研究者詳細 - 山本　敏央

Detection and molecular cloning of genes underlying quantitative phenotypic variations in rice 査読

Toshio Yamamoto, Masahiro Yano

Biotechnology in Agriculture and Forestry 62 295 - 308 2008年

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

Scopus

Marker-assisted selection and evaluation of the QTL for stigma exsertion under japonica rice genetic background 査読

Maiko Miyata, Toshio Yamamoto, Toshiyuki Komori, Naoto Nitta

THEORETICAL AND APPLIED GENETICS 114 ( 3 ) 539 - 548 2007年2月

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

Mapping QTLs that control the performance of rice tissue culture and evaluation of derived near-isogenic lines 査読

F Taguchi-Shiobara, T Yamamoto, M Yano, S Oka

THEORETICAL AND APPLIED GENETICS 112 ( 5 ) 968 - 976 2006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：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 < 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

Development of isogenic lines of rice cultivar Koshihikari with early and late heading by marker-assisted selection 査読

Yoshinobu Takeuchi, Takeshi Ebitani, Toshio Yamamoto, Hiroyuki Sato, Hisatoshi Ohta, Hideyuki Hirabayashi, Hiroshi Kato, Ikuo Ando, Hiroshi Nemoto, Tokio Imbe, Masahiro Yano

Breeding Science 56 ( 4 ) 405 - 413 2006年

Isolation of a rice regeneration quantitative trait loci gene and its application to transformation systems 査読

A Nishimura, M Ashikari, S Lin, T Takashi, ER Angeles, T Yamamoto, M Matsuoka

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 ( 33 ) 11940 - 11944 2005年8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：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

Cytokinin oxidase regulates rice grain production 査読

M Ashikari, H Sakakibara, SY Lin, T Yamamoto, T Takashi, A Nishimura, ER Angeles, Q Qian, H Kitano, M Matsuoka

SCIENCE 309 ( 5735 ) 741 - 745 2005年7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：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

Fine scale and physical mapping of Spk(t) controlling spreading stub in rice 査読

M Miyata, T Komori, T Yamamoto, T Ueda, M Yano, N Nitta

BREEDING SCIENCE 55 ( 2 ) 237 - 239 2005年6月

Construction and evaluation of chromosome segment substitution lines carrying overlapping chromosome segments of indica rice cultivar ‘Kasalath’ in a genetic background of Japonica elite cultivar ‘Koshihikari’ 査読

Ebitani T, Takeuchi Y, Nonoue Y, Yamamoto T, Takeuchi K, Yano M

Breeding Science 55 ( 1 ) 65 - 73 2005年3月

Isolation of a rice regeneration QTL gene and its application to new transformation system

A Nishimura, M Ashikari, SY Lin, T Takashi, ER Angeles, T Yamamoto, M Matsuoka

PLANT AND CELL PHYSIOLOGY 46 S193 - S193 2005年

Fine genetic mapping of the nuclear gene, Rf-1, that restores the BT-type cytoplasmic male sterility in rice (Oryza sativa L.) by PCR-based markers 査読

T Komori, T Yamamoto, N Takemori, M Kashihara, H Matsushima, N Nitta

EUPHYTICA 129 ( 2 ) 241 - 247 2003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：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

Mapping quantitative trait loci for days-to-heading, and culm, panicle and internode lengths in a BC1F3 population using an elite rice variety, Koshihikari, as the recurrent parent 査読

T Yamamoto, F Taguchi-Shiobara, Y Ukai, T Sasaki, M Yano

BREEDING SCIENCE 51 ( 2 ) 63 - 71 2001年6月

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 < 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

Characterization and detection of epistatic interactions of 3 QTLs, Hd1, Hd2, and Hd3,controlling heading date in rice using nearly isogenic lines 査読

HX Lin, T Yamamoto, T Sasaki, M Yano

THEORETICAL AND APPLIED GENETICS 101 ( 7 ) 1021 - 1028 2000年11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-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

Identification of heading date quantitative trait locus Hd6 and characterization of its epistatic interactions with Hd2 in rice using advanced backcross progeny 査読

T Yamamoto, HX Lin, T Sasaki, M Yano

GENETICS 154 ( 2 ) 885 - 891 2000年2月

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.

Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice, as single Mendelian factors 査読

T Yamamoto, Y Kuboki, SY Lin, T Sasaki, M Yano

THEORETICAL AND APPLIED GENETICS 97 ( 1-2 ) 37 - 44 1998年7月

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

A high-density rice genetic linkage map with 2275 markers using a single F-2 population 査読

Y Harushima, M Yano, P Shomura, M Sato, T Shimano, Y Kuboki, T Yamamoto, SY Lin, BA Antonio, A Parco, H Kajiya, N Huang, K Yamamoto, Y Nagamura, N Kurata, GS Khush, T Sasaki

GENETICS 148 ( 1 ) 479 - 494 1998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：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 >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.

Genetic analysis of spreading stub using indica/japonica backcrossed progenies in rice 査読

T Yamamoto, T Sasaki, M Yano

BREEDING SCIENCE 47 ( 2 ) 141 - 144 1997年6月

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.

Genetic Analysis of Spreading Stub Using indica/japonica Backcrossed Progenies in Rice. 査読

Yamamoto T, Sasaki T, Yano M

Breeding Science 47 ( 2 ) 141 - 144 1997年6月

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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