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Wang L, Yang H, Wu M, Zhang J, Zhang H, Mao Z, Chen X. Integrative transcriptome and proteome revealed high-yielding mechanisms of epsilon-poly-L-lysine by Streptomyces albulus. Front Microbiol 2023; 14:1123050. [PMID: 37152744 PMCID: PMC10157215 DOI: 10.3389/fmicb.2023.1123050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction ε-poly-L-lysine (ε-PL) is a high value, widely used natural antimicrobial peptide additive for foods and cosmetic products that is mainly produced by Streptomyces albulus. In previous work, we developed the high-yield industrial strain S. albulus WG-608 through successive rounds of engineering. Methods Here, we use integrated physiological, transcriptomic, and proteomics association analysis to resolve the complex mechanisms underlying high ε-PL production by comparing WG-608 with the progenitor strain M-Z18. Results Our results show that key genes in the glycolysis, pentose phosphate pathway, glyoxylate pathway, oxidative phosphorylation, and L-lysine biosynthesis pathways are differentially upregulated in WG-608, while genes in the biosynthetic pathways for fatty acids, various branched amino acids, and secondary metabolite by-products are downregulated. This regulatory pattern results in the introduction of more carbon atoms into L-lysine biosynthesis and ε-PL production. In addition, significant changes in the regulation of DNA replication, transcription, and translation, two component systems, and quorum sensing may facilitate the adaptability to environmental pressure and the biosynthesis of ε-PL. Overexpression of ppk gene and addition of polyP6 further enhanced the ε-PL production. Discussion This study enables comprehensive understanding of the biosynthetic mechanisms of ε-PL in S. albulus WG-608, while providing some genetic modification and fermentation strategies to further improve the ε-PL production.
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Imaizumi T, Ebana K, Kawahara Y, Muto C, Kobayashi H, Koarai A, Olsen KM. Genomic divergence during feralization reveals both conserved and distinct mechanisms of parallel weediness evolution. Commun Biol 2021; 4:952. [PMID: 34376793 PMCID: PMC8355325 DOI: 10.1038/s42003-021-02484-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/23/2021] [Indexed: 12/28/2022] Open
Abstract
Agricultural weeds are the most important biotic constraints to global crop production, and chief among these is weedy rice. Despite increasing yield losses from weedy rice in recent years worldwide, the genetic basis of weediness evolution remains unclear. Using whole-genome sequence analyses, we examined the origins and adaptation of Japanese weedy rice. We find evidence for a weed origin from tropical japonica crop ancestry, which has not previously been documented in surveys of weedy rice worldwide. We further show that adaptation occurs largely through different genetic mechanisms between independently-evolved temperate japonica- and tropical japonica-derived strains; most genomic signatures of positive selection are unique within weed types. In addition, some weedy rice strains have evolved through hybridization between weedy and cultivated rice with adaptive introgression from the crop. Surprisingly, introgression from cultivated rice confers not only crop-like adaptive traits (such as shorter plant height, facilitating crop mimicry) but also weedy-like traits (such as seed dormancy). These findings reveal how hybridization with cultivated rice can promote persistence and proliferation of weedy rice.
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Affiliation(s)
- Toshiyuki Imaizumi
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan.
| | - Kaworu Ebana
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Yoshihiro Kawahara
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Chiaki Muto
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Hiroyuki Kobayashi
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Tsukuba, Japan
- Center for Weed and Wildlife Management, Utsunomiya University, Utsunomiya, Japan
| | - Akira Koarai
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, USA
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Hayashi S, Kuramata M, Abe T, Yamaguchi N, Takagi H, Tanikawa H, Iino M, Sugimoto K, Ishikawa S. Deficiency in alcohol dehydrogenase 2 reduces arsenic in rice grains by suppressing silicate transporters. PLANT PHYSIOLOGY 2021; 186:611-623. [PMID: 33620496 PMCID: PMC8154085 DOI: 10.1093/plphys/kiab086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/02/2021] [Indexed: 05/14/2023]
Abstract
Paddy fields are anaerobic and facilitate arsenite (As(III)) elution from the soil. Paddy-field rice accumulates arsenic (As) in its grains because silicate transporters actively assimilate As(III) during the reproductive stage. Reducing the As level in rice grains is an important challenge for agriculture. Using a forward genetic approach, we isolated a rice (Oryza sativa) mutant, low arsenic line 3 (las3), whose As levels were decreased in aerial tissues, including grains. The low-As phenotype was not observed in young plants before heading (emergence of the panicle). Genetic analyses revealed that a deficiency in alcohol dehydrogenase (ADH) 2 by mutation is responsible for the phenotype. Among the three rice ADH paralogues, ADH2 was the most efficiently produced in root tissue under anaerobic conditions. In wild-type (WT), silicon and As concentrations in aerial tissues increased with growth. However, the increase was suppressed in las3 during the reproductive stage. Accordingly, the gene expression of two silicate transporters, Lsi1 and Lsi2, was increased in WT around the time of heading, whereas the increase was suppressed in las3. These results indicate that the low-As phenotype in las3 is due to silicate transporter suppression. Measurement of intracellular pH by 31P-nuclear magnetic resonance revealed intracellular acidification of las3 roots under hypoxia, suggesting that silicate transporter suppression in las3 might arise from an intracellular pH decrease, which is known to be facilitated by a deficiency in ADH activity under anaerobic conditions. This study provides valuable insight into reducing As levels in rice grains.
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Affiliation(s)
- Shimpei Hayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Masato Kuramata
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Tadashi Abe
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Noriko Yamaguchi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Hiroki Takagi
- Ishikawa Prefectural University, Ishikawa 921-8836, Japan
| | - Hachidai Tanikawa
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Manaka Iino
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Kazuhiko Sugimoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8518, Japan
| | - Satoru Ishikawa
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
- Author for communication:
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Ogawa D, Sakamoto T, Tsunematsu H, Yamamoto T, Kanno N, Nonoue Y, Yonemaru JI. Surveillance of panicle positions by unmanned aerial vehicle to reveal morphological features of rice. PLoS One 2019; 14:e0224386. [PMID: 31671163 PMCID: PMC6822732 DOI: 10.1371/journal.pone.0224386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/13/2019] [Indexed: 02/06/2023] Open
Abstract
Rice plant architecture affects biomass and grain yield. Thus, it is important to select rice genotypes with ideal plant architecture. High-throughput phenotyping by use of an unmanned aerial vehicle (UAV) allows all lines in a field to be observed in less time than with traditional procedures. However, discrimination of plants in dense plantings is difficult, especially during the reproductive stage, because leaves and panicles overlap. Here, we developed an original method that relies on using UAV to identify panicle positions for dissecting plant architecture and to distinguish rice lines by detecting red flags attached to panicle bases. The plant architecture of recombinant inbred lines derived from Japanese cultivars ‘Hokuriku 193’ and ‘Mizuhochikara’, which differ in plant architecture, was assessed using a commercial camera-UAV system. Orthomosaics were made from UAV digital images. The center of plants was plotted on the image during the vegetative stage. The horizontal distance from the center to the red flag during the reproductive stage was used as the panicle position (PP). The red flags enabled us to recognize the positions of the panicles at a rate of 92%. The PP phenotype was related to but was not identical with the phenotypes of the panicle base angle, leaf sheath angle, and score of spreading habit. These results indicate that PP on orthomosaics could be used as an index of plant architecture under field conditions.
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Affiliation(s)
- Daisuke Ogawa
- Institute of Crop Science, National Agricultural and Food Research Organization, Tsukuba, Japan
- * E-mail: (DO); (TS)
| | - Toshihiro Sakamoto
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
- * E-mail: (DO); (TS)
| | - Hiroshi Tsunematsu
- Institute of Crop Science, National Agricultural and Food Research Organization, Tsukuba, Japan
| | - Toshio Yamamoto
- Institute of Crop Science, National Agricultural and Food Research Organization, Tsukuba, Japan
| | - Noriko Kanno
- Institute of Crop Science, National Agricultural and Food Research Organization, Tsukuba, Japan
| | - Yasunori Nonoue
- Institute of Crop Science, National Agricultural and Food Research Organization, Tsukuba, Japan
| | - Jun-ichi Yonemaru
- Institute of Crop Science, National Agricultural and Food Research Organization, Tsukuba, Japan
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Yang G, Chen S, Chen L, Sun K, Huang C, Zhou D, Huang Y, Wang J, Liu Y, Wang H, Chen Z, Guo T. Development of a core SNP arrays based on the KASP method for molecular breeding of rice. RICE (NEW YORK, N.Y.) 2019; 12:21. [PMID: 30963280 PMCID: PMC6453994 DOI: 10.1186/s12284-019-0272-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/20/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND The development and utilization of genetic markers play a pivotal role in marker-assisted breeding of rice cultivars during pyramiding of valuable genes. Among molecular markers, SNPs have become the most promising due to their wide distribution within genomes and suitability for high -throughput automated genotyping. Although metadata of SNPs have been identified via next generation sequencing in rice, a large gap between the development of SNP markers and the application in breeding still exists. To promote the application of SNP markers based on the KASP (Kompetitive Allele-Specific PCR) method in rice breeding, a set of core SNP arrays was built via the screening of SNP databases and literature resources based on the KASP method. RESULTS Five hundred and ninety six SNPs classified into eight subsets including quality control, indica-indica variation, highly polymorphic, functional genes, key genes targeting sites, gene cloned region, important trait associated and gap filling sites were chosen to design KASP primers and 565 out of them were successfully designed, and the assay design success rate was 94.8%. Finally, 467 out of the 565 successfully-designed SNPs can display diversity at the loci were used to develop a set of core SNP arrays. To evaluate the application value of the core SNP markers in rice breeding, 481 rice germplasms were genotyped with three functional KASP markers designed from the sequences of GBSSI, SSIIa, and Badh2 from the core SNP arrays for estimation of their grain quality performance. Eighteen rice lines, including Xiangwanxian 13, Basmati 370, Ruanhua A, and PR 33319-9-1-1-5-3-5-4-1, harbor all three favorable alleles. The core KASP arrays were also used for rice germplasm assessment, genetic diversity and population evaluation. Four hundred and eighty-one rice germplasms were divided into 3 groups: POP1, POP2 and POP3. POP1 and POP2 were indica rice subgroups consisting of 263 and 186 rice germplasms, respectively. POP3 was a japonica rice subgroup consisting of 32 rice germplasms. The average FST value for the three subgroups was 0.3501; the FST value of POP1 and POP3 was the largest (0.5482), while that of POP1 and POP2 was the smallest (0.0721). The results showed that the genetic distance between the japonica and indica rice subspecies was large, indicating that the core SNP markers were effective at discriminating the population structure of the germplasms. Finally, the core KASP arrays were used for association analysis with milled grain traits. A total of 31 KASP markers were significantly associated (P < 0.01) with ML and the LWR. Among the 31 markers, 13 were developed based on cloned genes or on identified loci related to yield traits. Notably, several KASP markers associated with grain quality were also found to be associated with brown planthopper resistance or green leafhopper resistance simultaneously. CONCLUSIONS The core KASP arrays developed in our study were efficient and versatile for rice germplasm assessment, genetic diversity and population evaluation and are valuable for promoting SNP molecular breeding in rice. Our study demonstrated that useful assays combined with molecular breeding can be exploited for important economic trait improvement in rice breeding.
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Affiliation(s)
- Guili Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Siping Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Likai Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Kai Sun
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Cuihong Huang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Danhua Zhou
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Yuting Huang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Jiafeng Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Yongzhu Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China.
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China.
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Kitazawa N, Shomura A, Mizubayashi T, Ando T, Nagata K, Hayashi N, Takahashi A, Yamanouchi U, Fukuoka S. Rapid DNA-genotyping system targeting ten loci for resistance to blast disease in rice. BREEDING SCIENCE 2019; 69:68-83. [PMID: 31086485 PMCID: PMC6507720 DOI: 10.1270/jsbbs.18143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/13/2018] [Indexed: 06/09/2023]
Abstract
The fungal pathogen Pyricularia oryzae causes blast, a severe disease of rice (Oryza sativa L.). Improving blast resistance is important in rice breeding programs. Inoculation tests have been used to select for resistance genotypes, with DNA marker-based selection becoming an efficient alternative. No comprehensive DNA marker system for race-specific resistance alleles in the Japanese rice breeding program has been developed because some loci contain multiple resistance alleles. Here, we used the Fluidigm SNP genotyping platform to determine a set of 96 single nucleotide polymorphism (SNP) markers for 10 loci with race-specific resistance. The markers were then used to evaluate the presence or absence of 24 resistance alleles in 369 cultivars; results were 93.5% consistent with reported inoculation test-based genotypes in japonica varieties. The evaluation system was successfully applied to high-yield varieties with indica genetic backgrounds. The system includes polymorphisms that distinguish the resistant alleles at the tightly linked Pita and Pita-2 loci, thereby confirming that all the tested cultivars with Pita-2 allele carry Pita allele. We also developed and validated insertion/deletion (InDel) markers for ten resistance loci. Combining SNP and InDel markers is an accurate and efficient strategy for selection for race-specific resistance to blast in breeding programs.
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Affiliation(s)
- Noriyuki Kitazawa
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Ayahiko Shomura
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Tatsumi Mizubayashi
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Tsuyu Ando
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Kazufumi Nagata
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Nagao Hayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Akira Takahashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Utako Yamanouchi
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Shuichi Fukuoka
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
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TA KN, KHONG NG, HA TL, NGUYEN DT, MAI DC, HOANG TG, PHUNG TPN, BOURRIE I, COURTOIS B, TRAN TTH, DINH BY, LA TN, DO NV, LEBRUN M, GANTET P, JOUANNIC S. A genome-wide association study using a Vietnamese landrace panel of rice (Oryza sativa) reveals new QTLs controlling panicle morphological traits. BMC PLANT BIOLOGY 2018; 18:282. [PMID: 30428844 PMCID: PMC6234598 DOI: 10.1186/s12870-018-1504-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/26/2018] [Indexed: 05/20/2023]
Abstract
CONTEXT Yield improvement is an important issue for rice breeding. Panicle architecture is one of the key components of rice yield and exhibits a large diversity. To identify the morphological and genetic determinants of panicle architecture, we performed a detailed phenotypic analysis and a genome-wide association study (GWAS) using an original panel of Vietnamese landraces. RESULTS Using a newly developed image analysis tool, morphological traits of the panicles were scored over two years: rachis length; primary, secondary and tertiary branch number; average length of primary and secondary branches; average length of internode on rachis and primary branch. We observed a high contribution of spikelet number and secondary branch number per panicle to the overall phenotypic diversity in the dataset. Twenty-nine stable QTLs associated with seven traits were detected through GWAS over the two years. Some of these QTLs were associated with genes already implicated in panicle development. Importantly, the present study revealed the existence of new QTLs associated with the spikelet number, secondary branch number and primary branch number traits. CONCLUSIONS Our phenotypic analysis of panicle architecture variation suggests that with the panel of samples used, morphological diversity depends largely on the balance between indeterminate vs. determinate axillary meristem fate on primary branches, supporting the notion of differences in axillary meristem fate between rachis and primary branches. Our genome-wide association study led to the identification of numerous genomic sites covering all the traits studied and will be of interest for breeding programs aimed at improving yield. The new QTLs detected in this study provide a basis for the identification of new genes controlling panicle development and yield in rice.
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Affiliation(s)
- Kim Nhung TA
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- Present address: Plant Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Ngan Giang KHONG
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- Present address: Department of Molecular Biology, Palacký University, Olomouc, Czech Republic
| | - Thi Loan HA
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Dieu Thu NGUYEN
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Duc Chung MAI
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Thi Giang HOANG
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Thi Phuong Nhung PHUNG
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | | | - Brigitte COURTOIS
- CIRAD, UMR AGAP, University of Montpellier, INRA, Montpellier, France
| | | | | | | | - Nang Vinh DO
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Michel LEBRUN
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- UMR LSTM, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Pascal GANTET
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
| | - Stefan JOUANNIC
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
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Discovery of QTL Alleles for Grain Shape in the Japan-MAGIC Rice Population Using Haplotype Information. G3-GENES GENOMES GENETICS 2018; 8:3559-3565. [PMID: 30194091 PMCID: PMC6222584 DOI: 10.1534/g3.118.200558] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A majority of traits are determined by multiple quantitative trait loci (QTL) that can have pleiotropic effects. A multi-parent advanced generation inter-cross (MAGIC) population is well suited for genetically analyzing the effects of multiple QTL on traits of interest because it contains a higher number of QTL alleles than a biparental population. We previously produced the JAPAN-MAGIC (JAM) population, derived from eight rice (Oryza sativa L.) cultivars with high yield and biomass in Japan, and developed the method of genome-wide association study (GWAS) using haplotype information on the JAM lines. This method was effective for identifying major genes such as Waxy for eating quality and Sd1 for culm length. Here, we show that haplotype-based GWAS is also effective for the evaluation of multiple QTL with small effects on rice grain shape in the JAM lines. Although both the haplotype- and SNP-based GWAS identified multiple QTL for grain length and width, the sum of the estimated trait values of each allele for the QTL detected by haplotype-based GWAS had higher correlation with observed values than those detected by SNP-based GWAS, indicating high-accuracy QTL detection in the haplotype-based GWAS. Furthermore, the study revealed pleiotropic effects of some QTL regions in regulation of grain shape, suggesting that the haplotype-based GWAS using the JAM lines is an effective means to evaluate the main and side effects of haplotypes at each QTL. Information on the pleiotropic effects of haplotypes on various traits will be useful for designing ideal lines in a breeding program.
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Matsubara K, Yonemaru JI, Kobayashi N, Ishii T, Yamamoto E, Mizobuchi R, Tsunematsu H, Yamamoto T, Kato H, Yano M. A follow-up study for biomass yield QTLs in rice. PLoS One 2018; 13:e0206054. [PMID: 30352074 PMCID: PMC6198978 DOI: 10.1371/journal.pone.0206054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 10/07/2018] [Indexed: 12/22/2022] Open
Abstract
The biomass yield (plant weight) of rice fluctuates from year to year. In a previous study, we demonstrated that six quantitative trait loci (QTLs) contribute to the variation in the plant weight of recombinant inbred lines (RILs) of high-yielding Japanese rice cultivars. However, it remains unclear whether the effects of those QTLs are stable over multiple years. Therefore, we evaluated the effect of the alleles on the plant weight of RILs over multiple years, including a change of fertilization level (i.e., in different environments). Even though the biomass yields of all RILs fluctuated among environments, RILs that were selected on the basis of the genotypes of the detected QTLs had a stable rank order of plant weight that corresponded to their genotypes. This multiple-environment experiment reveals the highly significant contribution of both genotypic and environmental variances to the observed variance in plant weight. A marginally significant QTL–environment interaction was detected at only one of the six QTLs, with a subtle contribution. These results support the idea that the biomass yield of rice can be improved through QTL-based allele selection.
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Affiliation(s)
- Kazuki Matsubara
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Jun-ichi Yonemaru
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
| | - Nobuya Kobayashi
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
| | - Takuro Ishii
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
| | - Eiji Yamamoto
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Ritsuko Mizobuchi
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
| | - Hiroshi Tsunematsu
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
| | - Toshio Yamamoto
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
| | - Hiroshi Kato
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
| | - Masahiro Yano
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
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10
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Reig-Valiente JL, Marqués L, Talón M, Domingo C. Genome-wide association study of agronomic traits in rice cultivated in temperate regions. BMC Genomics 2018; 19:706. [PMID: 30253735 PMCID: PMC6156875 DOI: 10.1186/s12864-018-5086-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/17/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Rice plants are sensitive to the agro-climate conditions, being photoperiod one of main factor contributing to their adaptation to the region where they are grown. Dissecting the genetic bases underlying diversity in rice populations adapted to specific environmental conditions is a fundamental resource for breeding. In this study we have analysed a collection of japonica varieties adapted to temperate regions to perform association studies with traits of high agronomical interest such as heading date, plant height, number of panicles, panicle length and number of grains per panicle. RESULTS We have performed a genome wide association study using a panel of 1713 SNPs that, based on previous linkage disequilibrium estimations, provides a full coverage of the whole genome. We have found a total of 43 SNPs associated with variations in the different traits. The identified SNPs were distributed across the genome except in chromosome 12, where no associated SNPs were found. The inspection of the vicinity of these markers also revealed a set of genes associated with physiological functions strongly linked to agronomic traits. Of special relevance are two genes involved in gibberellin homeostasis that are associated with plant height and panicle length. We also detected novel associated sites with heading date, panicle length and number of grain per panicle. CONCLUSION We have identified loci associated with important agronomic traits among cultivars adapted to temperate conditions. Some of these markers co-localized with already known genes or QTLs, but the association also provided novel molecular markers that can be of help to elucidate the complicated genetic mechanism controlling important agronomic traits, as flowering regulation in the non-dependent photoperiod pathway. The detected associated markers may provide important tools for the genetic improvement of rice cultivars in temperate regions.
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Affiliation(s)
- Juan L Reig-Valiente
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7, 46113, Moncada, Spain
| | - Luis Marqués
- Cooperativa de Productores de Semillas de Arroz, Sueca, Spain
| | - Manuel Talón
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7, 46113, Moncada, Spain
| | - Concha Domingo
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7, 46113, Moncada, Spain.
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Ogawa D, Yamamoto E, Ohtani T, Kanno N, Tsunematsu H, Nonoue Y, Yano M, Yamamoto T, Yonemaru JI. Haplotype-based allele mining in the Japan-MAGIC rice population. Sci Rep 2018. [PMID: 29531264 PMCID: PMC5847589 DOI: 10.1038/s41598-018-22657-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Multi-parent advanced generation inter-cross (MAGIC) lines have broader genetic variation than bi-parental recombinant inbred lines. Genome-wide association study (GWAS) using high number of DNA polymorphisms such as single-nucleotide polymorphisms (SNPs) is a popular tool for allele mining in MAGIC populations, in which the associations of phenotypes with SNPs are investigated; however, the effects of haplotypes from multiple founders on phenotypes are not considered. Here, we describe an improved method of allele mining using the newly developed Japan-MAGIC (JAM) population, which is derived from eight high-yielding rice cultivars in Japan. To obtain information on the haplotypes in the JAM lines, we predicted the haplotype blocks in the whole chromosomes using 16,345 SNPs identified via genotyping-by-sequencing analysis. Using haplotype-based GWAS, we clearly detected the loci controlling the glutinous endosperm and culm length traits. Information on the alleles of the eight founders, which was based on the effects of mutations revealed by the analysis of next-generation sequencing data, was used to narrow down the candidate genes and reveal the associations between alleles and phenotypes. The haplotype-based allele mining (HAM) proposed in this study is a promising approach to the detection of allelic variation in genes controlling agronomic traits in MAGIC populations.
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Affiliation(s)
- Daisuke Ogawa
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan.,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Eiji Yamamoto
- Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Toshikazu Ohtani
- Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Noriko Kanno
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan.,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Hiroshi Tsunematsu
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Yasunori Nonoue
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Masahiro Yano
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan.,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Toshio Yamamoto
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan. .,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan.
| | - Jun-Ichi Yonemaru
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan. .,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan.
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12
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Hayashi S, Kuramata M, Abe T, Takagi H, Ozawa K, Ishikawa S. Phytochelatin synthase OsPCS1 plays a crucial role in reducing arsenic levels in rice grains. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:840-848. [PMID: 28621830 DOI: 10.1111/tpj.13612] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/16/2017] [Accepted: 05/22/2017] [Indexed: 05/18/2023]
Abstract
Reduction of the level of arsenic (As) in rice grains is an important challenge for agriculture. A recent study reported that the OsABCC1 transporter prevents the accumulation of As in grains by sequestering As-phytochelatin complexes into vacuoles in the upper nodes. However, how phytochelatins are provided in response to As remains unclear. Here, we show that the phytochelatin synthase OsPCS1 plays a crucial role in reducing As levels in rice grains. Using a forward genetic approach, we isolated two rice mutants (has1 and has2) in which As levels were much higher in grains but significantly lower in node I compared with the wild type. Map-based cloning identified the genes responsible as OsABCC1 in has1 and OsPCS1 in has2. The levels of As in grains and node I were similar between the two mutants, suggesting that OsABCC1 preferentially cooperates with OsPCS1 to sequester As, although rice has another phytochelatin synthase, OsPCS2. An in vitro phytochelatin synthesis assay indicated that OsPCS1 was more sensitive to activation by As than by cadmium, whereas OsPCS2 was more weakly activated by As than by cadmium. Transgenic plants highly expressing OsPCS1 showed significantly lower As levels in grains than did wild-type plants. Our results provide new knowledge of the relative contribution of rice PCS paralogs to As sequestration and suggest a good candidate tool to reduce As levels in rice grains.
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Affiliation(s)
- Shimpei Hayashi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8604, Japan
- Institute of Agrobiological Sciences, NARO, Tsukuba, 305-8604, Japan
| | - Masato Kuramata
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8604, Japan
| | - Tadashi Abe
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8604, Japan
| | - Hiroki Takagi
- Iwate Biotechnology Research Center, Kitakami, 024-0003, Japan
- Ishikawa Prefectural University, Ishikawa, 921-8836, Japan
| | - Kenjirou Ozawa
- Institute of Agrobiological Sciences, NARO, Tsukuba, 305-8604, Japan
| | - Satoru Ishikawa
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8604, Japan
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13
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Alternative functions of Hd1 in repressing or promoting heading are determined by Ghd7 status under long-day conditions. Sci Rep 2017; 7:5388. [PMID: 28710485 PMCID: PMC5511259 DOI: 10.1038/s41598-017-05873-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/05/2017] [Indexed: 11/12/2022] Open
Abstract
Previous studies suggested that Hd1 promoted heading under short-day conditions (SD) and delayed heading under long-day conditions (LD). However in this study, Hd1 was demonstrated to consistently promote heading date in Zhenshan 97 (ZS97) background by upregulating Ehd1, Hd3a and RFT1 expression under both SD and LD. While the high photoperiod sensitivity of Hd1 was observed in Minghui 63 (MH63) background, with heading being suppressed in LD but promoted in SD. Comparative analysis of two sets of near isogenic lines of Hd1 in MH63 and ZS97 backgrounds indicated that the alternative functions of Hd1 in promoting or suppressing heading under LD are dependent on the previously cloned flowering repressor gene Ghd7. The interaction between proteins Ghd7 and Hd1 occurred through binding of the CCT domain of Ghd7 to the transcription-activating domain of Hd1, resulting in suppression of Ehd1 and florigen gene expression. The involvement of the transcription-activating domain of Hd1 in this protein-protein interaction probably blocked or weakened its transcriptional activity. These findings suggest that Hd1 alone essentially acts as a promoter of heading date, and the protein interaction between Ghd7 and Hd1 determines photoperiod sensitivity and integrated Hd1-mediated and Ehd1-mediated flowering pathways in rice.
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14
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Genome-wide association study of outcrossing in cytoplasmic male sterile lines of rice. Sci Rep 2017; 7:3223. [PMID: 28607357 PMCID: PMC5468336 DOI: 10.1038/s41598-017-03358-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/26/2017] [Indexed: 11/23/2022] Open
Abstract
Stigma exsertion and panicle enclosure of male sterile lines are two key determinants of outcrossing in hybrid rice seed production. Based on 43,394 single nucleotide polymorphism markers, 217 cytoplasmic male sterile lines were assigned into two subpopulations and a mixed-group where the linkage disequilibrium decay distances varied from 975 to 2,690 kb. Genome-wide association studies (GWAS) were performed for stigma exsertion rate (SE), panicle enclosure rate (PE) and seed-setting rate (SSR). A total of 154 significant association signals (P < 0.001) were identified. They were situated in 27 quantitative trait loci (QTLs), including 11 for SE, 6 for PE, and 10 for SSR. It was shown that six of the ten QTLs for SSR were tightly linked to QTLs for SE or/and PE with the expected allelic direction. These QTL clusters could be targeted to improve the outcrossing of female parents in hybrid rice breeding. Our study also indicates that GWAS-base QTL mapping can complement and enhance previous QTL information for understanding the genetic relationship between outcrossing and its related traits.
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15
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Kinoshita N, Takano S, Shimoda N, Takamure I, Sato T, Kato K. Development of genome-wide PCR-based markers from insertion, deletion and single nucleotide polymorphisms for closely related Japanese rice cultivars and identification of QTLs for the appearance of cooked rice and polished rice. BREEDING SCIENCE 2016; 66:742-751. [PMID: 28163590 PMCID: PMC5282762 DOI: 10.1270/jsbbs.16108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/08/2016] [Indexed: 05/17/2023]
Abstract
Appearance of rice grain is an important property, affecting its acceptance by consumers. Moreover, appearance is a complex characteristic involving many components, including glossiness and whiteness. The genetic bases for the glossiness of cooked rice and the whiteness of polished rice (WPR) were determined using 133 recombinant inbred lines (RILs) derived from a cross between two closely related cultivars from Hokkaido, Joiku462, with high glossiness and whiteness, and Yukihikari, an ancestor of Joiku462 with low glossiness and whiteness. Analyses identified 167 genome-wide InDel markers, five cleaved amplified polymorphic sequences (CAPS) and eight derived CAPS markers differentiating the parental lines. The glossiness area (GLA) and glossiness strength (GLS) of cooked rice and WPR were determined for RILs in two locations, Pippu and Sapporo, Hokkaido. Four QTLs were detected. qGLA10 and qGLS9 were detected on chromosomes 10 and 9, respectively, with both being significant at both geographic locations. qWPR1 on chromosome 1 was significant at Pippu, and qWPR4 on chromosome 4 was significant at Sapporo. The Joiku462 alleles at all QTLs increased each trait. The PCR-based markers flanking these four QTLs may be useful for improvement of GLA, GLS and WPR.
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Affiliation(s)
- Noriko Kinoshita
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine,
Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555,
Japan
| | - Sho Takano
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine,
Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555,
Japan
| | - Naomi Shimoda
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine,
Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555,
Japan
| | - Itsuro Takamure
- Graduate School of Agriculture, Hokkaido University,
Kita 9 Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
| | - Takashi Sato
- Rice Breeding Group, Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization,
Minami 1-5, Pippu, Hokkaido 078-0397,
Japan
| | - Kiyoaki Kato
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine,
Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555,
Japan
- Corresponding author (e-mail: )
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16
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Matsubara K, Yamamoto E, Kobayashi N, Ishii T, Tanaka J, Tsunematsu H, Yoshinaga S, Matsumura O, Yonemaru JI, Mizobuchi R, Yamamoto T, Kato H, Yano M. Improvement of Rice Biomass Yield through QTL-Based Selection. PLoS One 2016; 11:e0151830. [PMID: 26986071 PMCID: PMC4795639 DOI: 10.1371/journal.pone.0151830] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 03/06/2016] [Indexed: 12/31/2022] Open
Abstract
Biomass yield of rice (Oryza sativa L.) is an important breeding target, yet it is not easy to improve because the trait is complex and phenotyping is laborious. Using progeny derived from a cross between two high-yielding Japanese cultivars, we evaluated whether quantitative trait locus (QTL)-based selection can improve biomass yield. As a measure of biomass yield, we used plant weight (aboveground parts only), which included grain weight and stem and leaf weight. We measured these and related traits in recombinant inbred lines. Phenotypic values for these traits showed a continuous distribution with transgressive segregation, suggesting that selection can affect plant weight in the progeny. Four significant QTLs were mapped for plant weight, three for grain weight, and five for stem and leaf weight (at α = 0.05); some of them overlapped. Multiple regression analysis showed that about 43% of the phenotypic variance of plant weight was significantly explained (P < 0.0001) by six of the QTLs. From F2 plants derived from the same parental cross as the recombinant inbred lines, we divergently selected lines that carried alleles with positive or negative additive effects at these QTLs, and performed successive selfing. In the resulting F6 lines and parents, plant weight significantly differed among the genotypes (at α = 0.05). These results demonstrate that QTL-based selection is effective in improving rice biomass yield.
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Affiliation(s)
- Kazuki Matsubara
- NARO Institute of Crop Science, Tsukuba, Ibaraki 305–8518, Japan
- * E-mail:
| | - Eiji Yamamoto
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305–8602, Japan
| | - Nobuya Kobayashi
- NARO Institute of Crop Science, Tsukuba, Ibaraki 305–8518, Japan
| | - Takuro Ishii
- NARO Institute of Crop Science, Tsukuba, Ibaraki 305–8518, Japan
| | - Junichi Tanaka
- NARO Institute of Crop Science, Tsukuba, Ibaraki 305–8518, Japan
| | | | | | | | - Jun-ichi Yonemaru
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305–8602, Japan
| | - Ritsuko Mizobuchi
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305–8602, Japan
| | - Toshio Yamamoto
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305–8602, Japan
| | - Hiroshi Kato
- NARO Institute of Crop Science, Tsukuba, Ibaraki 305–8518, Japan
| | - Masahiro Yano
- NARO Institute of Crop Science, Tsukuba, Ibaraki 305–8518, Japan
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17
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Hori K, Suzuki K, Iijima K, Ebana K. Variation in cooking and eating quality traits in Japanese rice germplasm accessions. BREEDING SCIENCE 2016; 66:309-18. [PMID: 27162502 PMCID: PMC4785008 DOI: 10.1270/jsbbs.66.309] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/01/2015] [Indexed: 05/19/2023]
Abstract
The eating quality of cooked rice is important and determines its market price and consumer acceptance. To comprehensively describe the variation of eating quality in 183 rice germplasm accessions, we evaluated 33 eating-quality traits including amylose and protein contents, pasting properties of rice flour, and texture of cooked rice grains. All eating-quality traits varied widely in the germplasm accessions. Principal-components analysis (PCA) revealed that allelic differences in the Wx gene explained the largest proportion of phenotypic variation of the eating-quality traits. In 146 accessions of non-glutinous temperate japonica rice, PCA revealed that protein content and surface texture of the cooked rice grains significantly explained phenotypic variations of the eating-quality traits. An allelic difference based on simple sequence repeats, which was located near a quantitative trait locus (QTL) on the short arm of chromosome 3, was associated with differences in the eating quality of non-glutinous temperate japonica rice. These results suggest that eating quality is controlled by genetic factors, including the Wx gene and the QTL on chromosome 3, in Japanese rice accessions. These genetic factors have been consciously selected for eating quality during rice breeding programs in Japan.
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Affiliation(s)
- Kiyosumi Hori
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
- Corresponding author (e-mail: )
| | - Keitaro Suzuki
- NARO Institute of Crop Science,
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Ken Iijima
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Kaworu Ebana
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
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18
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Zhang P, Zhong K, Shahid MQ, Tong H. Association Analysis in Rice: From Application to Utilization. FRONTIERS IN PLANT SCIENCE 2016; 7:1202. [PMID: 27582745 PMCID: PMC4987372 DOI: 10.3389/fpls.2016.01202] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/28/2016] [Indexed: 05/03/2023]
Abstract
Association analysis based on linkage disequilibrium (LD) is an efficient way to dissect complex traits and to identify gene functions in rice. Although association analysis is an effective way to construct fine maps for quantitative traits, there are a few issues which need to be addressed. In this review, we will first summarize type, structure, and LD level of populations used for association analysis of rice, and then discuss the genotyping methods and statistical approaches used for association analysis in rice. Moreover, we will review current shortcomings and benefits of association analysis as well as specific types of future research to overcome these shortcomings. Furthermore, we will analyze the reasons for the underutilization of the results within association analysis in rice breeding.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
- *Correspondence: Peng Zhang
| | - Kaizhen Zhong
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural UniversityGuangzhou, China
| | - Hanhua Tong
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
- Hanhua Tong
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Shinada H, Yamamoto T, Sato H, Yamamoto E, Hori K, Yonemaru J, Sato T, Fujino K. Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping. BREEDING SCIENCE 2015; 65:388-95. [PMID: 26719741 PMCID: PMC4671699 DOI: 10.1270/jsbbs.65.388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/26/2015] [Indexed: 05/20/2023]
Abstract
Plant breeding programs aim to develop cultivars with high adaptability to the specific conditions in a local region. As a result, unique genes and gene combinations have been accumulated in local elite breeding populations during the long history of plant breeding. Genetic analyses on such genes and combinations may be useful for developing new cultivars with more-desirable agronomic traits. Here, we attempted to detect quantitative trait loci (QTL) for rice blast resistance (BR) using a local breeding rice population from Hokkaido, Japan. Using genotyping data on single nucleotide polymorphisms and simple sequence repeat markers distributed throughout the whole genomic region, we detected genetic regions associated with phenotypic variation in BR by a genome-wide association mapping study (GWAS). An additional association analysis using other breeding cultivars verified the effect and inheritance of the associated region. Furthermore, the existence of a gene for BR in the associated region was confirmed by QTL mapping. The results from these studies enabled us to estimate potential of the Hokkaido rice population as a gene pool for improving BR. The results of this study could be useful for developing novel cultivars with vigorous BR in rice breeding programs.
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Affiliation(s)
- Hiroshi Shinada
- Rice Breeding Group, Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization,
Minami 1-5, Pippu, Hokkaido 078-0397,
Japan
- Corresponding author (e-mail: )
| | - Toshio Yamamoto
- Rice Applied Genomics Research Unit, National Institute of Agrobiological Sciences,
Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Hirokazu Sato
- Rice Breeding Group, Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization,
Minami 1-5, Pippu, Hokkaido 078-0397,
Japan
| | - Eiji Yamamoto
- Rice Applied Genomics Research Unit, National Institute of Agrobiological Sciences,
Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Kiyosumi Hori
- Rice Applied Genomics Research Unit, National Institute of Agrobiological Sciences,
Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Junichi Yonemaru
- Rice Applied Genomics Research Unit, National Institute of Agrobiological Sciences,
Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Takashi Sato
- Rice Breeding Group, Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization,
Minami 1-5, Pippu, Hokkaido 078-0397,
Japan
| | - Kenji Fujino
- NARO Hokkaido Agricultural Research Center, National Agricultural Research Organization,
Sapporo, Hokkaido 062-8555,
Japan
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20
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Yonemaru JI, Choi SH, Sakai H, Ando T, Shomura A, Yano M, Wu J, Fukuoka S. Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar 'Koshihikari'. BREEDING SCIENCE 2015; 65:249-56. [PMID: 26175622 PMCID: PMC4482175 DOI: 10.1270/jsbbs.65.249] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/24/2015] [Indexed: 05/06/2023]
Abstract
Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used as DNA markers to identify QTLs and genes and to facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. Here, re-sequencing of 5 indica, 2 aus, and 3 tropical japonica cultivars and Japanese elite cultivar 'Koshihikari' was performed to extract regions containing large indels (10-51 bp) shared by diverse cultivars. To design indel markers for the discrimination of genomic regions between 'Koshihikari' and other diverse cultivars, we subtracted the indel regions detected in 'Koshihikari' from those shared in other cultivars. Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including 'Khao Nam Jen' as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively. Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers. The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.
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Affiliation(s)
- Jun-ichi Yonemaru
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
- Corresponding author (e-mail: )
| | - Sun Hee Choi
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Hiroaki Sakai
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Tsuyu Ando
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Ayahiko Shomura
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Masahiro Yano
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
- NARO Institute of Crop Science,
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Jianzhong Wu
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Shuichi Fukuoka
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
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Kitomi Y, Kanno N, Kawai S, Mizubayashi T, Fukuoka S, Uga Y. QTLs underlying natural variation of root growth angle among rice cultivars with the same functional allele of DEEPER ROOTING 1. RICE (NEW YORK, N.Y.) 2015; 8:16. [PMID: 25844121 PMCID: PMC4385264 DOI: 10.1186/s12284-015-0049-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 02/27/2015] [Indexed: 05/17/2023]
Abstract
BACKGROUND The functional allele of the rice gene DEEPER ROOTING 1 (DRO1) increases the root growth angle (RGA). However, wide natural variation in RGA is observed among rice cultivars with the functional DRO1 allele. To elucidate genetic factors related to such variation, we quantitatively measured RGA using the basket method and analyzed quantitative trait loci (QTLs) for RGA in three F2 mapping populations derived from crosses between the large RGA-type cultivar Kinandang Patong and each of three accessions with varying RGA: Momiroman has small RGA and was used to produce the MoK-F2 population; Yumeaoba has intermediate RGA (YuK-F2 population); Tachisugata has large RGA (TaK-F2 population). All four accessions belong to the same haplotype group of functional DRO1 allele. RESULTS We detected the following statistically significant QTLs: one QTL on chromosome 4 in MoK-F2, three QTLs on chromosomes 2, 4, and 6 in YuK-F2, and one QTL on chromosome 2 in TaK-F2. Among them, the two QTLs on chromosome 4 were located near DRO2, which has been previously reported as a major QTL for RGA, whereas the two major QTLs for RGA on chromosomes 2 (DRO4) and 6 (DRO5) were novel. With the LOD threshold reduced to 3.0, several minor QTLs for RGA were also detected in each population. CONCLUSION Natural variation in RGA in rice cultivars carrying functional DRO1 alleles may be controlled by a few major QTLs and by several additional minor QTLs.
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Affiliation(s)
- Yuka Kitomi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Noriko Kanno
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Sawako Kawai
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Tatsumi Mizubayashi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Shuichi Fukuoka
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Yusaku Uga
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
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Begum H, Spindel JE, Lalusin A, Borromeo T, Gregorio G, Hernandez J, Virk P, Collard B, McCouch SR. Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa). PLoS One 2015; 10:e0119873. [PMID: 25785447 PMCID: PMC4364887 DOI: 10.1371/journal.pone.0119873] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 02/02/2015] [Indexed: 11/18/2022] Open
Abstract
Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.
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Affiliation(s)
- Hasina Begum
- International Rice Research Institute, Los Baños, Philippines
| | - Jennifer E. Spindel
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Antonio Lalusin
- Crop Science Cluster, University of the Philippines Los Baños, Los Baños, Philippines
| | - Teresita Borromeo
- Crop Science Cluster, University of the Philippines Los Baños, Los Baños, Philippines
| | - Glenn Gregorio
- International Rice Research Institute, Los Baños, Philippines
| | - Jose Hernandez
- Crop Science Cluster, University of the Philippines Los Baños, Los Baños, Philippines
| | - Parminder Virk
- International Center for Tropical Agriculture, Cali, Colombia
| | | | - Susan R. McCouch
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States of America
- * E-mail:
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Salvi S, Tuberosa R. The crop QTLome comes of age. Curr Opin Biotechnol 2015; 32:179-185. [PMID: 25614069 DOI: 10.1016/j.copbio.2015.01.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 12/31/2014] [Accepted: 01/02/2015] [Indexed: 12/15/2022]
Abstract
Recent progress in genomics and phenomics allows for a more accurate and comprehensive characterization of the Quantitative Trait Loci (QTLs)—hereafter defined 'QTLome' as a whole—that govern the variation targeted in breeding programs. High-density genotyping now provides unambiguous identification of QTL alleles, and for several traits beneficial alleles at major QTLs have already been deployed in marker-assisted breeding. However, the amount of QTLome information is enormous and approaches to distill and translate this information to breeders remain to be refined. Improved QTL meta-analyses, better estimation of QTL effects, improved crop modelling and full sharing of raw QTL data will enable a more effective exploitation of the QTLome.
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Affiliation(s)
- Silvio Salvi
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
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Matsubara K, Yamamoto E, Mizobuchi R, Yonemaru JI, Yamamoto T, Kato H, Yano M. Hybrid breakdown caused by epistasis-based recessive incompatibility in a cross of rice (Oryza sativa L.). J Hered 2014; 106:113-22. [PMID: 25429024 DOI: 10.1093/jhered/esu065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Viability and fertility in organisms depend on epistatic interactions between loci maintained in lineages. Here, we describe reduced fitness of segregants (hybrid breakdown, HB) that emerged in an F2 population derived from a cross between 2 rice (Oryza sativa L.) cultivars, "Tachisugata" (TS) and "Hokuriku 193" (H193), despite both parents and F1s showing normal fitness. Quantitative trait locus (QTL) analyses detected 13 QTLs for 4 morphological traits associated with the HB and 6 associated with principal component scores calculated from values of the morphological traits in the F2 population. Two-way analysis of variance of the putative QTLs identified 4 QTL pairs showing significant epistasis; among them, a pair on chromosomes 1 and 12 made the greatest contribution to HB. The finding was supported by genetic experiments using F3 progeny. HB emerged only when a plant was homozygous for the TS allele at the QTL on chromosome 1 and homozygous for the H193 allele at the QTL on chromosome 12, indicating that each allele behaves as recessive to the other. Our results support the idea that epistasis is an essential part of hybrid fitness.
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Affiliation(s)
- Kazuki Matsubara
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan.
| | - Eiji Yamamoto
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
| | - Ritsuko Mizobuchi
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
| | - Jun-ichi Yonemaru
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
| | - Toshio Yamamoto
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
| | - Hiroshi Kato
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan.
| | - Masahiro Yano
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
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