研究者詳細 - 土井　一行

論文 - 土井　一行

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Development of rice breeding and cultivation technology tailored for Kenya's environment

Makihara D., Kimani J., Samejima H., Kikuta M., Menge D., Doi K., Inukai Y., Maekawa M., Masunaga T., Sasaki Y., Katsura K., Kitano H., Mitsuya S., Kano-Nakata M., Wainaina C., Gichuhi E., Njinju S., Kagito S., Magoti R., Kundu C., Yamauchi A.

Crop Production under Stressful Conditions: Application of Cutting-edge Science and Technology in Developing Countries 頁： 27 - 47 2018年8月

Regional population differences of the brown planthopper (Nilaparvata lugens Stål) in Cambodia using genotyping-by-sequencing. 査読有り

Matsukawa M, Tasaki M, Doi K, Ito K, Kawakita K, Tanaka T

Bulletin of entomological research 108 巻 ( 4 ) 頁： 471 - 478 2018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：Bulletin of Entomological Research

The brown planthopper Nilaparvata lugens Stål (BPH) can be found year-round in tropical region and causes severe damage to rice. Although there has been documented BPH damage to rice crops in the past decade in Cambodia, the extent of this epidemic is poorly understood. Here, we examined the time variation of BPH population in the abundance of morphotypes in 13 main rice-producing provinces (86 sites) by aspirator method and in the Takeo Province (five sites) by yellow sticky trap method. At least three generations were observed during the 3-month collection period in the rainy growing season. Regarding the occurrence of BPH morphotypes, in July the macropterous adults were restricted to south Cambodia and in August all morphotypes, adults (macropterous and brachypterous) and nymphs, appeared in all sampling sites. To explain the difference of regional distribution, the genetic differentiation was analyzed in south and northwest Cambodia (three sites) by using single nucleotide polymorphisms (SNP) analysis via genotyping-by-sequencing (GBS) using next-generation sequencing. The 2455 SNPs obtained by GBS clarified the three sub-populations and they corresponded to the expected dissemination patterns. These results provide a clue to understand the differentiation and epidemic of BPH in Cambodia.

DOI： 10.1017/S0007485317000992

Web of Science

Scopus

PubMed

Identification and validation of QTLs for cold tolerance at the booting stage and other agronomic traits in a rice cross of a Japanese tolerant variety, Hananomai and a NERICA parent, WAB56-104 査読有り Open Access

Cornelius Mbathi Wainaina, Daigo Makihara, Mitsuru Nakamura, Akihiro Ikeda, Taro Suzuki, Yuko Mizukami, Toshihiro Nonoyama, Kazuyuki Doi, Mayumi Kikuta, Hiroaki Samejima, Daniel Makori Menge, Akira Yamauchi, Akira Yamauchi, John Munji Kimani, Yoshiaki Inukai

Plant Production Science 21 巻 ( 2 ) 頁： 132 - 143 2018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：Plant Production Science

In Africa, cold temperatures occur in the highlands of East and Southern Africa and in some areas of the Sahel region of West Africa leading to substantial rice yield losses. Cold tolerance (CT) at booting stage on basis of spikelet fertility after cold water irrigation was evaluated using F2 population derived from a cross between temperate japonica, Hananomai, and tropical japonica, WAB56-104. Two Quantitative trait loci (QTLs) for CT were detected on chromosome 8 and 10 with enhanced effects on the trait coming from Hananomai and WAB56-104 allele, respectively. The QTLs explained 30% and 33% of phenotypic variation in spikelet fertility, respectively. CT was negatively correlated with panicle number (r = −0.35, p < 0.01) and positively correlated with panicle weight (r = 0.61, p < 0.001). Selected BC1F4 and BC1F5 genotypes having homozygous alleles for both CT QTLs exhibited higher spikelet fertility under cold stress. The identified QTLs will be useful in the development of cold-tolerant varieties for production in high altitude areas through marker-assisted selection.

DOI： 10.1080/1343943X.2018.1440970

Open Access

Web of Science

Scopus

Root plasticity under fluctuating soil moisture stress exhibited by backcross inbred line of a rice variety, Nipponbare carrying introgressed segments from KDML105 and detection of the associated QTLs Open Access

Owusu-Nketia Stella, Inukai Yoshiaki, Ohashi Satomi, Rodriguez Suralta Roel, Doi Kazuyuki, Mitsuya Shiro, Kano-Nakata Mana, Manito Niones Jonathan, Dinh Thi Ngoc Nguyen, Takuya Kabuki, Makihara Daigo, Yamauchi Akira

PLANT PRODUCTION SCIENCE 21 巻 ( 2 ) 頁： 106-122 - 122 2018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：Plant Production Science

In rainfed lowland rice ecosystem, rice plants are often exposed to alternating recurrences of waterlogging and drought due to erratic rainfall. Such soil moisture fluctuation (SMF) which is completely different from simple or progressive drought could be stressful for plant growth, thereby causing reduction in yield. Root plasticity is one of the key traits that play important roles for plant adaptation under such conditions. This study aimed to evaluate root plasticity expression and its functional roles in dry matter production and yield under SMF using Nipponbare, KDML 105 and three backcross inbred lines (BILs) and to identify QTL(s) associated with root traits in response to SMF at two growth stages using Nipponbare/KDML105 F2 plants. A BIL, G3-3 showed higher shoot dry matter production and yield than Nipponbare due to its greater ability to maintain stomatal conductance concomitant with greater root system development caused by promoted production of nodal and lateral roots under SMF. QTLs were identified for total nodal root length, total lateral root length, total root length, number of nodal roots, and branching index under SMF at vegetative and reproductive stages. The QTLs detected at vegetative and reproductive stages were different. We discuss here that relationship between root system of G3-3 and the detected QTLs. Therefore, G3-3 and the identified QTLs could be useful genetic materials in breeding program for improving the adaptation of rice plants in target rainfed lowland areas.

DOI： 10.1080/1343943X.2018.1446759

Open Access

Web of Science

Scopus

Duplication and loss of function of genes encoding RNA polymerase III subunit C4 causes hybrid incompatibility in rice 査読有り Open Access

Nguyen G.N., Yamagata Y., Shigematsu Y., Watanabe M., Miyazaki Y., Doi K., Tashiro K., Kuhara S., Kanamori H., Wu J., Matsumoto T., Yasui H., Yoshimura A.

G3: Genes, Genomes, Genetics 7 巻 ( 8 ) 頁： 2565 - 2575 2017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：G3: Genes, Genomes, Genetics

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-offunction 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.

DOI： 10.1534/g3.117.043943

Adapting Genotyping-by-Sequencing for Rice F2 Populations. 査読有り Open Access

Furuta T, Ashikari M, Jena KK, Doi K, Reuscher S

G3 (Bethesda, Md.) 7 巻 ( 3 ) 頁： 881 - 893 2017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：G3: Genes, Genomes, Genetics

Rapid and cost-effective genotyping of large mapping populations can be achieved by sequencing a reduced representation of the genome of every individual in a given population, and using that information to generate genetic markers. A customized genotyping-by-sequencing (GBS) pipeline was developed to genotype a rice F2 population from a cross of Oryza sativa ssp. japonica cv. Nipponbare and the African wild rice species O. longistaminata. While most GBS pipelines aim to analyze mainly homozygous populations, we attempted to genotype a highly heterozygous F2 population. We show how species- and population-specific improvements of established protocols can drastically increase sample throughput and genotype quality. Using as few as 50,000 reads for some individuals (134,000 reads on average), we were able to generate up to 8154 informative SNP markers in 1081 F2 individuals. Additionally, the effects of enzyme choice, read coverage, and data postprocessing are evaluated. Using GBS-derived markers, we were able to assemble a genetic map of 1536 cM. To demonstrate the usefulness of our GBS pipeline, we determined quantitative trait loci (QTL) for the number of tillers. We were able to map four QTL to chromosomes 1, 3, 4, and 8, and partially confirm their effects using introgression lines. We provide an example of how to successfully use GBS with heterozygous F2 populations. By using the comparatively low-cost MiSeq platform, we show that the GBS method is flexible and cost-effective, even for smaller laboratories.

DOI： 10.1534/g3.116.038190

A single base change explains the independent origin of and selection for the nonshattering gene in African rice domestication. 査読有り Open Access

Win KT, Yamagata Y, Doi K, Uyama K, Nagai Y, Toda Y, Kani T, Ashikari M, Yasui H, Yoshimura A

The New phytologist 213 巻 ( 4 ) 頁： 1925 - 1935 2017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：New Phytologist

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.

DOI： 10.1111/nph.14290

Web of Science

Scopus

PubMed

Identification of QTLs for yield-related traits in RILs derived from the cross between pLIA-1 carrying Oryza longistaminata chromosome segments and Norin 18 in rice 査読有り

Gichuhi, E., E. Himi, H. Takahashi, S. Zhu, K. Doi, K. Tsugane and M. Maekawa

Breed Sci. 66 巻頁： 720-733 2016年12月

Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice 査読有り

Bessho-Uehara, K., D.R. Wang, T. Furuta, A. Minami, K. Nagai, R. Gamuyao, K. Asano, R.B. Angeles-Shim, Y. Shimizu, M. Ayano, N. Komeda, K. Doi, K. Miura, Y. Toda, T. Kinoshita, S. Okuda, T. Higashiyama, M. Nomoto, Y. Tada, H. Shinohara, Y. Matsubayashi, A. Greenberg, J. Wu, H. Yasui, A. Yoshimura, H. Mori, S.R. McCouch and M. Ashikari

Proc. Natl. Acad. Sci. USA 113 巻頁： 8969-8974 2016年8月

Construction of a versatile SNP array for pyramiding useful genes of rice 招待有り査読有り

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

Plant Science 2015年9月

Oryza sativaとO. glumaepatulaの種間交雑後代に見出された染色体２に座乗する２個の連鎖するF1花粉不稔遺伝子査読有り

Sakata, M., Y. Yamagata, K. Doi and A. Yoshimura

Breeding Science 64 巻 ( 4 ) 頁： 309-320 2014年12月

Validation of QTLs for eating quality of japonica rice `Koshihikari' using backcross inbred lines 査読有り

1. Wada, T., H. Yasui, T. Inoue, M. Tsubone, T. Ogata, K. Doi, A. Yoshimura and Y. Matsue

Plant Prod. Sci. 16 巻頁： 131-140 2013年3月

イネGS3遺伝子の短粒アレルは複数の別々の由来をもつ査読有り

63 巻頁： 77-85 2013年3月

Molecular mapping of two loci conferring F1 pollen sterility in inter- and intraspecific crosses of rice 査読有り

Win, K.T., Kubo, T., Miyazaki, Y., Doi, K., Yasui, H., Yamagata, Y. and Yoshimura, A.

Genes Genomes and Genomics 6 巻頁： 16-21 2012年

GS3 participates in stigma exsertion as well as seed length in rice 査読有り

Takano-Kai, N., Doi, K. and Yoshimura A

Breed Sci 61 巻頁： 244-250 2011年9月

Independent evolution of a new allele of F1 pollen sterility gene S27 encoding mitochondrial ribosomal protein L27 in Oryza nivara 査読有り

4. K.T. Win, Y. Yamagata, Y. Miyazaki, K. Doi, H. Yasui and A. Yoshimura

Theor. Appl. Genet. 122 巻 ( 2 ) 頁： 385-394 2011年2月

Artificial selection for a green revolution gene during japonica rice domestication 査読有り

1. K. Asano, M. Yamasaki, S. Takuno, K. Miura, S. Katagiri, T. Ito, K. Doi, J. Wu, K. Ebana, T. Matsumoto, H. Innan, H. Kitano, M. Ashikari and M. Matsuoka

Proc Natl Acad Sci USA. 2011年

Introgression lines of rice (Oryza sativa L.) carrying a donor genome from the wild species, O. glumaepatula Steud. and O. meridionalis Ng. 査読有り

2. A. Yoshimura, H. Nagayama, Sobrizal, T. Kurakazu, P.L. Sanchez, K. Doi, Y. Yamagata and H. Yasui

Breed. Sci. 60 巻頁： 597-603 2010年

Analysis of rice panicle traits and detection of QTLs using an image analyzing method 査読有り

M. Ikeda, Y. Hirose, T. Takashi, Y. Shibata, T. Yamamura, T. Komura, K. Doi, M. Ashikari, M. Matsuoka and H. Kitano

Breed. Sci. 60 巻頁： 55-64 2010年

Mitochondrial gene in the nuclear genome induces reproductive barrier in rice 査読有り

Y. Yamagata, E. Yamamoto, K. Aya, K.T. Win, K. Doi, Sobrizal, T. Ito, H. Kanamori, J. Wu, T. Matsumoto, M. Matsuoka, M. Ashikari, A. Yoshimura

Proc. Natl. Acad. Sci. U.S.A. 107 巻頁： 1494-1499 2010年

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