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

Web of Science