研究者詳細 - 土井　一行

Leaf Na+ effects and multi-trait GWAS point to salt exclusion as the key mechanism for reproductive stage salinity tolerance in rice.

de Ocampo MP, Tam BP, Egdane JA, Chebotarov D, Doi K, Yamauchi A, Ismail AM, Henry A, Mitsuya S

Annals of botany 2024年12月

Detection of QTLs regulating the second internode length in rice dwarf mutant d1. Open Access

Ha QT, Moe S, Reyes VP, Doi K, Miura K, Mizushima M, Maeno A, Tsuda K, Nagai K, Ashikari M

Breeding science 74 巻 ( 5 ) 頁： 443 - 453 2024年12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：日本育種学会

Stem length is a crucial agronomic trait in rice breeding. The short stature of rice dwarf mutants is caused by shortening of internodes, resulting in five distinct internode elongation patterns: dn, dm, d6, nl and sh. Several genetic studies have been conducted; however, the genetic mechanisms underlying these internode elongation patterns remain unclear. In this study, we examined two Daikoku dwarf (d1) mutants, T65(d1-1) and Kin(d1-7), which display contrasting internode elongation phenotypes. Anatomical observation revealed that T65(d1-1) exhibits a dm-type internode elongation pattern due to the lack of the second internode counted from the top, while Kin(d1-7) shows a dn-type pattern with a relatively elongated second internode. To identify the genetic factors influencing these phenotypes, we conducted a quantitative trait locus (QTL) analysis using two F2 populations derived from reciprocal crosses between them. The QTL analysis showed that the second internode length is regulated by three QTLs on chromosomes 4, 5, and 6. Epistatic effects were observed through the analysis of F3 progenies, indicating that the combination of Kin(d1-7) alleles at these QTLs is associated with an increased second internode length. Furthermore, specific combinations of alleles result in varying degrees of elongation in the second internode, significantly impacting the internode elongation pattern. These findings contribute to a deeper understanding of the genetic factors influencing the internode elongation patterns in rice.

DOI： 10.1270/jsbbs.24036

Evaluation of Grain-Filling-Related Traits Using Taichung 65 x DV85 Chromosome Segment Substitution Lines (TD-CSSLs) of Rice. 査読有り Open Access

Mabreja AD, Reyes VP, Soe TK, Shimakawa K, Makihara D, Nishiuchi S, Doi K

Plants (Basel, Switzerland) 13 巻 ( 2 ) 2024年1月

記述言語：英語出版者・発行元：Plants

Grain yield of rice consists of sink capacity and grain filling. There are some genes known to contribute to sink capacity, but few genes associated with grain filling are known. We conducted a genetic analysis on yield-related traits by using a chromosome segment substitution line population that have introgression from DV85, an aus variety of rice, in the background of T65, a japonica variety. Refined whole-genome genotypes of the 43 TD-CSSLs were obtained by genotyping-by-sequencing. The effects of previously detected quantitative trait loci (QTLs), qNSC1 and qNSC2, were confirmed by the amount of non-structural carbohydrate (NSC) at 5 days after heading (DAH). The CSSL for qSWTR11, the QTL for decrease in shoot weight during the maturity stage, showed the highest NSC at 5 DAH and lowest at 35 DAH. The brown rice yield of these lines were not stably significant. Most of the sink-related traits correlated between the 2 tested years, but most of the grain-filling traits did not show correlation between the 2 years. Correlation analysis revealed that the sink capacity is stable and primarily determines the yield, and grain filling is more affected by the environment. In addition, biomass production before heading and during the maturity stage contributes to higher yield in TD-CSSLs, and the amount of translocation of stem reserve does not affect much to the yield. We conclude that higher NSC at the heading stage and rapid decrease in shoot biomass during the maturity stage did not directly contribute to the yield formation in the japonica genetic background.

DOI： 10.3390/plants13020289

Contribution of genes related to grain number (Gn1a and WFP) introgressed into NERICA 1 to grain yield under tropical highland conditions in central Kenya 査読有り Open Access

Kikuta M., Menge D.M., Gichuhi E.W., Samejima H., Tomita R., Kimani J.M., Musila R.N., Doi K., Ashikari M., Angeles-Shim R., Jena K.K., Makihara D.

Plant Production Science 26 巻 ( 3 ) 頁： 309 - 319 2023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：Plant Production Science

In Kenya and many other African countries, improving rice productivity is vital for future food security. To improve rice productivity in Kenya, near-isogenic lines (NIL) were developed by introducing Gn1a and WFP, genes that function to increase grain number per panicle by increasing secondary and primary rachis-branches, into NERICA 1, a registered variety in Kenya. The aim of this study was to determine whether the introduction of these genes has the potential to improve rice productivity under tropical highland conditions in central Kenya. Field experiments were conducted in 2016 and 2017 at a lowland rice field in Mwea, Kenya, under different nitrogen fertilization conditions using three lines of NERICA 1 introgressed with Gn1a and/or WFP (NIL-Gn1a, NIL-WFP, and NIL-Gn1a+WFP) and their recurrent parents, NERICA 1. Two years of field experiments revealed that the introgression lines enhanced grain yield by increasing the number of primary and secondary rachis-branches and the number of grains per panicle. Gn1a and WFP showed additive effects and the introgression of both genes alleviated the negative effects on yield components observed in the introgressed lines, resulting in higher grain yield. Sufficient nitrogen fertilization was required to increase yield in the single-gene introgression lines. However, the line with both Gn1a and WFP achieved reasonable yields even under low fertilizer conditions in Mwea, Kenya. As these introgression lines have similar growing characteristics to their parent variety, they are expected to contribute to increased rice production in Kenya and similar environments in sub-Saharan Africa.

DOI： 10.1080/1343943x.2023.2245127

Genetic Variation of Blast (Pyricularia oryzae Cavara) Resistance in the Longistaminata Chromosome Segment Introgression Lines (LCSILs) and Potential for Breeding Use in Kenya. Open Access

Tomita R, Reyes VP, Fukuta Y, Gichuhi EW, Kikuta M, Menge DM, Doi K, Makihara D

Plants (Basel, Switzerland) 12 巻 ( 4 ) 2023年2月

記述言語：英語出版者・発行元：Plants

In Kenya’s rice-growing areas, Basmati varieties have been produced in monoculture since the late 1980s. This has resulted in the breakdown of the resistance (R) gene-mediated response of the local Basmati varieties to blast disease caused by Pyricularia oryzae. To improve blast resistance in Kenyan Basmati varieties, continuous identification of R genes and suitable breeding materials for Basmati are necessary. Longistaminata chromosome segment introgression lines (LCSILs) with the Kernel Basmati genetic background, developed using a rice line called potential low-input adaptable-1 (pLIA-1) derived from a cross between Taichung 65 (T65) (a rice variety in the Japonica Group) and O. longistaminata, are expected to contain useful blast R genes derived from O. longistaminata or T65. In this study, we investigated the genetic variation of blast R genes in LCSILs and their parents by using a new international differential system for designating blast races based on the gene-for-gene theory and molecular characterization using single nucleotide polymorphism (SNP) markers. LCSILs and their parents were classified into three groups—A, B1, and B2—based on reaction patterns to the standard differential blast isolates (SDBIs). Group A, including pLIA-1, showed the highest resistance in all groups, followed by groups B1 and B2. Kernel Basmati in group B1 was considered to possess Pik-p or Pi7(t), Pi19(t), and other unknown R genes. In addition to these R genes, LCSIL 6, 12, 27, 28, and 40, in group A, were determined to possess one of Pish, Piz-t, or both genes that confer resistance to the Kenyan blast races. These lines can be used for efficiently pyramiding blast R genes in the local Basmati varieties.

DOI： 10.3390/plants12040863

Utilization of Genotyping-by-Sequencing (GBS) for Rice Pre-Breeding and Improvement: A Review. 査読有り Open Access

Reyes VP, Kitony JK, Nishiuchi S, Makihara D, Doi K

Life (Basel, Switzerland) 12 巻 ( 11 ) 頁： 1752 2022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：Life

Molecular markers play a crucial role in the improvement of rice. To benefit from these markers, genotyping is carried out to identify the differences at a specific position in the genome of individuals. The advances in sequencing technologies have led to the development of different genotyping techniques such as genotyping-by-sequencing. Unlike PCR-fragment-based genotyping, genotyping-by-sequencing has enabled the parallel sequencing and genotyping of hundreds of samples in a single run, making it more cost-effective. Currently, GBS is being used in several pre-breeding programs of rice to identify beneficial genes and QTL from different rice genetic resources. In this review, we present the current advances in the utilization of genotyping-by-sequencing for the development of rice pre-breeding materials and the improvement of existing rice cultivars. The challenges and perspectives of using this approach are also highlighted.

DOI： 10.3390/life12111752

Estimating Yield-Related Traits Using UAV-Derived Multispectral Images to Improve Rice Grain Yield Prediction 査読有り Open Access

Bascon M.V., Nakata T., Shibata S., Takata I., Kobayashi N., Kato Y., Inoue S., Doi K., Murase J., Nishiuchi S.

Agriculture (Switzerland) 12 巻 ( 8 ) 頁： 1141 2022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：Agriculture (Switzerland)

Rice grain yield prediction with UAV-driven multispectral images are re-emerging interests in precision agriculture, and an optimal sensing time is an important factor. The aims of this study were to (1) predict rice grain yield by using the estimated aboveground biomass (AGB) and leaf area index (LAI) from vegetation indices (VIs) and (2) determine the optimal sensing time in estimating AGB and LAI using VIs for grain yield prediction. An experimental trial was conducted in 2020 and 2021, involving two fertility conditions and five japonica rice cultivars (Aichinokaori, Asahi, Hatsushimo, Nakate Shinsenbon, and Nikomaru). Multi-temporal VIs were used to estimate AGB and LAI throughout the growth period with the extreme gradient boosting model and Gompertz model. The optimum time windows for predicting yield for each cultivar were determined using a single-day linear regression model. The results show that AGB and LAI could be estimated from VIs (R2: 0.56–0.83 and 0.57–0.73), and the optimum time window for UAV flights differed between cultivars, ranging from 4 to 31 days between the tillering stage and the initial heading stage. These findings help researchers to save resources and time for numerous UAV flights to predict rice grain yield.

DOI： 10.3390/agriculture12081141

A novel combination of genes causing temperature sensitive hybrid weakness in rice 査読有り

2. Than Kutay Soe, M. Kunieda, H. Sunohara, Y. Inukai, V.P. Reyes, S. Nishiuchi and K. Doi

Front. Plant Sci. 13 巻頁： 908000 2022年5月

QTL analysis for sodium removal ability in rice leaf sheaths under salinity using an IR-44595/318 F(2) population. 査読有り国際共著 Open Access

Goto I, Neang S, Kuroki R, Reyes VP, Doi K, Skoulding NS, Taniguchi M, Yamauchi A, Mitsuya S

Frontiers in plant science 13 巻頁： 1002605 2022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：Frontiers in Plant Science

Over-accumulation of salt in rice plants is an effect of salt stress which decreases growth and grain yield. Salt removal ability in leaf sheaths is a tolerance mechanism to decrease salt entry and accumulation in leaf blades and maintain photosynthesis under salinity. In this study, a QTL analysis of removal ability of sodium ions (Na+) in leaf sheaths and Na+ accumulation-related traits, was conducted using F2 population between two rice varieties, IR-44595 with superior Na+ removal ability, and 318 with contrasting Na+ removal ability in leaf sheaths under salinity. Suggestive QTLs for Na+ removal ability in leaf sheaths were found on chromosomes 4 and 11. The suggestive QTL on chromosome 11 overlapped with other significant QTLs for Na+ concentration in shoots, leaf blades and leaf sheaths, and Na+/K+ ratio in leaf blades. Correlation analysis indicated that Na+ removal ability in leaf sheaths is important in reducing Na+ accumulation in leaf blades. The varietal difference of Na+ removal ability in leaf sheaths at the whole plant level was greater at lower NaCl concentrations and became smaller as the treatment NaCl concentration increased. Although the Na+ removal ability in leaf sheath was comparable between IR-44595 and 318 under high salinity at the whole plant level, the younger leaves of IR-44595 still showed a higher Na+ sheath-blade ratio than 318, which implied the Na+ removal ability functions in the younger leaves in IR-44595 to reduce Na+ entry in young leaf blades even under high salinity.

DOI： 10.3389/fpls.2022.1002605

Marker-Assisted Introgression and Stacking of Major QTLs Controlling Grain Number (Gn1a) and Number of Primary Branching (WFP) to NERICA Cultivars. 査読有り国際共著 Open Access

Reyes VP, Angeles-Shim RB, Mendioro MS, Manuel MCC, Lapis RS, Shim J, Sunohara H, Nishiuchi S, Kikuta M, Makihara D, Jena KK, Ashikari M, Doi K

Plants (Basel, Switzerland) 10 巻 ( 5 ) 頁： 844 - 844 2021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：Plants

The era of the green revolution has significantly improved rice yield productivity. However, with the growing population and decreasing arable land, rice scientists must find new ways to improve rice productivity. Although hundreds of rice yield-related QTLs were already mapped and some of them were cloned, only a few were utilized for actual systematic introgression breeding programs. In this study, the major yield QTLs Grain Number 1a (Gn1a) and Wealthy Farmer’s Panicle (WFP) were introgressed and stacked in selected NERICA cultivars by marker-assisted backcross breeding (MABB). The DNA markers RM3360, RM3452, and RM5493 were used for foreground selection. At BC3 F4 and BC3 F5 generation, a combination of marker-assisted selection and phenotypic evaluation were carried out to select lines with target alleles and traits. Further, genotyping-by-sequencing (GBS) was conducted to validate the introgression and determine the recurrent parent genome recovery (RPGR) of the selected lines. The Gn1a and/or WFP introgression lines showed significantly higher numbers of spikelets per panicle and primary branching compared to the recurrent parents. In addition, lines with Gn1a and/or WFP alleles were comparatively similar to the recurrent parents (RP) in most yield-related traits. This study demonstrates the success of utilizing yield QTLs and marker-assisted selection to develop and improve rice cultivars.

DOI： 10.3390/plants10050844

Marker-Assisted Introgression of Quantitative Resistance Gene pi21 Confers Broad Spectrum Resistance to Rice Blast Open Access

Diverse panicle architecture results from various combinations of Prl5/GA20ox4 and Pbl6/APO1 alleles. 査読有り Open Access

Agata A, Ando K, Ota S, Kojima M, Takebayashi Y, Takehara S, Doi K, Ueguchi-Tanaka M, Suzuki T, Sakakibara H, Matsuoka M, Ashikari M, Inukai Y, Kitano H, Hobo T

Communications biology 3 巻 ( 1 ) 頁： 302 2020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：Communications Biology

Panicle architecture directly affects crop productivity and is a key target of high-yield rice breeding. Panicle length strongly affects panicle architecture, but the underlying regulatory mechanisms are largely unknown. Here, we show that two quantitative trait loci (QTLs), PANICLE RACHIS LENGTH5 (Prl5) and PRIMARY BRANCH LENGTH6 (Pbl6), independently regulate panicle length in rice. Prl5 encodes a gibberellin biosynthesis enzyme, OsGA20ox4. The expression of Prl5 was higher in young panicles resulting in panicle rachis elongation. Pbl6 is identical to ABERRANT PANICLE ORGANIZATION 1 (APO1), encoding an F-box-containing protein. We found a novel function that higher expression of Pbl6 is responsible for primary branch elongation. RNA-seq analysis revealed that these two genes independently regulate panicle length at the level of gene expression. QTL pyramiding of both genes increased panicle length and productivity. By combining these two genes in various combinations, we designed numerous panicle architecture without trade-off relationship.

DOI： 10.1038/s42003-020-1036-8

その他リンク： http://www.nature.com/articles/s42003-020-1036-8

Evaluation of backcrossed pyramiding lines of the yield-related gene and the bacterial leaf blight resistant genes 招待有り査読有り

J. Intl. Cooper. Agric. Dev. 2020年3月

Angeles-Shim R.B., Reyes V.P., del Valle M.M., Lapis R.S., Shim J., Sunohara H., Jena K.K., Ashikari M., Doi K.

Rice Science 27 巻 ( 2 ) 頁： 113 - 123 2020年3月

出版者・発行元：Rice Science

The quantitative resistance gene pi21 from Sensho was introgressed to an indica breeding line IR63307-4B-13-2, a pyramiding line IRBB4/5/13/21, and a tropical japonica line Kinandang Patong by marker-assisted backcrossing. A total of 192 improved lines at the BC4F3 and BC4F4 generations were developed and confirmed to have the gene introgression via genotyping using a pi21-specific InDel marker. Thirteen randomly selected improved lines, representing all the three genetic backgrounds, demonstrated resistance against leaf blast composites in the field and a broader spectrum resistance against individual isolates compared to the recurrent parents in the glasshouse. Specifically, the tested lines exhibited pi21-acquired resistance against 11 leaf blast isolates that elicited susceptible reactions from the recurrent parents. All the tested lines maintained a comparative heading date, and similar or improved panicle length, number of primary branches per panicle and number of total grains per panicle relative to the recurrent parents. The physical grain characteristics of the recurrent parents were also maintained in the 13 lines tested, although variability in the amylose content and chalkiness degree was observed. The successful marker-assisted introgression of pi21 in diverse genetic backgrounds and the resulting broader spectrum resistance of improved lines against leaf blast indicate the potential of pi21 for deployment in cultivars grown across other rice growing regions in Asia.

DOI： 10.1016/j.rsci.2020.01.002

Domain Unknown Function DUF1668-Containing Genes in Multiple Lineages Are Responsible for F(1) Pollen Sterility in Rice. Open Access

Sakata M, Takano-Kai N, Miyazaki Y, Kanamori H, Wu J, Matsumoto T, Doi K, Yasui H, Yoshimura A, Yamagata Y

Frontiers in plant science 11 巻頁： 632420 2020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：Frontiers in Plant Science

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.

DOI： 10.3389/fpls.2020.632420

Evaluation of backcrossed pyramiding lines of the yield-related gene and the bacterial leaf blight resistant genes 査読有り

Shuto Yamada, Yusuke Kurokawa, Keisuke Nagai, Rosalyn B Angeles-Shim, Hideshi Yasui, Naruto Furuya, Atsushi Yoshimura, Kazuyuki Doi, Motoyuki Ashikari, Hidehiko Sunohara

農学国際協力誌 18 巻 ( 18 ) 頁： 18 - 28 2020年

記述言語：英語出版者・発行元：名古屋大学農学国際教育研究センター

The yield-related gene, WFP increases grain number by increasing the primary branch number per panicle in rice. In the present study, WFP was introgressed from ST-12 to IRBB60, a pyramiding line having the genes Xa4, xa5, xa13 and Xa21 for BLB resistance in the IR24 genetic background. The pyramided lines PL-1, PL-4 and PL-5 that were included in the initial BC2F2 selections based on their improved PBN were selected for further agronomic evaluation and generation advance up to BC2F3. All three lines recorded significantly higher PBN and GN due WFP introgression, although the loss of at least two BLB genes during the breeding process resulted in the variable response of the lines to the different BLB races. Among the lines, only PL-5 showed a significantly higher estimate of actual yield measured in terms of panicle weight per square meter compared to IRBB60. PL-5 also exhibited resistance to five out of the six BLB races used for resistance screening. Despite the negative effects in grain size, the improved yield estimates, as well as the validated BLB resistance of PL-5 makes it a suitable candidate for cultivar adoption under the tropical rice ecosystem of Southeast Asia.イネ収量関連遺伝子WFPは、一次枝梗数増加による着粒数増加をもたらす。IR24に白葉枯病抵抗性遺伝子群（Xa4、xa5、xa13、Xa21）を集積したIRBB60へ、ST-12が持つWFPの導入を行った。IRBB60を反復親とした戻し交雑後代BC2F2とBC2F3世代で、DNAマーカーの利用と一次枝梗数を含む収量形質の評価から、3ピラミディング系統（PL-1、PL-4、PL-5）を選抜した。BC2F4において、これらはWFPによる一次枝梗数と着粒数の増加を示したが、4白葉枯病抵抗性遺伝子の集積が不完全で、白葉枯病レース群への反応の差が見られた。しかし、PL-5はIRBB60よりも収量増加が見込まれ、今回供試した白葉枯病レース（ベトナム、ミャンマー、インド由来6レース）の内5レースに対して抵抗性を示したことから、PL-5は東南アジアの熱帯地域での展開を見込んだ候補系統となり得ると考えられた。

DOI： 10.18999/jouica.18.18

NERICA1に<i>Gn1a</i>および<i>WFP</i>を導入した準同質遺伝子系統のケニアの異なる施肥条件下における生育および収量

菊田真由実, 鮫島啓彰, 芦苅基行, 土井一行, 槇原大悟

日本作物学会講演会要旨集 248 巻 ( 0 ) 頁： 99 - 99 2019年9月

QTL analysis for carbon assimilate translocation-related traits during maturity in rice (Oryza sativa L.). Open Access

Phung HD, Sugiura D, Sunohara H, Makihara D, Kondo M, Nishiuchi S, Doi K

Breeding science 69 巻 ( 2 ) 頁： 289 - 296 2019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：日本育種学会

Problems with carbon assimilate translocation from source organs to sink (grains) during ripening cause yield losses in rice (Oryza sativa L.), especially in high-sink-capacity varieties. We conducted a genetic analysis of traits related to such translocation by using recombinant inbred lines. Shoot weight (SW) of T65, a japonica parent, was retained from heading to late maturity, whereas that of DV85, an aus parent, was greater than that of T65 at 5 days after heading (DAH) and then decreased until 20 DAH. This difference was observed clearly under standard-fertilizer but not low-fertilizer conditions. Non-structural carbohydrate (NSC) contents in the parents showed a tendency similar to that for SW. QTL analysis revealed pleiotropic QTLs on chromosomes 5 and 10, probably by associations with heading date QTLs. A QTL associated with harvest index and NSC at 5 DAH was detected on chromosome 1. By considering the temporal changes of the traits, we found a QTL for decrease in SW on chromosome 11; the DV85 allele of this QTL facilitated assimilate translocation and suppressed biomass growth. A suggestive QTL for NSC decrease was located on chromosome 2. These QTLs could represent potential targets for controlling carbon assimilate translocation in breeding programs.

DOI： 10.1270/jsbbs.18203

Effect of GN1a and WFP Introgression on the Yield and Yield Components in Two Rice Varieties in Kenya

Menge Daniel Makori, Kikuta Mayumi, Samejima Hiroaki, Gichuhi Emily W, Kimani John M, Ashikari Motoyuki, Angeles-Shim Rosalyn, Sunohara Hidehiko, Jena Kshirod K, Yamauchi Akira, Doi Kazuyuki, Makihara Daigo

Abstracts of Meeting of the CSSJ 247 巻 ( 0 ) 頁： 110 2019年

Marker-assisted Introgression of the Quantitative Resistance Gene pi21 Confers Broad Spectrum Resistance of Rice to Blast 査読有り

Rosalyn B ANGELES-SHIM, Vincent P REYES, Marilyn M del VALLE, Ruby S LAPIS, Junghyun SHIM, Hidehiko SUNOHARA, Kshirod K JENA, Motoyuki ASHIKARI, Kazuyuki DOI

Rice Science 26 巻 2019年

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

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

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

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