   出版者・発行元：Springer International Publishing  

Sequencing of the entire rice genome has made remarkable progress (IRGSP 2005). This sequence information has provided new tools for genetics and has created a new paradigm of plant breeding. Many phenotypic traits of economic interest are controlled by multiple genes and often show complex and quantitative inheritance. Recent progress in rice genomics has had a great impact on the genetic dissection of such traits into single genetic factors, or quantitative trait loci (QTLs) (Tanksley 1993
Yano and Sasaki 1997). Such genetic factors can subsequently be identified at the molecular level by map-based strategies (Yano 2001). Many QTL mapping studies in rice have been conducted during the last decade. Information on individual QTLs is collected and summarized in a cereal genome database, Gramene (http://www.gramene.org/Oryza_sativa/). It is difficult to review all progress due to the tremendous amount of QTL information in this database. Thus, in this chapter, we summarize QTLs with relatively large effects of economic or agronomic interest. Some of them have already been cloned at the molecular level (Table 1). In addition, we describe the platform for use in the systematic exploitation of natural variations and QTLs and in further analyses of QTLs, such as molecular cloning and marker assisted selection (MAS) for the biological study and breeding of rice.

DOI： 10.1007/978-3-540-74250-0_22

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

Stigma exsertion is one of the important traits which contribute to the efficient improvement of commercial seed production in hybrid rice. In order to understand the genetic factors involved in the stigma exsertion of an indica variety-IR24-a QTL analysis was conducted using the F-2 population between a japonica variety-Koshihikari-and a breeding line showing exserted stigma selected from the backcross population between IR24 as a donor and japonica varieties. As a result, a highly significant QTL (qES3), which had been predicted in the recombinant inbred population of IR24, was confirmed at the centromeric region on chromosome 3. qES3 increases about 20% of the frequency of the exserted stigmas at the IR24 allele and explains about 32% of the total phenotypic variance. A QTL near-isogenic line for qES3 increased the frequency of the exserted stigma by 36% compared to that of Koshihikari in a field evaluation, which suggests that qES3 is a promising QTL for the development of a maternal line for hybrid rice.

DOI： 10.1007/s00122-006-0454-4

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

Quantitative trait loci (QTLs) that control the performance of tissue culture in rice were detected by using 116 RFLP markers and 183 BC1F3 lines derived from two varieties, Koshihikari and Kasalath. With time, the seed callus of Koshihikari tends to turn brown and stop growing, while that of Kasalath remains yellowish-white and proliferates continuously. The performance of tissue culture in the induction of calli from seed, the subculture of induced calli, and shoot regeneration were evaluated by five indices: induced-callus weight, induced-callus color, subcultured-callus volume, subcultured-callus color, and regeneration rate. Through callus induction and subculture, eight putative QTLs (P &lt; 0.001) were located on chromosomes 1, 4, and 9. Among these QTLs, five Kasalath alleles and three Koshihikari alleles improved tissue culture performance. No QTL for regeneration was found. Among all the QTLs, qSv1 explained the largest phenotypic variance, 33%, in subcultured-callus volume. In induced-callus color, two detected QTLs accounted for 36.4% of the total phenotypic variance; this was the highest score among the five indices used to evaluate the performance of tissue culture. Three near-isogenic lines for QTLs, located in two regions on chromosome 1, were developed to evaluate their tissue culture performance. The Kasalath alleles in qSv1 and qSc1-1 improved callus color through callus induction and subculture, and increased the subcultured-callus volume and the fresh weight of regenerated calli, including shoots, roots, and differentiated structures. In qSc1-2, the Kasalath allele improved callus color through induction and subculture. These results verified the presence of QTLs for the volume and color of subcultured callus on chromosome 1, qSv1, qSc1-1, and qSc1-2.

DOI： 10.1007/s00122-005-0200-3

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1270/jsbbs.56.405

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：NATL ACAD SCIENCES  

Regeneration of plant organs is often the essential step in genetic transformation; however, the regeneration ability of a plant varies depending on the genetic background. By conventional crosses of low-regeneration rice strain Koshihikari with high-regeneration rice strain Kasalath, we identified some quantitative trait loci, which control the regeneration ability in rice. Using a map-based cloning strategy, we isolated a main quantitative trait loci gene encoding ferredoxin-nitrite reductase (NiR) that determines regeneration ability in rice. Molecular analyses revealed that the poor regeneration ability of Koshihikari is caused by lower expression than in Kasalath and the specific activity of NiR. Using the NiR gene as a selection marker, we succeeded in selectively transforming a foreign gene into rice without exogenous marker genes. Our results demonstrate that nitrate assimilation is an important process in rice regeneration and also provide an additional selectable marker for rice transformation.

DOI： 10.1073/pnas.0504220102

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER ASSOC ADVANCEMENT SCIENCE  

Most agriculturally important traits are regulated by genes known as quantitative trait loci (QTLs) derived from natural allelic variations. We here show that a QTL that increases grain productivity in rice, Gn1a, is a gene for cytokinin oxidase/ dehydrogenase (OsCKX2), an enzyme that degrades the phytohormone cytokinin. Reduced expression of OsCKX2 causes cytokinin accumulation in inflorescence meristems and increases the number of reproductive organs, resulting in enhanced grain yield. QTL pyramiding to combine loci for grain number and plant height in the same genetic background generated lines exhibiting both beneficial traits. These results provide a strategy for tailormade crop improvement.

DOI： 10.1126/science.1113373

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：JAPANESE SOC BREEDING  

DOI： 10.1270/jsbbs.55.237

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1270/jsbbs.55.65

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記述言語：英語   出版者・発行元：OXFORD UNIV PRESS  

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：KLUWER ACADEMIC PUBL  

The Rf-1 gene restores the pollen fertility disturbed by the BT-type male sterile cytoplasm. Nine restriction fragment length polymorphism( RFLP) markers on chromosome 10, where the Rf-1 gene is located, were converted to PCR-based markers. Genetic analysis was conducted using the nine markers and a segregating population consisting of 1042 plants. As a result, the Rf-1 gene was mapped between S12564 Tsp509I and C1361 MwoI. The genetic distance of the two marker loci was estimated as 0.3 cM. Based on the map information of the Rf-1 gene, it will be possible to introduce a limited chromosomal segment of the Rf-1 region derived from a donor into japonica rice varieties efficiently and effectively by marker-assisted selection (MAS). Also, examination of seed purity of hybrid rice varieties and their parental lines will be facilitated. Furthermore, judging from the genetic distance from the Rf-1 locus to S12564 Tsp509I and C1361 MwoI loci, it seems that the Rf-1 gene could be isolated by chromosomal walking from either or both of the two marker loci.

DOI： 10.1023/A:1021915611210

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：JAPANESE SOC BREEDING  

An RFLP linkage map was constructed using a BC1F3 population, which was developed by backcrossing between an elite Japonica rice variety, Koshihikari, as the recurrent parent and an Indica rice variety, Kasalath, as a donor parent. The map was constructed using data from 187 plants and 116 RFLP markers. Quantitative trait loci (QTL) analyses were carried out for days-to-heading, and culm, panicle, and internode lengths. Four QTLs (p &lt; 0.001) for days-to-heading, six for culm length, and four for panicle length were detected. Seventeen QTLs were detected for the internode length. Chromosomal locations of putative QTLs in this study were compared with those in other studies. Several QTLs for these traits, showing a correlation with phenotypic values, were mapped in the same chromosomal regions. However, the sets and relative effects of QTLs for internode length were different among the corresponding QTLs for culm length. The implications of QTL analysis in the BC1F3 generation for rice chromosome introgression breeding are discussed.

DOI： 10.1270/jsbbs.51.63

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER-VERLAG  

To characterize quantitative trait loci (QTLs), we used marker-assisted selection (MAS) to develop three nearly isogenic lines (NILs) differing only for the presence of a single, specific QTL (QTL-NILs) - Hd1, Hd2, and Hd3 - for heading date in rice. The three lines contained the chromosomal region of the target QTL from donor variety Kasalath (indica) in the genetic background of var. Nipponbare (japonica). To analyze epistatic interactions in pairs of these QTLs, we also used MAS to develop four combined QTL-NILs with 2 of the 3 QTLs or with all 3. Different daylength treatment testing of the QTL-NILs revealed that the three QTLs control photoperiod sensitivity. Genetic analysis of F-2 populations derived from crosses between the three QTL-NILs with a single QTL using molecular markers revealed the existence of epistatic interactions between Hd1 and Hd2, and Hd2 and Hd3. These interactions were also confirmed by the analysis of combined QTL-NILs under different daylength conditions. The existence of an epistatic interaction between Hd1 and Hd3 was also clarified. Based on these results, we suggest that the Kasalath allele of Hd3 does not affect photoperiod sensitivity by itself but that it is involved in enhancement of the expression of the Nipponbare alleles of Hd1 and Hd2.

DOI： 10.1007/s001220051576

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：GENETICS  

A backcrossed population (BC4F2) derived from a cross between a japonica rice variety, Nipponbare, as the recurrent parent and an indica rice variety, Kasalath, as the donor parent showed a long-range variation in days to heading. Quantitative trait loci (QTL) analysis revealed that two QTL, one on chromosome 3, designated Hd6, and another on chromosome 2, designated Hd7 were involved in this variation; and Hd6 was precisely mapped as a single Mendelian factor by using progeny testing (BC4F8). The nearly isogenic line with QTL (QTL-NIL) that carries the chromosomal segment from Kasalath for the Hd6 region in Nipponhare's genetic background was developed by marker-assisted selection. In a day-length treatment test, the QTL-NIL for Hd6 prominently increased days to heading under a 13.5-hr day length compared with the recurrent parent, Nipponbare, suggesting that Hd6 controls photoperiod sensitivity. QTL analysis of the F-2 population derived from a cross between the QTL-NILs revealed existence of an epistatic interaction between Hd2, which is one of the photoperiod sensitivity genes detected in a previous analysis, and Hd6. The day-length treatment tests of these QTL-NILs, including the line introgressing both Hd2 and Hd6, also indicated an epistatic interaction for photoperiod sensitivity between them.

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER VERLAG  

Fine mapping was carried out on three putative QTLs (tentatively designated as Hd-l to Hd-3) of five such QTLs controlling heading date in rice that had been earlier identified using an F-2 population derived from a cross between a japonica variety, 'Nipponbare', and an indica variety,'Kasalath', using progeny backcrossed with 'Nipponbare' as the recurrent parent. One BC3F2 and two BC3F1 plants, in which the target QTL regions were heterozygous and most other chromosomal regions were homozygous for the 'Nipponbare' allele, were selected as the experimental material. Self-pollinated progeny (BC3F2 and BC3F3) Of the BC3F1 or BC3F2 showed continuous variation in days to heading. By means of progeny testing based on BC3F3 or BC3F4 lines, we determined the genotypes of each BC3F2 or BC3F3 individual at target QTLs. Their segregation patterns fitted Mendelian inheritance ratios. When the results obtained by RFLP analysis and progeny tests were combined, Hd-1, Hd-2 and Hd-3 were mapped precisely on chromosomes 6, 7 and 6, respectively, of a rice RFLP linkage map. The results demonstrated that QTLs can be treated as Mendelian factors. Moreover, these precise locations were in good agreement with the regions estimated by QTL analysis of the initial Fz population, demonstrating the high reliability of QTL mapping using a high-density linkage map.

DOI： 10.1007/s001220050864

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：GENETICS  

A 2275-marker genetic map of rice (Oryza sativa L.) covering 1521.6 cM in the Kosambi function has been constructed using 186 F-2 plants from a single cross between the japonica variety Nipponbare and the indica variety Kasalath. The map provides the most detailed and informative genetic map of any plant. Centromere locations on 12 linkage groups were determined by dosage analysis of secondary and telotrisomics using &gt;130 DNA markers located on respective chromosome arms. A limited influence on meiotic recombination inhibition by the centromere in the genetic map was discussed. The main sources of the markers in this map were expressed sequence tag (EST) clones from Nipponbare callus, root, and shoot libraries. We mapped 1455 loci using ESTs; 615 of these loci showed significant similarities to known, genes, including single-copy genes, family genes, and isozyme genes. The high-resolution genetic map permitted us to characterize meiotic recombinations in the whole genome. Positive interference of meiotic recombination was detected both by the distribution of recombination number per each chromosome and by the distribution of double crossover interval lengths.

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：JAPANESE SOC BREEDING  

Improving plant type is one of the principal objectives of rice breeding programs. However, little information about the genetic basis of plant type is available. For progenies derived from indica/japonica crosses, the variation of plant type is continuous and complex, so genetic analysis of such traits is often difficult. This study was undertaken to clarify the genetic basis of spreading stub, an inferior plant type character for recent Japanese elite rice varieties, Two different plant types, spreading stub and erect, were observed in one population (BC3F2) derived from a selected backcrossed plant, in which a japonica variety, Nipponbare, was the recurrent parent and an indica variety, Kasalath, was the donor parent. BC3F3 lines derived from each BC3F2 individual were also classified into 3 distinct types, erect (9 lines), spreading (12 lines) and segregating into both types (29 lines). Spreading type was observed about 3 times more frequently than erect type in each segregated line. These results suggest that spreading stub was controlled by a single dominant gene. Moreover the tentatively designated locus, Spk(t), was mapped, with RFLP markers, on chromosome 9.

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記述言語：英語   出版者・発行元：Japanese Society of Breeding  

栽培イネにおける草型の改良は重要な育種目標のひとつであるにもかかわらず,一般には雑種後代で連続的かつ複雑な変異を示すため,その遺伝学的な知見は少ない。本研究では草型の構成要因のひとつである株の開張性(spreading stub)について遺伝子分析を試みた。日本型品種日本晴とインド型品種Kasalathの交雑F₁個体に日本晴を反復親として育成した戻し交雑後代個体BC₃F₁-11の自殖集団(BC₃F₂-11,n=50)は遺伝的背景が日本晴型に近づいたため株の開張性に関して単因子様の分離が認められた。BC₂F₃後代検定を実施したところ,この形質の遺伝子型評価が可能になり,その系統数の内訳は直立型:分離型:開張型=9:29:12(1:2:1,χ²=1.64)であった。また分離系統内では開張個体と直立個体がほぼ3:1の割合で観察された。これらの結果から,この集団における株の開張性はKasalathが有する優性の1遺伝子によって支配されることが明らかとなった。またRFLPマーカーを用いた連鎖分析によってこの遺伝子座(Spk(t)と仮称)は第9染色体に座乗することが判明した。

DOI： 10.1270/jsbbs1951.47.141

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記述言語：日本語  

DOI： 10.1270/jsbbr.16.13

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記述言語：日本語  

DOI： 10.14829/jcsproc.233.0.178.0

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記述言語：日本語  

DOI： 10.14829/jcsproc.232.0.170.0

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記述言語：日本語   出版者・発行元：農林水産技術情報協会  

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記述言語：日本語  

DOI： 10.14829/jcsproc.231.0.148.0

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記述言語：日本語   出版者・発行元：農林水産技術情報協会  

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記述言語：英語   出版者・発行元：Institute of Radiation Breeding, Ministry of Agriculture & Forestry  

ゲノム塩基配列情報は、遺伝子機能解析や比較ゲノム解析などの基礎的な研究への貢献ばかりではなく、作物育種への貢献も期待されている。自殖性作物では、有用遺伝子の連鎖解析による選抜マーカーの同定ならびにマーカー選抜(Marker-assisted selection: MAS)による優良品種への導入が進み、その集積がいくつかの形質で試みられている。イネでは、出穂期、半矮性、いもち病圃場抵抗性、トビイロウンカ抵抗性、洪水耐性などの改良がMASによって進められてきた。特に、いもち病圃場抵抗性においては、抵抗性遺伝子の近傍に存在する不良形質に関わる遺伝子の連鎖(連鎖のひきずり)をマーカー支援により解消することに成功している。またMASにより導入された遺伝子を組み合わせる、いわゆる遺伝子ピラミディングも現実的な作業になってきた。育種上重要な形質の一部は、効果の比較的小さな多数の遺伝子が関与し、それらの遺伝子作用の組み合わせによってそれらの形質が最適化されている。このような効果の小さな遺伝子についても、染色体断片置換系統に代表される実験系統群の作出と利用によって、遺伝子解析のみならずマーカー選抜も可能になっている。近年、ゲノム塩基配列解析手法の飛躍的な進歩によって、一塩基多型(SNP)の大規模検出が可能になり、近縁な品種間も含めた様々なイネ品種系統間のゲノムワイドなSNPの検出が進められている。また、アレイ技術を活用したゲノムワイドなSNPの一斉解析も可能になっている。これらの新しい手法は、ゲノムのある特定の部分(遺伝子)だけに注目して選抜操作を行う従来のMASから、ゲノム全体にわたるハプロタイプあるいは複数の染色体領域に注目して、選抜操作を行うゲノム選抜の可能性を示唆している。その一方、研究が進んでMASの限界も見えてきた。その限界は、マーカーに代表されるゲノムツールの問題と言うよりはむしろ、いかにして望ましい遺伝子を見いだすか、育種形質に関していかに信頼性の高い評価手法を作り出すか、あるいは精度の高い遺伝解析を可能にする実験材料の準備など、遺伝育種に関わる研究者の工夫の問題になってきた。今後、新たな作物育種の展開には、新しい形質評価法の模索や広範な遺伝資源の利活用を基盤にして、ゲノミクスを背景とした形質の理解を深める基礎的な研究(生理学)、多様な実験系統群、育種が培ってきた経験や知識、ゲノミクスにおける新しいツールや方法などの効果的な融合が不可欠であろう。

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記述言語：日本語   出版者・発行元：農林水産先端技術産業振興センター  

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記述言語：日本語  

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記述言語：日本語   出版者・発行元：岩波書店  

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記述言語：英語   掲載種別：研究発表ペーパー・要旨（国際会議）   出版者・発行元：FEDERATION AMER SOC EXP BIOL  

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出願番号：第20119号  出願日：2006年8月22日

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出願人：本田技研工業株式会社

出願番号：JP2003014434  出願日：2003年11月13日

公開番号：WO2004-044200  公開日：2004年5月27日

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出願人：本田技研工業株式会社

出願番号：特願2004-551229  出願日：2003年11月13日

特許番号/登録番号：特許第4448031号  発行日：2010年1月29日

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出願番号：第10870号  出願日：2002年12月16日

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出願人：日本たばこ産業株式会社, シンジェンタ リミテッド

出願番号：特願2001-281109  出願日：2001年9月17日

公開番号：特開2002-291488  公開日：2002年10月8日

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出願人：日本たばこ産業株式会社, シンジェンタ リミテッド

出願番号：特願2001-247600  出願日：2001年8月17日

公開番号：特開2002-345485  公開日：2002年12月3日

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出願番号：第8631号  出願日：2001年2月9日

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出願番号：第8632号  出願日：2001年2月9日

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出願番号：第8630号  出願日：2001年2月9日

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出願番号：第7690号  出願日：2000年2月22日

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出願番号：第7691号  出願日：2000年2月22日

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出願番号：第5189号  出願日：1996年10月15日

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