九州大学 研究者情報
論文一覧
山形 悦透(やまがた よしゆき) データ更新日:2023.11.27

准教授 /  農学研究院 資源生物科学部門 農業生物資源学講座


原著論文
1. Takahiko Kubo, Yoshiyuki Yamagata, Hiroaki Matsusaka, Atsushi Toyoda, Yutaka Sato, Toshihiro Kumamaru, Whole-Genome Sequencing of Rice Mutant Library Members Induced by N-Methyl-N-Nitrosourea Mutagenesis of Fertilized Egg Cells., Rice (New York, N.Y.), 10.1186/s12284-022-00585-1, 15, 1, 38-38, 2022.07, Although targeted genome editing technology has become a powerful reverse genetic approach for accelerating functional genomics, conventional mutant libraries induced by chemical mutagens remain valuable for plant studies. Plants containing chemically induced mutations are simple yet effective genetic tools that can be grown without regard for biosafety issues. Whole-genome sequencing of mutant individuals reduces the effort required for mutant screening, thereby increasing their utility. In this study, we sequenced members of a mutant library of Oryza sativa cv. Nipponbare derived from treating single fertilized egg cells with N-methyl-N-nitrosourea (MNU). By whole-genome sequencing 266 M1 plants in this mutant library, we identified a total of 0.66 million induced point mutations. This result represented one mutation in every 146-kb of genome sequence in the 373 Mb assembled rice genome. These point mutations were uniformly distributed throughout the rice genome, and over 70,000 point mutations were located within coding sequences. Although this mutant library was a small population, nonsynonymous mutations were found in nearly 61% of all annotated rice genes, and 8.6% (3248 genes) had point mutations with large effects on gene function, such as gaining a stop codon or losing a start codon. WGS showed MNU-mutagenesis using rice fertilized egg cells induces mutations efficiently and is suitable for constructing mutant libraries for an in silico mutant screening system. Expanding this mutant library and its database will provide a useful in silico screening tool that facilitates functional genomics studies with a special emphasis on rice..
2. Kanako Bessho-Uehara, Kengo Masuda, Diane R Wang, Rosalyn B Angeles-Shim, Keisuke Obara, Keisuke Nagai, Riri Murase, Shin-Ichiro Aoki, Tomoyuki Furuta, Kotaro Miura, Jianzhong Wu, Yoshiyuki Yamagata, Hideshi Yasui, Michael B Kantar, Atsushi Yoshimura, Takumi Kamura, Susan R McCouch, Motoyuki Ashikari, Regulator of Awn Elongation 3, an E3 ubiquitin ligase, is responsible for loss of awns during African rice domestication., Proceedings of the National Academy of Sciences of the United States of America, 10.1073/pnas.2207105120, 120, 4, e2207105120, 2023.01, Two species of rice have been independently domesticated from different ancestral wild species in Asia and Africa. Comparison of mutations that underlie phenotypic and physiological alterations associated with domestication traits in these species gives insights into the domestication history of rice in both regions. Asian cultivated rice, Oryza sativa, and African cultivated rice, Oryza glaberrima, have been modified and improved for common traits beneficial for humans, including erect plant architecture, nonshattering seeds, nonpigmented pericarp, and lack of awns. Independent mutations in orthologous genes associated with these traits have been documented in the two cultivated species. Contrary to this prevailing model, selection for awnlessness targeted different genes in O. sativa and O. glaberrima. We identify Regulator of Awn Elongation 3 (RAE3) a gene that encodes an E3 ubiquitin ligase and is responsible for the awnless phenotype only in O. glaberrima. A 48-bp deletion may disrupt the substrate recognition domain in RAE3 and diminish awn elongation. Sequencing analysis demonstrated low nucleotide diversity in a ~600-kb region around the derived rae3 allele on chromosome 6 in O. glaberrima compared with its wild progenitor. Identification of RAE3 sheds light on the molecular mechanism underlying awn development and provides an example of how selection on different genes can confer the same domestication phenotype in Asian and African rice..
3. Justine K. Kitony, Hidehiko Sunohara, Mikako Tasaki, Jun-Ichi Mori, Akihisa Shimazu, Vincent P. Reyes, Hideshi Yasui, Yoshiyuki Yamagata, Atsushi Yoshimura, Masanori Yamasaki, Shunsaku Nishiuchi, Kazuyuki Doi, Development of an Aus-Derived Nested Association Mapping (Aus-NAM) Population in Rice, Plants, 10.3390/plants10061255, 10, 6, 1255-1255, 2021.06, A genetic resource for studying genetic architecture of agronomic traits and environmental adaptation is essential for crop improvements. Here, we report the development of a rice nested association mapping population (aus-NAM) using 7 aus varieties as diversity donors and T65 as the common parent. Aus-NAM showed broad phenotypic variations. To test whether aus-NAM was useful for quantitative trait loci (QTL) mapping, known flowering genes (Ehd1, Hd1, and Ghd7) in rice were characterized using single-family QTL mapping, joint QTL mapping, and the methods based on genome-wide association study (GWAS). Ehd1 was detected in all the seven families and all the methods. On the other hand, Hd1 and Ghd7 were detected in some families, and joint QTL mapping and GWAS-based methods resulted in weaker and uncertain peaks. Overall, the high allelic variations in aus-NAM provide a valuable genetic resource for the rice community..
4. Kanako Bessho-Uehara, Yoshiyuki Yamagata, Tomonori Takashi, Takashi Makino, Hideshi Yasui, Atsushi Yoshimura, Motoyuki Ashikari, Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species, Plants, 10.3390/plants10040725, 10, 4, 725-725, 2021.04, Wild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution of the loss of awn to modern rice agriculture. Therefore, identifying the genes regulating awn development would facilitate the elucidation of a part of the domestication process in rice and increase our understanding of the complex mechanism in awn morphogenesis. To identify the novel loci regulating awn development and understand the conservation of genes in other wild rice relatives belonging to the AA genome group, we analyzed the chromosome segment substitution lines (CSSL). In this study, we compared a number of CSSL sets derived by crossing wild rice species in the AA genome group with the cultivated species Oryza sativa ssp. japonica. Two loci on chromosomes 7 and 11 were newly discovered to be responsible for awn development. We also found wild relatives that were used as donor parents of the CSSLs carrying the functional alleles responsible for awn elongation, REGULATOR OF AWN ELONGATION 1 (RAE1) and RAE2. To understand the conserveness of RAE1 and RAE2 in wild rice relatives, we analyzed RAE1 and RAE2 sequences of 175 accessions among diverse AA genome species retrieved from the sequence read archive (SRA) database. Comparative sequence analysis demonstrated that most wild rice AA genome species maintained functional RAE1 and RAE2, whereas most Asian rice cultivars have lost either or both functions. In addition, some different loss-of-function alleles of RAE1 and RAE2 were found in Asian cultivated species. These findings suggest that different combinations of dysfunctional alleles of RAE1 and RAE2 were selected after the speciation of O. sativa, and that two-step loss of function in RAE1 and RAE2 contributed to awnlessness in Asian cultivated rice..
5. Nilsa Emilia Munguambe, Shouta Inoue, Zita Demeter, Yoshiyuki Yamagata, Hideshi Yasui, Shao-Hui Zheng, Daisuke Fujita, Substitution Mapping of a Locus Responsible for Hybrid Breakdown in Populations Derived From Interspecific Introgression Line, Frontiers in Plant Science, 10.3389/fpls.2021.633247, 12, 633247-633247, 2021.04, Hybrid breakdown, a form of postzygotic reproductive barrier, has been reported to hinder gene flow in many crosses between wild and cultivated rice. Here, the phenomenon of hybrid breakdown was observed as low-tillering (i.e., low tiller number) in some progeny of an interspecific cross produced in an attempt to introduce Oryza meridionalis Ng (W1625) chromosomal segments into Oryza sativa L. ssp. japonica “Taichung 65” (T65). Low-tillering lines were obtained in BC4-derived progeny from a cross between W1625 and “Taichung 65,” but the locus for low-tillering could not be mapped in segregating populations. As a second approach to map the locus for low-tillering, we analyzed an F2 population derived from a cross between the low-tillering lines and a high-yielding indica cultivar, “Takanari.” A major QTL for low-tillering, qLTN4, was detected between PCR-based markers MS10 and RM307 on the long arm of chromosome 4, with a LOD score of 15.6. The low-tillering phenotype was associated with weak growth and pale yellow phenotype; however, low-tillering plant had less reduction of grain fertility. In an F4 population (4896 plants), 563 recombinant plants were identified and the low-tillering locus was delimited to a 4.6-Mbp region between markers W1 and C5-indel3729. This region could not be further delimited because recombination is restricted in this region of qLTN4, which is near the centromere. Understanding the genetic basis of hybrid breakdown, including the low-tillering habit, will be important for improving varieties in rice breeding..
6. Mitsukazu Sakata, Noriko Takano-Kai, Yuta Miyazaki, Hiroyuki Kanamori, Jianzhong Wu, Takashi Matsumoto, Kazuyuki Doi, Hideshi Yasui, Atsushi Yoshimura, Yoshiyuki Yamagata, Domain Unknown Function DUF1668-Containing Genes in Multiple Lineages Are Responsible for F1 Pollen Sterility in Rice, Frontiers in Plant Science, 10.3389/fpls.2020.632420, 11, 632420-632420, 2021.01, Postzygotic reproductive isolation maintains species integrity and uniformity and contributes to speciation by restricting the free gene flow between divergent species. In this study we identify causal genes of two Mendelian factors S22A and S22B on rice chromosome 2 inducing F1 pollen sterility in hybrids between Oryza sativa japonica-type cultivar Taichung 65 (T65) and a wild relative of rice species Oryza glumaepatula. The causal gene of S22B in T65 encodes a protein containing DUF1668 and gametophytically expressed in the anthers, designated S22B_j. The O. glumaepatula allele S22B-g, allelic to S22B_j, possesses three non-synonymous substitutions and a 2-bp deletion, leading to a frameshifted translation at the S22B C-terminal region. Transcription level of S22B-j and/or S22B_g did not solely determine the fertility of pollen grains by genotypes at S22B. Western blotting of S22B found that one major band with approximately 46 kDa appeared only at the mature stage and was reduced on semi-sterile heterozygotes at S22B, implying that the 46 kDa band may associated in hybrid sterility. In addition, causal genes of S22A in T65 were found to be S22A_j1 and S22A_j3 encoding DUF1668-containing protein. The allele of a wild rice species Oryza meridionalis Ng at S22B, designated S22B_m, is a loss-of-function allele probably due to large deletion of the gene lacking DUF1668 domain and evolved from the different lineage of O. glumaepatula. Phylogenetic analysis of DUF1668 suggested that many gene duplications occurred before the divergence of current crops in Poaceae, and loss-of-function mutations of DUF1668-containing genes represent the candidate causal genetic events contributing to hybrid incompatibilities. The duplicated DUF1668-domain gene may provide genetic potential to induce hybrid incompatibility by consequent mutations after divergence..
7. Tomoyuki Fujii, Yoshiyuki Yamagata, Tin Tin Myint, Yasufumi Kunihiro, Yuji Matsue, Thidar Win, Zaw Moe Aung, Win Sander Htay, Hideshi Yasui, Atsushi Yoshimura, Kazuo Ogata, Improvement of Genetic Purity of Breeder Seed by Introducing Line Cultivation Method for Myanmar’s Major Rice Cultivars, Journal of Experimental Agriculture International, 10.9734/jeai/2020/v42i430494, 42, 4, 1-13, 2020.05, Aims: Since the genetic purity of rice seed significantly affects paddy yield and quality, many rice production countries have been attempting to improve seed quality. This study aimed to demonstrate the effectiveness of breeder seed production using line cultivation to ensure traceability of ancestral information by line and individual selection, to improve the genetic purity of breeder seed in Myanmar that has been degraded due to pedigree mixtures.
Study Design: Observational and analytic study design was used to evaluate the effect of the introduction of line cultivation method in practical activities of breeder seed production in Myanmar under the project for improvement of seed purity of breeder seed.
Place and Duration of Study: Department of Agricultural Research at Yezin, Ministry of Agriculture, Livestock and Irrigation, Myanmar, from June 2012 to December 2016.
Methodology: Using nine major rice cultivars in Myanmar, the line cultivation method was evaluated through measurement of the standard deviation and the variance component ratio in heading date, culm length, panicle length, and panicle number from 2012 to 2016. DNA polymorphism analysis by simple sequence repeat (SSR) markers was also conducted using breeder seed of the Sinthukha variety multiplied in 2013, 2014, 2015, and 2016 for the evaluation.
Results: Standard deviations of heading date, culm length, panicle length and panicle number in 2016 were significantly decreased compared to the first year of the introduction of the line cultivation method. Average heading duration among sister lines of all varieties was reduced from 8.25 days in 2013 to 5.25 days in 2016, and the uniformity of heading time among sister lines was improved. The variance component ratio of each trait in 2016 was the highest since 2013. The analysis of breeder seed by SSR markers revealed that the DNA polymorphism ratio of Sinthukha seed in 2016 was lower than that of 2013. This demonstrated that Sinthukha seed in 2016 had improved genetic purity. Consequently, it is considered that other cultivars multiplied by the line cultivation method have improved their genetic purity as well.
Conclusion: Line cultivation is an effective method to improve genetic purity and maintain genetic stability of the breeder seed in Myanmar’s rice cultivars. Genetically pure breeder seed would improve quality of downstream seed such as certified seed. Consequently, it is expected that productivity and quality of rice will be improved thus income of farmers will increase..
8. Miki Kihara, Tomokazu Ushijima, Yoshiyuki Yamagata, Yukinari Tsuruda, Takeshi Higa, Tomomi Abiko, Takahiko Kubo, Masamitsu Wada, Noriyuki Suetsugu, Eiji Gotoh, Light-induced chloroplast movements in Oryza species., Journal of plant research, 10.1007/s10265-020-01189-w, 2020.04, [URL], Light-induced chloroplast movements control efficient light utilization in leaves, and thus, are essential for leaf photosynthesis and biomass production under fluctuating light conditions. Chloroplast movements have been intensively analyzed using wild-type and mutant plants of Arabidopsis thaliana. The molecular mechanism and the contribution to biomass production were elucidated. However, the knowledge of chloroplast movements is very scarce in other plant species, especially grass species including crop plants. Because chloroplast movements are efficient strategy to optimize light capture in leaves and thus promote leaf photosynthesis and biomass, analysis of chloroplast movements in crops is required for biomass production. Here, we analyzed chloroplast movements in a wide range of cultivated and wild species of genus Oryza. All examined Oryza species showed the blue-light-induced chloroplast movements. However, O. sativa and its ancestral species O. rufipogon, both of which are AA-genome species and usually grown in open condition where plants are exposed to full sunlight, showed the much weaker chloroplast movements than Oryza species that are usually grown under shade or semi-shade conditions, including O. officinalis, O. eichingeri, and O. granulata. Further detailed analyses of different O. officinalis accessions, including sun, semi-shade, and shade accessions, indicated that the difference in chloroplast movement strength between domesticated rice plants and wild species might result from the difference in habitat, and the shape of mesophyll chlorenchyma cells. The findings of this study provide useful information for optimizing Oryza growth conditions, and lay the groundwork for improving growth and yield in staple food crop Oryza sativa..
9. Hnin Wah Thein, Yoshiyuki Yamagata, Tan Van Mai, Hideshi Yasui, Four resistance alleles derived from Oryza longistaminata (A. Chev. & Roehrich) against green rice leafhopper, Nephotettix cincticeps (Uhler) identified using novel introgression lines., Breeding science, 10.1270/jsbbs.19060, 69, 4, 573-584, 2019.12, [URL], The green rice leafhopper (GRH, Nephotettix cincticeps Uhler) is a serious insect pest of rice (Oryza sativa L.) in temperate regions of Asia. Wild Oryza species are the main source of resistance to insects. The W1413 accession of African wild rice (O. longistaminata A. Chev. & Roehrich) is resistant to GRH. To analyze its resistance, we developed 28 BC3F3 introgression lines carrying W1413 segments in the genetic background of Nipponbare, a susceptible rice cultivar, and evaluated their GRH resistance. Five BC3F3 populations were used for quantitative trait locus (QTL) analysis and seven BC3F4 populations for QTL validation. Four significant QTLs on the long arm of chromosome 2 (qGRH2), short arm of chromosome 4 (qGRH4), short arm of chromosome 5 (qGRH5), and long arm of chromosome 11 (qGRH11) were identified. The contribution of the W1413 allele at qGRH11 was the largest among the four QTLs; the other QTLs also contributed to GRH resistance. Chromosomal locations suggested that qGRH11 corresponds to the previously reported GRH resistance gene Grh2, qGRH4 to Grh6, and qGRH5 to Grh1. qGRH2 is a novel QTL for resistance to GRH. Thus, resistance of O. longistaminata to GRH can be explained by at least four QTLs..
10. Takayuki Ogami, Hideshi Yasui, Atsushi Yoshimura, Yoshiyuki Yamagata, Identification of Anther Length QTL and Construction of Chromosome Segment Substitution Lines of Oryza longistaminata., Plants (Basel, Switzerland), 10.3390/plants8100388, 8, 10, 2019.09, [URL], Life histories and breeding systems strongly affect the genetic diversity of seed plants, but the genetic architectures that promote outcrossing in Oryza longistaminata, a perennial wild species in Africa, are not understood. We conducted a genetic analysis of the anther length of O. longistaminata accession W1508 using advanced backcross quantitative trait locus (QTL) analysis and chromosomal segment substitution lines (CSSLs) in the genetic background of O. sativa Taichung 65 (T65), with simple sequence repeat markers. QTL analysis of the BC3F1 population (n = 100) revealed that four main QTL regions on chromosomes 3, 5, and 6 were associated to anther length. We selected a minimum set of BC3F2 plants for the development of CSSLs to cover as much of the W1508 genome as possible. The additional minor QTLs were suggested in the regional QTL analysis, using 21 to 24 plants in each of the selected BC3F2 population. The main QTLs found on chromosomes 3, 5, and 6 were validated and designated qATL3, qATL5, qATL6.1, and qATL6.2, as novel QTLs identified in O. longistaminata in the mapping populations of 94, 88, 70, and 95 BC3F4 plants. qATL3, qATL5, and qATL6.1 likely contributed to anther length by cell elongation, whereas qATL6.2 likely contributed by cell multiplication. The QTLs were confirmed again in an evaluation of the W1508ILs. In several chromosome segment substitution lines without the four validated QTLs, the anthers were also longer than those of T65, suggesting that other QTLs also increase anther length in W1508. The cloning and diversity analyses of genes conferring anther length QTLs promotes utilization of the genetic resources of wild species, and the understanding of haplotype evolution on the differentiation of annuality and perenniality in the genus Oryza..
11. Phi CN, Fujita D, Yamagata Y, Yoshimura A, Yasui H, High-resolution mapping of GRH6, a gene from Oryza nivara (Sharma et Shastry) conferring resistance to green rice leafhopper (Nephotettix cincticeps Uhler)., Breeding science, 10.1270/jsbbs.19029, 69, 3, 439-446, 2019.09, [URL].
12. Fujii T, Y. Matsue, Y. Kunihiro, T. T. Myint, A. Chit, T. Win, H. L. Tun, K. Ogata, Y. Yamagata, Z. M. Aung, L. Z. Myo, W. S. Htay., Variation in agronomic traits of Myanmar’s major rice cultivars in wet season and dry season, J. Fac. Agr., Kyushu Univ., 64, 2, 237-245, 2019.09, [URL], In Myanmar, the double cropping area using photoperiod insensitive rice cultivars is gradually expanding with the development of irrigation facilities. However, performance of agronomic traits of these rice cultivars between wet season (WS) and dry season (DS) have not been clarified. The objective of this study is to evaluate variation of heading date, culm length, panicle length, panicle number and paddy yield of rice cultivars in WS and DS, and to identify main components explaining phenotypic variations by genotypes, locations, cropping seasons and year in Myanmar to establish efficient cropping system. We used eight major cultivars (Theedatyin, Manawthukha, Sinthukha, Sinthwelatt, Kyawzeya, Shwewartun, Ayeyarmin and Pawsanyin) and planted in 2014 and 2015 for DS, in 2015 and 2016 for WS. As the results of experiments at three locations; Yezin, Hmawbi and Myaungmya, we found that heading date of all cultivars grown in WS at Yezin and Myaungmya were about 10 to 16 days earlier than those in DS except for Theedatyin, although Yezin is located about 320 km north of Myaungmya. Further, the difference in heading date between WD and DS was larger in middle matured cultivar group than that of middle/late matured cultivar group at Yezin and Myaungmya. On the other hand, heading dates in WS and DS were almost the same in all cultivars grown at Hmawbi which is located about 100 km east of Myaungmya. These variations in heading date could be attributed to difference of day and night temperature in WS and DS at each location. Culm length in WS was longer than that of DS in all cultivars at all locations except for 2015 DS at Myaungmya. An air–dry effect is likely to be a cause do this variation. Analysis of variance revealed that phenotypic variance of heading date and culm length was highly associated to genotype, season and location as well as their interactions. Genotypes and interaction of genotypes by season were significant component of phenotypic variance of yield. In analysis of variance separately conducted in WS and DS showed that genotype, location and interaction between genotypes and location were found to be associated to heading date and yield. The results suggest that the cultivar trials at different locations need to be conducted both in WS and DS to improve the efficiency of selection for widely adopted cultivars as well as to make efficient cropping system in Myanmar..
13. Yoshiyuki Yamagata, Khin Thanda Win, Yuta Miyazaki, Chika Ogata, Hideshi Yasui, Atsushi Yoshimura, Development of introgression lines of AA genome Oryza species, O. glaberrima, O. rufipogon, and O. nivara, in the genetic background of O. sativa L. cv. Taichung 65., Breeding science, 10.1270/jsbbs.19002, 69, 2, 359-363, 2019.06, [URL], To evaluate and utilize potentially valuable quantitative trait loci or genes of wild relatives in the genetic background of domesticated crop species, chromosome segment substitution lines (CSSLs) are a valuable tool. CSSLs can be constructed through the exchange of chromosome segments of AA genome species of the genus Oryza with cultivated rice, Oryza sativa L. Here we report the development of three sets of CSSLs carrying segments of AA genome species closely related to Oryza sativa-O. glaberrima (IRGC 103777 from Mali), O. rufipogon (W1962 from China), and O. nivara (IRGC 105715 from Cambodia)-in the genetic background of ssp. japonica cultivar Taichung 65 through the use of 101 to 121 simple-sequence-repeat markers in whole-genome genotyping and marker-assisted selection. The materials are available via the National Bioresource Project (Rice) Oryzabase Web page..
14. Yoshiyuki Yamagata, Atsushi Yoshimura, Toyoaki Anai, Satoshi Watanabe, Selection criteria for SNP loci to maximize robustness of high-resolution melting analysis for plant breeding., Breeding science, 10.1270/jsbbs.18048, 68, 4, 488-498, 2018.09, [URL], DNA markers are useful for identifying genes and developing new genetic materials for breeding and genetic research. High-resolution melting (HRM) analysis can detect a single nucleotide polymorphism (SNP) in two polymerase chain reaction (PCR) fragments as a melting temperature (Tm) difference without additional experimental steps, such as gel electrophoresis. To design a method for developing reliable HRM markers that discriminate between homozygous alleles containing SNPs, we tested new evaluation indexes related to the thermodynamics of double-stranded DNA to find one that maximizes the difference in Tm values between PCR fragments. We found that differences in the change in Gibbs free energy (ΔG°) correlated with actual differences in Tm values. Optimization of the nearest neighboring nucleotide (NNN) of a SNP by nucleotide substitution in the primer and reducing the size of the PCR fragment both enlarged the actual differences in Tm. The genetic DNA markers we developed by NNN substitution, termed NNNs-HRM markers, could be precisely mapped within soybean chromosomes by linkage analysis. We developed a Perl script pipeline to enable the automatic design of a massive number of NNNs-HRM markers; these scripts are freely available and would be useful for practical breeding programs for other plant species..
15. Atsushi Yoshimura, Hideshi Yasui, Pham Van Cuong, Motoyuki Ashikari, Enric E. Angeres, Nguyen Van Hoan, Tran Tan Phuong, Yoshiyuki Yamagata, Norimitsu Hamaoka, Kazuyuki Doi, Tang Thi Hanh, Mai Van Tan, Nguyen Quoc Trung, Nobuyuki Iseri, Kazuo Ogata, Development of rice promising lines using genomic technology and information in Vietnam, Crop Production under Stressful Conditions
Application of Cutting-edge Science and Technology in Developing Countries
, 10.1007/978-981-10-7308-3_2, 11-25, 2018.08, [URL].
16. Yohei Koide, Atsushi Ogino, Takanori Yoshikawa, Yuki Kitashima, Nozomi Saito, Yoshitaka Kanaoka, Kazumitsu Onishi, Yoshihiro Yoshitake, Takuji Tsukiyama, Hiroki Saito, Masayoshi Teraishi, Yoshiyuki Yamagata, Aiko Uemura, Hiroki Takagi, Yoriko Hayashi, Tomoko Abe, Yoshimichi Fukuta, Yutaka Okumoto, Akira Kanazawa, Lineage-specific gene acquisition or loss is involved in interspecific hybrid sterility in rice., Proceedings of the National Academy of Sciences of the United States of America, 10.1073/pnas.1711656115, 115, 9, E1955-E1962-E1962, 2018.02, [URL], Understanding the genetic basis of reproductive barriers between species has been a central issue in evolutionary biology. The S
1
locus in rice causes hybrid sterility and is a major reproductive barrier between two rice species, Oryza sativa and Oryza glaberrima The O. glaberrima-derived allele (denoted S1g) on the S
1
locus causes preferential abortion of gametes with its allelic alternative (denoted S1s) in S
1
g/S
1
s heterozygotes. Here, we used mutagenesis and screening of fertile hybrid plants to isolate a mutant with an allele, S
1
mut, which does not confer sterility in the S
1
mut/S
1
g and S
1
mut/S
1
s hybrids. We found that the causal mutation of the S
1
mut allele was a deletion in the peptidase-coding gene (denoted "SSP") in the S
1
locus of O. glaberrima No orthologous genes of SSP were found in the O. sativa genome. Transformation experiments indicated that the introduction of SSP in carriers of the S
1
s allele did not induce sterility. In S
1
mut/S
1
s heterozygotes, the insertion of SSP led to sterility, suggesting that SSP complemented the loss of the functional phenotype of the mutant and that multiple factors are involved in the phenomenon. The polymorphisms caused by the lineage-specific acquisition or loss of the SSP gene were implicated in the generation of hybrid sterility. Our results demonstrated that artificial disruption of a single gene for the reproductive barrier creates a "neutral" allele, which facilitates interspecific hybridization for breeding programs..
17. Mbaraka, R. S., Y. Yamagata, A. Yoshimura, H. Yasui, Genetic mapping and characterization of lethal necrotic mutants in rice, American Journal of Plant Science, 10.4236/ajps.2017.813226, 8, 13, 3350-3376, 2017.12, [URL].
18. Norimitsu Hamaoka, Hideshi Yasui, Yoshiyuki Yamagata, Yoko Inoue, Naruto Furuya, Takuya Araki, Osamu Ueno, Atsushi Yoshimura, A hairy-leaf gene, BLANKET LEAF, of wild Oryza nivara increases photosynthetic water use efficiency in rice., Rice (New York, N.Y.), 10.1186/s12284-017-0158-1, 10, 1, 20-20, 2017.12, [URL], BACKGROUND: High water use efficiency is essential to water-saving cropping. Morphological traits that affect photosynthetic water use efficiency are not well known. We examined whether leaf hairiness improves photosynthetic water use efficiency in rice. RESULTS: A chromosome segment introgression line (IL-hairy) of wild Oryza nivara (Acc. IRGC105715) with the genetic background of Oryza sativa cultivar 'IR24' had high leaf pubescence (hair). The leaf hairs developed along small vascular bundles. Linkage analysis in BC5F2 and F3 populations showed that the trait was governed by a single gene, designated BLANKET LEAF (BKL), on chromosome 6. IL-hairy plants had a warmer leaf surface in sunlight, probably due to increased boundary layer resistance. They had a lower transpiration rate under moderate and high light intensities, resulting in higher photosynthetic water use efficiency. CONCLUSION: Introgression of BKL on chromosome 6 from O. nivara improved photosynthetic water use efficiency in the genetic background of IR24..
19. Giao Ngoc Nguyen, Yoshiyuki Yamagata, Yuko Shigematsu, Miyako Watanabe, Yuta Miyazaki, Kazuyuki Doi, Kosuke Tashiro, Satoru Kuhara, Hiroyuki Kanamori, Jianzhong Wu, Takashi Matsumoto, Hideshi Yasui, Atsushi Yoshimura, Duplication and Loss of Function of Genes Encoding RNA Polymerase III Subunit C4 Causes Hybrid Incompatibility in Rice., G3 (Bethesda, Md.), 10.1534/g3.117.043943, 7, 8, 2565-2575, 2017.08, [URL], Reproductive barriers are commonly observed in both animals and plants, in which they maintain species integrity and contribute to speciation. This report shows that a combination of loss-of-function alleles at two duplicated loci, DUPLICATED GAMETOPHYTIC STERILITY 1 (DGS1) on chromosome 4 and DGS2 on chromosome 7, causes pollen sterility in hybrid progeny derived from an interspecific cross between cultivated rice, Oryza sativa, and an Asian annual wild rice, O. nivara Male gametes carrying the DGS1 allele from O. nivara (DGS1-nivaras ) and the DGS2 allele from O. sativa (DGS2-T65s ) were sterile, but female gametes carrying the same genotype were fertile. We isolated the causal gene, which encodes a protein homologous to DNA-dependent RNA polymerase (RNAP) III subunit C4 (RPC4). RPC4 facilitates the transcription of 5S rRNAs and tRNAs. The loss-of-function alleles at DGS1-nivaras and DGS2-T65s were caused by weak or nonexpression of RPC4 and an absence of RPC4, respectively. Phylogenetic analysis demonstrated that gene duplication of RPC4 at DGS1 and DGS2 was a recent event that occurred after divergence of the ancestral population of Oryza from other Poaceae or during diversification of AA-genome species..
20. Khin Thanda Win, Yoshiyuki Yamagata, Kazuyuki Doi, Kazuhiro Uyama, Yasuko Nagai, Yosuke Toda, Takahiro Kani, Motoyuki Ashikari, Hideshi Yasui, Atsushi Yoshimura, A single base change explains the independent origin of and selection for the nonshattering gene in African rice domestication., The New phytologist, 10.1111/nph.14290, 213, 4, 1925-1935, 2017.03, [URL], Reduced seed shattering was a critical evolutionary step in crop domestication. Two cultivated rice species, Oryza sativa and Oryza glaberrima, were independently domesticated from the wild species Oryza rufipogon in Asia and Oryza barthii in Africa, respectively. A single nucleotide polymorphism (SNP) in the c gene, which encodes a trihelix transcription factor, causes nonshattering in O. sativa. However, the genetic mechanism of nonshattering in O. glaberrima is poorly understood. We conducted an association analysis for the coding sequences of SH3/SH4 in AA- genome rice species and the mutation suggested to cause nonshattering was demonstrated to do so using a positional-cloning approach in the O. sativa genetic background. We found that the loss of seed shattering in O. glaberrima was caused by an SNP resulting in a truncated SH3/SH4 protein. This mutation appears to be endemic and to have spread in the African gene pool by hybridization with some O. barthii accessions. We showed that interaction between the O. sativa and O. glaberrima domestication alleles of SH3 in heterozygotes induces a 'throwback' seed-shattering phenotype similar to that in the wild species. Identification of the causative SNP provides new insights into the molecular basis of seed shattering in crops and may facilitate investigation of the history of African rice domestication..
21. Mitsukazu Sakata, Mari Seno, Hiroaki Matsusaka, Kiyomi Takahashi, Yuki Nakamura, Yoshiyuki Yamagata, Enrique R Angeles, Toshihiro Mochizuki, Toshihiro Kumamaru, Masao Sato, Akiko Enomoto, Kosuke Tashiro, Satoru Kuhara, Hikaru Satoh, Atsushi Yoshimura, Development and evaluation of rice giant embryo mutants for high oil content originated from a high-yielding cultivar 'Mizuhochikara'., Breeding science, 10.1270/jsbbs.15135, 66, 3, 425-33, 2016.06, Rice bran oil is a byproduct of the milling of rice (Oryza sativa L.). It offers various health benefits and has a beneficial fatty acid composition. To increase the amount of rice bran as a sink for triacylglycerol (TAG), we developed and characterized new breeding materials with giant embryos. To induce mutants, we treated fertilized egg cells of the high-yielding cultivar 'Mizuhochikara' with N-methyl-N-nitrosourea (MNU). By screening M2 seeds, we isolated four giant embryo mutant lines. Genetic analysis revealed that the causative loci in lines MGE12 and MGE13 were allelic to giant embryo (ge) on chromosome 7, and had base changes in the causal gene Os07g0603700. On the other hand, the causative loci in lines MGE8 and MGE14 were not allelic to ge, and both were newly mapped on chromosome 3. The TAG contents of all four mutant lines increased relative to their wild type, 'Mizuhochikara'. MGE13 was agronomically similar to 'Mizuhochikara' and would be useful for breeding for improved oil content..
22. Yusuke Kurokawa, Tomonori Noda, Yoshiyuki Yamagata, Rosalyn Angeles-Shim, Hidehiko Sunohara, Kanako Uehara, Tomoyuki Furuta, Keisuke Nagai, Kshirod Kumar Jena, Hideshi Yasui, Atsushi Yoshimura, Motoyuki Ashikari, Kazuyuki Doi, Construction of a versatile SNP array for pyramiding useful genes of rice., Plant science : an international journal of experimental plant biology, 10.1016/j.plantsci.2015.09.008, 242, 131-139, 2016.01, [URL], DNA marker-assisted selection (MAS) has become an indispensable component of breeding. Single nucleotide polymorphisms (SNP) are the most frequent polymorphism in the rice genome. However, SNP markers are not readily employed in MAS because of limitations in genotyping platforms. Here the authors report a Golden Gate SNP array that targets specific genes controlling yield-related traits and biotic stress resistance in rice. As a first step, the SNP genotypes were surveyed in 31 parental varieties using the Affymetrix Rice 44K SNP microarray. The haplotype information for 16 target genes was then converted to the Golden Gate platform with 143-plex markers. Haplotypes for the 14 useful allele are unique and can discriminate among all other varieties. The genotyping consistency between the Affymetrix microarray and the Golden Gate array was 92.8%, and the accuracy of the Golden Gate array was confirmed in 3 F2 segregating populations. The concept of the haplotype-based selection by using the constructed SNP array was proofed..
23. Gaihre, Y.R., Yamagata Y, Yoshimura A, Nose A, Identification of QTLs involved in resistance to sheath blight disease in rice line 32R derived from Tetep, Tropical Agriculture and Development, 59, 3, 154-160, 2015.10, [URL].
24. Mitsukazu Sakata, Yoshiyuki Yamagata, Kazuyuki Doi, Atsushi Yoshimura, Two linked genes on rice chromosome 2 for F1 pollen sterility in a hybrid between Oryza sativa and O. glumaepatula., Breeding science, 10.1270/jsbbs.64.309, 64, 4, 309-20, 2014.12, [URL], Hybrid incompatibility plays an important role in establishment of post-zygotic reproductive isolation. To unveil genetic basis of hybrid incompatibilities between diverged species of genus Oryza AA genome species, we conducted genetic dissection of hybrid sterility loci, S22(t), which had been identified in backcross progeny derived from Oryza sativa ssp. japonica (recurrent parent) and South American wild rice O. glumaepatula near the end of the short arm of chromosome 2. The S22(t) region was found to be composed of two loci, designated S22A and S22B, that independently induce F1 pollen sterility. Pollen grains containing either of the sterile alleles (S22A-glum (s) or S22B-glum (s) ) were sterile if produced on a heterozygous plant. No transmission of the S22A-glum (s) allele via pollen was observed, whereas a low frequency of transmission of S22B-glum (s) was observed. Cytological analysis showed that the sterile pollen grains caused by S22A could reach the bicellular or tricellular stage, and the nearly-sterile pollen grains caused by S22B could reach the tricellular stage. Our genetic analysis showed repulsion linkage effect is possible to induce strong reproductive barrier by high pollen sterility based on recombination value and transmission ratio of hybrid sterility gene to the progeny was influenced by frequency of competitors on fertilization..
25. Jirapong Jairin, Tetsuya Kobayashi, Yoshiyuki Yamagata, Sachiyo Sanada-Morimura, Kazuki Mori, Kosuke Tashiro, Satoru Kuhara, Seigo Kuwazaki, Masahiro Urio, Yoshitaka Suetsugu, Kimiko Yamamoto, Masaya Matsumura, Hideshi Yasui, A simple sequence repeat- and single-nucleotide polymorphism-based genetic linkage map of the brown planthopper, Nilaparvata lugens., DNA research : an international journal for rapid publication of reports on genes and genomes, 10.1093/dnares/dss030, 20, 1, 17-30, 2013.02, In this study, we developed the first genetic linkage map for the major rice insect pest, the brown planthopper (BPH, Nilaparvata lugens). The linkage map was constructed by integrating linkage data from two backcross populations derived from three inbred BPH strains. The consensus map consists of 474 simple sequence repeats, 43 single-nucleotide polymorphisms, and 1 sequence-tagged site, for a total of 518 markers at 472 unique positions in 17 linkage groups. The linkage groups cover 1093.9 cM, with an average distance of 2.3 cM between loci. The average number of marker loci per linkage group was 27.8. The sex-linkage group was identified by exploiting X-linked and Y-specific markers. Our linkage map and the newly developed markers used to create it constitute an essential resource and a useful framework for future genetic analyses in BPH..
26. Win, K. T., T. Kubo, Y. Miyazaki, K. Doi, H. Yasui, Y. Yamagata and A. Yoshimura, Molecular mapping of two loci conferring F1 pollen sterility in Inter- and intraspecific crosses of rice, Genes, Genomes and Genomics, 6, Special issue 1, 16-21, 2012.02.
27. Khin Thanda Win, Yoshiyuki Yamagata, Yuta Miyazaki, Kazuyuki Doi, Hideshi Yasui, Atsushi Yoshimura, Independent evolution of a new allele of F1 pollen sterility gene S27 encoding mitochondrial ribosomal protein L27 in Oryza nivara., TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 10.1007/s00122-010-1454-y, 122, 2, 385-94, 2011.02, Loss of function of duplicated genes plays an important role in the evolution of postzygotic reproductive isolation. The widespread occurrence of gene duplication followed by rapid loss of function of some of the duplicate gene copies suggests the independent evolution of loss-of-function alleles of duplicate genes in divergent lineages of speciation. Here, we found a novel loss-of-function allele of S27 in the Asian annual wild species Oryza nivara, designated S27-niv (s), that leads to F(1) pollen sterility in a cross between O. sativa and O. nivara. Genetic linkage analysis and complementation analysis demonstrated that S27-niv (s) lies at the same locus as the previously identified S27 locus and S27-niv (s) is a loss-of-function allele of S27. S27-niv (s) is composed of two tandem mitochondrial ribosomal protein L27 genes (mtRPL27a and mtRPL27b), both of which are inactive. The coding and promoter regions of S27-niv (s) showed a number of nucleotide differences from the functional S27-T65 (+) allele. The structure of S27-niv (s) is different from that of a previously identified null S27 allele, S27-glum (s), in the South American wild rice species O. glumaepatula, in which mtRPL27a and mtRPL27b are absent. These results show that the mechanisms for loss-of-function of S27-niv (s) and S27-glum (s) are different. Our results provide experimental evidence that different types of loss-of-function alleles are distributed in geographically and phylogenetically isolated species and represent a potential mechanism for postzygotic isolation in divergent species..
28. Atsushi Yoshimura, Hiroshi Nagayama, Sobrizal, Toshio Kurakazu, Paulino L. Sanchez, Kazuyuki Doi, Yoshiyuki Yamagata, Hideshi Yasui, Introgression lines of rice (Oryza sativa L.) carrying a donor genome from the wild species, O. glumaepatula Steud. and O. meridionalis Ng, BREEDING SCIENCE, 10.1270/jsbbs.60.597, 60, 5, 597-603, 2010.12, To broaden the available rice genetic resources, we developed two populations of introgression lines of cultivated rice (Oryza saliva) carrying donor segments from the wild species Oryza glumaepatula and Oryza meridionalis. These lines contain overlapped introgressed donor segments that covered most parts of the genome of the two donors in the same of O. sativa genetic background (ssp. japonica, cv. Taichung 65). The introgression lines were developed through repeated backcrossing with Taichung 65 as a pollen parent and marker assisted selection. O. glumaepatula introgression lines consist of two sets of the lines (with O. glumaepatula and Taichung 65 cytoplasm, respectively): these comprise a total of 69 lines that cover 79.5 to 89.2% of the Oryza glumaepatula genome. The O. meridionalis introgression lines also consist of two sets of the lines (with O. meridionalis and Taichung 65 cytoplasm, respectively): these comprise a total of 78 lines covering the 81.5 to 98.0% of the Oryza meridionalis genome. These introgression lines significantly broaden rice genetic resources, and will facilitate analyses of the genetics of traits specific to the donor species..
29. Hideshi Yasui, Yoshiyuki Yamagata, Atsushi Yoshimura, Development of chromosome segment substitution lines derived from indica rice donor cultivars DV85 and ARC10313 in the genetic background of japonica cultivar Taichung 65, BREEDING SCIENCE, 10.1270/jsbbs.60.620, 60, 5, 620-628, 2010.12, We have developed two sets of chromosome segment substitution lines (CSSLs) of cultivated rice (Oryza sativa) carrying donor segments from indica cultivars DV85 and ARC10313. The lines in each set contain chromosomal segments that cover most of the donor genome in a uniform genetic background (ssp. japonica cv. Taichung 65). The starting materials were several recombinant inbred lines derived from the crosses Taichung 65 x DV85 and Taichung 65 x ARC10313. The CSSLs were generated by repeated backcrossing to Taichung 65 (pollen parent), with marker-assisted selection applied at several marker loci. The CSSLs of DV85 (TD-CSSLs) comprise 45 lines that cover 76.6% of the DV85 genome, and the CSSLs of ARC10313 (TA-CSSLs) comprise 44 lines that cover 74.4% of the ARC10313 genome. We investigated the genetic control of days-to-heading in both sets of CSSLs and demonstrated the genetic contribution of several chromosome regions. These CSSLs provide a valuable tool for rice germplasm enhancement, and we expect them to reveal the genetic basis of traits specific to the donor cultivars..
30. Yamagata, Y., M. Watanabe, K. Doi and A. Yoshimura, Mapping of gametophytic pollen sterility mutant loci, gps4, gps5, gps6 and gps12 in rice, Rice Genetics Newsletter, 25, 50-51, 2010.05.
31. Yoshiyuki Yamagata, Eiji Yamamoto, Kohichiro Aya, Khin Thanda Win, Kazuyuki Doi, Sobrizal, Tomoko Ito, Hiroyuki Kanamori, Jianzhong Wu, Takashi Matsumoto, Makoto Matsuoka, Motoyuki Ashikari, Atsushi Yoshimura, Mitochondrial gene in the nuclear genome induces reproductive barrier in rice., Proceedings of the National Academy of Sciences of the United States of America, 10.1073/pnas.0908283107, 107, 4, 1494-9, 2010.01, [URL], Hybrid incompatibility in F(1) hybrids or later generations is often observed as sterility or inviability. This incompatibility acts as postzygotic reproductive isolation, which results in the irreversible divergence of species. Here, we show that the reciprocal loss of duplicated genes encoding mitochondrial ribosomal protein L27 causes hybrid pollen sterility in F(1) hybrids of the cultivated rice Oryza sativa and its wild relative O. glumaepatula. Functional analysis revealed that this gene is essential for the later stage of pollen development, and distribution analysis suggests that the gene duplication occurred before the divergence of the AA genome species. On the basis of these results, we discuss the possible contribution of the "founder effect" in establishing this reproductive barrier..
32. Khin Thanda Win, Takahiko Kubo, Yuta Miyazaki, Kazuyuki Doi, Yoshiyuki Yamagata, Atsushi Yoshimura, Identification of two loci causing F-1 pollen sterility in inter- and intraspecific crosses of rice, BREEDING SCIENCE, 10.1270/jsbbs.59.411, 59, 4, 411-418, 2009.12, [URL], F-1 sterility, one of the most common post-zygotic reproductive barriers, is frequently observed in both interspecific and intraspecific crosses of rice. Elucidating the genetic and cytological mechanisms of F-1 pollen sterility is important to exploit genetic resources and to understand the evolutionary dynamics of post-zygotic reproductive isolation in rice. Here, we report two F-1 pollen sterility loci, designated S36 and S25, found in an interspecific cross between O. sativa ssp. japonica (Taichung 65) and O. nivara (IRGC105444), and all intraspecific cross between O. sativa ssp. japonica (Asominori) and ssp. indica (IR24). Genetic analyses revealed that both loci are located on distal end of the short arm of chromosome 12 and that allelic interaction at the heterozygous locus caused the sterility of male gametes carrying the japonica alleles in both cases. Comparison of map positions of S36 and S25 suggested that these two loci might be the same locus. Cytological investigation revealed that abnormality of sterile pollen grains caused by S36 occurred mainly at the late bicellular stage after initiation of starch accumulation. This Study would provide the better understanding on the genetic nature and the cytological mechanism of F-1 pollen sterility in rice..
33. Khin Thanda Win, Takahiko Kubo, Yuta Miyazaki, Kazuyuki Doi, Yoshiyuki Yamagata, Atsushi Yoshimura, Identification of two loci causing F1 pollen sterility in inter- and intraspecific crosses of rice, Breeding Science, 10.1270/jsbbs.59.411, 59, 4, 411-418, 2009.12, [URL], F1 sterility, one of the most common post-zygotic reproductive barriers, is frequently observed in both inter-specific and intraspecific crosses of rice. Elucidating the genetic and cytological mechanisms of F1 pollen sterility is important to exploit genetic resources and to understand the evolutionary dynamics of post-zygotic reproductive isolation in rice. Here, we report two F1 pollen sterility loci, designated S36 and S25, found in an interspecific cross between O. sativa ssp. japonica (Taichung 65) and O. nivara (IRGC105444), and an intraspecific cross between O. sativa ssp. japonica (Asominori) and ssp. indica (IR24). Genetic analyses revealed that both loci are located on distal end of the short arm of chromosome 12 and that allelic interaction at the heterozygous locus caused the sterility of male gametes carrying the japonica alleles in both cases. Comparison of map positions of S36 and S25 suggested that these two loci might be the same locus. Cytological investigation revealed that abnormality of sterile pollen grains caused by S36 occurred mainly at the late bicellular stage after initiation of starch accumulation. This study would provide the better understanding on the genetic nature and the cytological mechanism of F1 pollen sterility in rice..
34. Takahiko Kubo, Yoshiyuki Yamagata, Maki Eguchi, Atsushi Yoshimura, A novel epistatic interaction at two loci causing hybrid male sterility in an inter-subspecific cross of rice (Oryza sativa L.)., Genes & genetic systems, 10.1266/ggs.83.443, 83, 6, 443-53, 2008.12, [URL], Postzygotic reproductive isolation (RI) often arises in inter-subspecific crosses as well as inter-specific crosses of rice (Oryza sativa L.). To further understand the genetic architecture of the postzygotic RI, we analyzed genes causing hybrid sterility and hybrid breakdown in a rice inter-subspecific cross. Here we report hybrid male sterility caused by epistatic interaction between two novel genes, S24 and S35, which were identified on rice chromosomes 5 and 1, respectively. Genetic analysis using near-isogenic lines (NILs) carrying IR24 (ssp. indica) segments with Asominori (ssp. japonica) genetic background revealed a complicated aspect of the epistasis. Allelic interaction at the S24 locus in the heterozygous plants caused abortion of male gametes carrying the Asominori allele (S24-as) independent of the S35 genotype. On the other hand, male gametes carrying the Asominori allele at the S35 locus (S35-as) showed abortion only when the IR24 allele at the S24 locus (S24-ir) was concurrently introgressed into the S35 heterozygous plants, indicating that the sterility phenotype due to S35 was dependent on the S24 genotype through negative epistasis between S24-ir and S35-as alleles. Due to the interaction between S24 and S35, self-pollination of the double heterozygous plants produced pollen-sterile progeny carrying the S24-ir/S24-ir S35-as/S35-ir genotype in addition to the S24 heterozygous plants. This result suggests that the S35 gene might function as a modifier of S24. This study presents strong evidence for the importance of epistatic interaction as a part of the genetic architecture of hybrid sterility in rice. In addition, it suggests that diverse systems have been developed as postzygotic RI mechanisms within the rice..
35. Takahiko Kubo, Yoshiyuki Yamagata, Maki Eguchi, Atsushi Yoshimura, A novel epistatic interaction at two loci causing hybrid male sterility in an inter-subspecific cross of rice (Oryza sativa L.), Genes and Genetic Systems, 10.1266/ggs.83.443, 83, 6, 443-453, 2008.12, [URL], Postzygotic reproductive isolation (RI) often arises in inter-subspecific crosses as well as inter-specific crosses of rice {Oryza sativa L.). To further understand the genetic architecture of the postzygotic RI, we analyzed genes causing hybrid ste- rility and hybrid breakdown in a rice inter-subspecific cross. Here we report hybrid male sterility caused by epistatic interaction between two novel genes, S24 and S35, which were identified on rice chromosomes 5 and 1, respectively. Genetic analysis using near-isogenic lines (NILs) carrying IR24 (ssp. indica) seg- ments with Asominori (ssp. japonica) genetic background revealed a complicated aspect of the epistasis. Allelic interaction at the S24 locus in the heterozygous plants caused abortion of male gametes carrying the Asominori allele (S24-as) independent of the S35 genotype. On the other hand, male gametes carrying the Asominori allele at the S35 locus (S35-as) showed abortion only when the IR24 allele at the S24 locus (S24-ir) was concurrently introgressed into the S35 het- erozygous plants, indicating that the sterility phenotype due to S35 was depen- dent on the S24 genotype through negative epistasis between S24-ir and S35-as alleles. Due to the interaction between S24 and S35, self-pollination of the double heterozygous plants produced pollen-sterile progeny carrying the S24-irl S24-ir S35-as/S35-ir genotype in addition to the S24 heterozygous plants. This result suggests that the S35 gene might function as a modifier of S24. This study presents strong evidence for the importance of epistatic interaction as a part of the genetic architecture of hybrid sterility in rice. In addition, it suggests that diverse systems have been developed as postzygotic RI mechanisms within the rice..
36. Y. Yamagata, K. Doi, H. Yasui, A. Yoshimura, Linkage analysis of SPS6, SPS9 and SPS12, the sporophytic rice genes acting in pollen development, Rice Genetics Newsletter, 24, 14-15, 24: 14-15, 2008.01.
37. Yoshiyuki Yamagata, Kazuyuki Doi, Hideshi Yasui, Atsushi Yoshimura, Identification of mutants for abnormal pollen development in rice, BREEDING SCIENCE, 10.1270/jsbbs.57.331, 57, 4, 331-337, 57: 331-337, 2007.12, To gain a comprehensive understanding of the genetic regulation of male gametogenesis, we screened and identified mutants for abnormal pollen development in rice (Oryza sativa L.). We gamma-irradiated spikelets of a japonica rice cultivar, Taichung 65, just before and after anthesis. Among 1,000 M-2 lines, 24 lines were identified as mutants for pollen sterility. Progeny tests in M-3 demonstrated that pollen sterility in 12 lines was controlled by single recessive genes, designated spsl-sps12 (sporophytic pollen sterility). In the remaining 12 lines, pollen semi-sterility was under the control of gametophytic genes, designated gps1-gps12 (gametophytic pollen sterility). Linkage analysis revealed that sps6, sps9, and sps12 were mapped on chromosomes 3, 9, and 7, respectively..
38. Yoshiyuki Yamagata, Kazuyuki Doi, Hideshi Yasui, Atsushi Yoshimura, Identification of mutants for abnormal pollen development in rice, Breeding Science, 10.1270/jsbbs.57.331, 57, 4, 331-337, 2007.12, [URL], To gain a comprehensive understanding of the genetic regulation of male gametogenesis, we screened and identified mutants for abnormal pollen development in rice (Oryza sativa L.). We gamma-irradiated spikelets of a japonica rice cultivar, Taichung 65, just before and after anthesis. Among 1,000 M2 lines, 24 lines were identified as mutants for pollen sterility. Progeny tests in M3 demonstrated that pollen sterility in 12 lines was controlled by single recessive genes, designated sps1-sps12 (sporophytic pollen sterility). In the remaining 12 lines, pollen semi-sterility was under the control of gametophytic genes, designated gps1-gps12 (gametophytic pollen sterility). Linkage analysis revealed that sps6, sps9, and sps12 were mapped on chromosomes 3, 9, and 7, respectively..
39. 山形 悦透, 松永 貴子, 吉村 淳, イグサ優良品種「ひのみどり」を識別する多型探索およびマーカー開発, DNA鑑定, 4, 39-47.

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