研究者詳細 - 山本　敏央

論文 - 山本　敏央

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Quantitative trait loci for whiteness of cooked rice detected in improved rice cultivars in Hokkaido 査読

Hiroshi Shinada, Toshio Yamamoto, Eiji Yamamoto, Kiyosumi Hori, Yuji Hirayama, Toshihiko Maekawa, Hitoshi Kiuchi, Hirokazu Sato, Takashi Sato

BREEDING SCIENCE 65 ( 3 ) 201 - 207 2015年6月

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

Detection of QTLs for white-back and basal-white grains caused by high temperature during ripening period in japonica rice 査読

Takuya Wada, Katsunori Miyahara, Jun-Ya Sonoda, Tadashi Tsukaguehi, Masayuki Miyazaki, Masao Tsubone, Tsuyu Ando, Kaworu Ebana, Toshio Yamamoto, Norio Iwasawa, Takayuki Umemoto, Motohiko Kondo, Masahiro Yano

BREEDING SCIENCE 65 ( 3 ) 216 - 225 2015年6月

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

Genetic architecture of variation in heading date among Asian rice accessions 査読

Kiyosumi Hori, Yasunori Nonoue, Nozomi Ono, Taeko Shibaya, Kaworu Ebana, Kazuki Matsubara, Eri Ogiso-Tanaka, Takanari Tanabata, Kazuhiko Sugimoto, Fumio Taguchi-Shiobara, Jun-ichi Yonemaru, Ritsuko Mizobuchi, Yusaku Uga, Atsunori Fukuda, Tadamasa Ueda, Shin-ichi Yamamoto, Utako Yamanouchi, Toshiyuki Takai, Takashi Ikka, Katsuhiko Kondo, Tomoki Hoshino, Eiji Yamamoto, Shunsuke Adachi, Hideki Nagasaki, Ayahiko Shomura, Takehiko Shimizu, Izumi Kono, Sachie Ito, Tatsumi Mizubayashi, Noriyuki Kitazawa, Kazufumi Nagata, Tsuyu Ando, Shuichi Fukuoka, Toshio Yamamoto, Masahiro Yano

BMC PLANT BIOLOGY 15 115 2015年5月

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

Isolation of a Novel Lodging Resistance QTL Gene Involved in Strigolactone Signaling and Its Pyramiding with a QTL Gene Involved in Another Mechanism 査読

Kenji Yano, Taiichiro Ookawa, Koichiro Aya, Yusuke Ochiai, Tadashi Hirasawa, Takeshi Ebitani, Takeshi Takarada, Masahiro Yano, Toshio Yamamoto, Shuichi Fukuoka, Jianzhong Wu, Tsuyu Ando, Reynante Lacsamana Ordonio, Ko Hirano, Makoto Matsuoka

MOLECULAR PLANT 8 ( 2 ) 303 - 314 2015年2月

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

Hybrid Breakdown Caused by Epistasis-Based Recessive Incompatibility in a Cross of Rice (Oryza sativa L.) 査読

Kazuki Matsubara, Eiji Yamamoto, Ritsuko Mizobuchi, Jun-ichi Yonemaru, Toshio Yamamoto, Hiroshi Kato, Masahiro Yano

JOURNAL OF HEREDITY 106 ( 1 ) 113 - 122 2015年1月

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

Genetic mechanisms underlying yield potential in the rice high-yielding cultivar Takanari, based on reciprocal chromosome segment substitution lines 査読

Toshiyuki Takai, Takashi Ikka, Katsuhiko Kondo, Yasunori Nonoue, Nozomi Ono, Yumiko Arai-Sanoh, Satoshi Yoshinaga, Hiroshi Nakano, Masahiro Yano, Motohiko Kondo, Toshio Yamamoto

BMC PLANT BIOLOGY 14 295 2014年11月

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

Isolation of a novel lodging resistance QTL gene involved in strigolactone signaling and its pyramiding with a QTL gene involved in another mechanism. 査読国際誌

Yano K, Ookawa T, Aya K, Ochiai Y, Hirasawa T, Ebitani T, Takarada T, Yano M, Yamamoto T, Fukuoka S, Wu J, Ando T, Ordonio RL, Hirano K, Matsuoka M

Molecular plant 2014年11月

Increased lodging resistance in long-culm, low-lignin gh2 rice for improved feed and bioenergy production 査読

Taiichiro Ookawa, Kazuya Inoue, Makoto Matsuoka, Takeshi Ebitani, Takeshi Takarada, Toshio Yamamoto, Tadamasa Ueda, Tadashi Yokoyama, Chisato Sugiyama, Satoshi Nakaba, Ryo Funada, Hiroshi Kato, Motoki Kanekatsu, Koki Toyota, Takashi Motobayashi, Mehran Vazirzanjani, Seishu Tojo, Tadashi Hirasawa

SCIENTIFIC REPORTS 4 6567 2014年10月

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

Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars 査読

Jun-Ichi Yonemaru, Ritsuko Mizobuchi, Hiroshi Kato, Toshio Yamamoto, Eiji Yamamoto, Kazuki Matsubara, Hideyuki Hirabayashi, Yoshinobu Takeuchi, Hiroshi Tsunematsu, Takuro Ishii, Hisatoshi Ohta, Hideo Maeda, Kaworu Ebana, Masahiro Yano

BMC GENOMICS 15 346 2014年5月

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

Introgression of two chromosome regions for leaf photosynthesis from an indica rice into the genetic background of a japonica rice 査読

Shunsuke Adachi, Leticia Z. Baptista, Tomohiro Sueyoshi, Kazumasa Murata, Toshio Yamamoto, Takeshi Ebitani, Taiichiro Ookawa, Tadashi Hirasawa

JOURNAL OF EXPERIMENTAL BOTANY 65 ( 8 ) 2049 - 2056 2014年5月

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

Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation 査読

Hiroshi Shinada, Toshio Yamamoto, Eiji Yamamoto, Kiyosumi Hori, Junichi Yonemaru, Shuichi Matsuba, Kenji Fujino

THEORETICAL AND APPLIED GENETICS 127 ( 4 ) 995 - 1004 2014年4月

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

Effect of advanced intercrossing on genome structure and on the power to detect linked quantitative trait loci in a multi-parent population: a simulation study in rice 査読

Eiji Yamamoto, Hiroyoshi Iwata, Takanari Tanabata, Ritsuko Mizobuchi, Jun-ichi Yonemaru, Toshio Yamamoto, Masahiro Yano

BMC GENETICS 15 50 2014年4月

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

The genetic architecture of hybrid breakdown emerged in progeny from a cross between Japanese rice varieties 査読

Matsubara Kazuki, Yamamoto Eiji, Kobayashi Nobuya, Tanaka Jun-ichi, Tsunematsu Hiroshi, Mizobuchi Ritsuko, Yonemaru Jun-ichi, Yamamoto Toshio, Yano Masahiro, Kato Hiroshi

GENES & GENETIC SYSTEMS 88 ( 6 ) 385 2013年12月

Detection of QTLs to reduce cadmium content in rice grains using LAC23/Koshihikari chromosome segment substitution lines 査読

Tadashi Abe, Yasunori Nonoue, Nozomi Ono, Motoyasu Omoteno, Masato Kuramata, Shuichi Fukuoka, Toshio Yamamoto, Masahiro Yano, Satoru Ishikawa

BREEDING SCIENCE 63 ( 3 ) 284 - 291 2013年9月

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

A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate 査読

Toshiyuki Takai, Shunsuke Adachi, Fumio Taguchi-Shiobara, Yumiko Sanoh-Arai, Norio Iwasawa, Satoshi Yoshinaga, Sakiko Hirose, Yojiro Taniguchi, Utako Yamanouchi, Jianzhong Wu, Takashi Matsumoto, Kazuhiko Sugimoto, Katsuhiko Kondo, Takashi Ikka, Tsuyu Ando, Izumi Kono, Sachie Ito, Ayahiko Shomura, Taiichiro Ookawa, Tadashi Hirasawa, Masahiro Yano, Motohiko Kondo, Toshio Yamamoto

SCIENTIFIC REPORTS 3 2149 2013年8月

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

QTL Analysis of Leaf Photosynthesis in Rice

Toshiyuki Takai, Akihiro Ohsumi, Yumiko Arai, Norio Iwasawa, Masahiro Yano, Toshio Yamamoto, Satoshi Yoshinaga, Motohiko Kondo

JARQ-JAPAN AGRICULTURAL RESEARCH QUARTERLY 47 ( 3 ) 227 - 235 2013年7月

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

ガンマ線照射による突然変異育種法を用いた難脱粒性カドミウムファイトレメディエーション用イネ系統「MJ3」および「MA22」の育成査読

安部匡, 倉俣正人, 岩崎行玄, 本間利光, 茨木俊行, 山本敏央, 矢野昌裕, 村上政治, 石川覚

育種学研究 = Breeding research 15 ( 2 ) 17 - 24 2013年6月

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

The mesophyll anatomy enhancing CO2 diffusion is a key trait for improving rice photosynthesis 査読

Shunsuke Adachi, Toru Nakae, Masaki Uchida, Kazuya Soda, Toshiyuki Takai, Takao Oi, Toshio Yamamoto, Taiichiro Ookawa, Hiroshi Miyake, Masahiro Yano, Tadashi Hirasawa

JOURNAL OF EXPERIMENTAL BOTANY 64 ( 4 ) 1061 - 1072 2013年2月

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

Genome-Wide Haplotype Changes Produced by Artificial Selection during Modern Rice Breeding in Japan 査読

Jun-ichi Yonemaru, Toshio Yamamoto, Kaworu Ebana, Eiji Yamamoto, Hideki Nagasaki, Taeko Shibaya, Masahiro Yano

PLOS ONE 7 ( 3 ) e32982 2012年3月

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

OGRO: The Overview of functionally characterized Genes in Rice online database 査読

Eiji Yamamoto, Jun-ichi Yonemaru, Toshio Yamamoto, Masahiro Yano

RICE 5 ( 1 ) 26 2012年

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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