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Xu Y, Chen S, Xue M, Chen X, Liu Z, Wei X, Gao JP, Chen C. Mapping and validation of quantitative trait loci associated with dorsal aleurone thickness in rice (Oryza sativa). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:117. [PMID: 37093272 DOI: 10.1007/s00122-023-04368-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Mapping of QTLs for dorsal aleurone thickness (DAT) was performed using chromosome segment substitution lines in rice. Three QTLs, qDAT3.1, qDAT3.2, and qDAT7.1, were detected in multiple environments. As a specified endosperm cell type, the aleurone has an abundance of various nutrients. Increasing the number of aleurone layers is a practicable way of developing highly nutritious cereals. Identifying genes that can increase aleurone thickness is useful for the breeding of aleurone traits to improve the nutritional and health values of rice. Here, we found that iodine staining could efficiently distinguish the aleurone layers, which revealed great variation of the aleurone thickness in rice, especially at the dorsal side of the seed. Therefore, we used a population of chromosome segmental substitution lines (CSSLs) derived from Koshihikari and Nona Bokra for quantitative trait locus (QTL) analysis of the dorsal aleurone thickness (DAT). Three QTLs, qDAT3.1, qDAT3.2, and qDAT7.1, were detected in multiple seasons. Among these, qDAT3.2 colocalizes with Hd6 and Hd16, two QTLs previously identified to regulate the heading date of Koshihikari, explaining the negative correlation between the DAT and days to heading (DTH) in rice. We also provide evidence that early-heading ensures the filling of rice seed under a relatively high temperature to promote aleurone thickening. qDAT7.1, the most stable QTL expressed in different environments, functions independently from heading date. Although Nona Bokra has a lower DAT, its qDAT7.1 allele significantly increased DAT in rice, which was further validated using two near-isogenic lines (NILs). These findings pave the way for further gene cloning of aleurone-related QTLs and may aid the development of highly nutritious rice.
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Affiliation(s)
- Yiwen Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Siming Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Mingming Xue
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Xingyu Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Zhibo Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Xuefeng Wei
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Ji-Ping Gao
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, China.
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China.
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, China.
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China.
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Xu Z, Li M, Du Y, Li X, Wang R, Chen Z, Tang S, Liu Q, Zhang H. Characterization of qPL5: a novel quantitative trait locus (QTL) that controls panicle length in rice ( Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:70. [PMID: 37313475 PMCID: PMC10248689 DOI: 10.1007/s11032-022-01339-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/20/2022] [Indexed: 06/15/2023]
Abstract
Panicle length (PL) is an important trait that determines panicle architecture and strongly affects grain yield and quality in rice. However, this trait has not been well characterized genetically, and its contribution to yield improvement is not well understood. Characterization of novel genes related to PL is of great significance for breeding high-yielding rice varieties. In our previous research, we identified qPL5, a quantitative trait locus for PL. In this study, we aimed to determine the exact position of qPL5 in the rice genome and identify the candidate gene. Through substitution mapping, we mapped qPL5 to a region of 21.86 kb flanked by the molecular marker loci STS5-99 and STS5-106 in which two candidate genes were predicted. By sequence analysis and relative expression analysis, LOC-Os05g41230, which putatively encodes a BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 precursor, was considered to be the most likely candidate gene for qPL5. In addition, we successfully developed a pair of near-isogenic lines (NILs) for qPL5 in different genetic backgrounds to evaluate the genetic effects of qPL5. Agronomic trait analysis of the NILs indicated that qPL5 positively contributes to plant height, grain number per panicle, panicle length, grain yield per plant, and flag leaf length, but it had no influence on heading date and grain-size-related traits. Therefore, qPL5 and the markers tightly linked to it should be available for molecular breeding of high-yielding varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01339-z.
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Affiliation(s)
- Zuopeng Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
| | - Meng Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Yuanyue Du
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Xixu Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Ruixuan Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Zhiai Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Shuzhu Tang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
| | - Honggen Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
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Genome wide screening and comparative genome analysis for Meta-QTLs, ortho-MQTLs and candidate genes controlling yield and yield-related traits in rice. BMC Genomics 2020; 21:294. [PMID: 32272882 PMCID: PMC7146888 DOI: 10.1186/s12864-020-6702-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/25/2020] [Indexed: 11/29/2022] Open
Abstract
Background Improving yield and yield-related traits is the crucial goal in breeding programmes of cereals. Meta-QTL (MQTL) analysis discovers the most stable QTLs regardless of populations genetic background and field trial conditions and effectively narrows down the confidence interval (CI) for identification of candidate genes (CG) and markers development. Results A comprehensive MQTL analysis was implemented on 1052 QTLs reported for yield (YLD), grain weight (GW), heading date (HD), plant height (PH) and tiller number (TN) in 122 rice populations evaluated under normal condition from 1996 to 2019. Consequently, these QTLs were confined into 114 MQTLs and the average CI was reduced up to 3.5 folds in compare to the mean CI of the original QTLs with an average of 4.85 cM CI in the resulted MQTLs. Among them, 27 MQTLs with at least five initial QTLs from independent studies were considered as the most stable QTLs over different field trials and genetic backgrounds. Furthermore, several known and novel CGs were detected in the high confident MQTLs intervals. The genomic distribution of MQTLs indicated the highest density at subtelomeric chromosomal regions. Using the advantage of synteny and comparative genomics analysis, 11 and 15 ortho-MQTLs were identified at co-linear regions between rice with barley and maize, respectively. In addition, comparing resulted MQTLs with GWAS studies led to identification of eighteen common significant chromosomal regions controlling the evaluated traits. Conclusion This comprehensive analysis defines a genome wide landscape on the most stable loci associated with reliable genetic markers and CGs for yield and yield-related traits in rice. Our findings showed that some of these information are transferable to other cereals that lead to improvement of their breeding programs.
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Nemoto Y, Hori K, Izawa T. Fine-tuning of the setting of critical day length by two casein kinases in rice photoperiodic flowering. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:553-565. [PMID: 29237079 PMCID: PMC5853454 DOI: 10.1093/jxb/erx412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/03/2017] [Indexed: 05/03/2023]
Abstract
Many short-day plants have a critical day length that fixes the schedule for flowering time, limiting the range of natural growth habitats (or growth and cultivation areas). Thus, fine-tuning of the critical day-length setting in photoperiodic flowering determines ecological niches within latitudinal clines; however, little is known about the molecular mechanisms controlling the fine-tuning of the critical day-length setting in plants. Previously, we determined that florigen genes are regulated by day length, and identified several key genes involved in setting the critical day length in rice. Using a set of chromosomal segment substitution lines with the genetic background of an elite temperate japonica cultivar, we performed a series of expression analyses of flowering-time genes to identify those responsible for setting the critical day-length in rice. Here, we identified two casein kinase genes, Hd16 and Hd6, which modulate the expression of florigen genes within certain restricted ranges of photoperiod, thereby fine-tuning the critical day length. In addition, we determined that Hd16 functions as an enhancer of the bifunctional action of Hd1 (the Arabidopsis CONSTANS ortholog) in rice. Utilization of the natural variation in Hd16 and Hd6 was only found among temperate japonica cultivars adapted to northern areas. Therefore, this fine-tuning of the setting of the critical day length may contribute to the potential northward expansion of rice cultivation areas.
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Affiliation(s)
- Yasue Nemoto
- Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kiyosumi Hori
- Rice Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Takeshi Izawa
- Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Japan
- University of Tokyo, Faculty of Agriculture, Laboratory of Plant Genetics and Breeding, Bunkyo-ku, Tokyo, Japan
- Correspondence:
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Hirotsu N, Ujiie K, Perera I, Iri A, Kashiwagi T, Ishimaru K. Partial loss-of-function of NAL1 alters canopy photosynthesis by changing the contribution of upper and lower canopy leaves in rice. Sci Rep 2017. [PMID: 29162918 DOI: 10.1038/s41598-017-15886-15885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
Little is known about the genetic basis of leaf and canopy photosynthesis. Here we aimed to detect novel quantitative trait loci (QTL) controlling photosynthesis by increasing leaf nitrogen content (LNC) per leaf area and analysed its effect on leaf and canopy photosynthesis. To identify QTL that increase photosynthetic rate in leaves, we screened chromosome segment substitution lines (CSSLs) of Oryza sativa ssp. japonica cultivar Koshihikari and O. sativa ssp. indica cultivar Nona Bokra using LNC per leaf area as the phenotype indicator. Locus leaf nitrogen content on chromosome four (qLNC4) is associated with increased LNC and photosynthetic rate per leaf area. Moreover, a non-synonymous amino acid substitution was identified in the NARROW LEAF 1 (NAL1) gene located in the qLNC4 region. This NAL1 allele increases LNC and photosynthetic rate per leaf area in flag leaves but does not increase whole-leaf photosynthesis. This NAL1 allele also increases light capture and whole-leaf nitrogen content of the lower leaves and is associated with slower senescence in flag leaves. These results suggest that this NAL1 allele does not increase whole-leaf photosynthesis but plays a role in regulating spatial and temporal trade-offs among traits at the whole-plant level.
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Affiliation(s)
- Naoki Hirotsu
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura, Gunma, 374-0193, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8518, Japan
| | - Kazuhiro Ujiie
- Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8518, Japan
| | - Ishara Perera
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura, Gunma, 374-0193, Japan
| | - Ayano Iri
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura, Gunma, 374-0193, Japan
| | - Takayuki Kashiwagi
- Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8518, Japan
| | - Ken Ishimaru
- Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8518, Japan.
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Partial loss-of-function of NAL1 alters canopy photosynthesis by changing the contribution of upper and lower canopy leaves in rice. Sci Rep 2017; 7:15958. [PMID: 29162918 PMCID: PMC5698313 DOI: 10.1038/s41598-017-15886-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/30/2017] [Indexed: 01/31/2023] Open
Abstract
Little is known about the genetic basis of leaf and canopy photosynthesis. Here we aimed to detect novel quantitative trait loci (QTL) controlling photosynthesis by increasing leaf nitrogen content (LNC) per leaf area and analysed its effect on leaf and canopy photosynthesis. To identify QTL that increase photosynthetic rate in leaves, we screened chromosome segment substitution lines (CSSLs) of Oryza sativa ssp. japonica cultivar Koshihikari and O. sativa ssp. indica cultivar Nona Bokra using LNC per leaf area as the phenotype indicator. Locus leaf nitrogen content on chromosome four (qLNC4) is associated with increased LNC and photosynthetic rate per leaf area. Moreover, a non-synonymous amino acid substitution was identified in the NARROW LEAF 1 (NAL1) gene located in the qLNC4 region. This NAL1 allele increases LNC and photosynthetic rate per leaf area in flag leaves but does not increase whole-leaf photosynthesis. This NAL1 allele also increases light capture and whole-leaf nitrogen content of the lower leaves and is associated with slower senescence in flag leaves. These results suggest that this NAL1 allele does not increase whole-leaf photosynthesis but plays a role in regulating spatial and temporal trade-offs among traits at the whole-plant level.
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Shibaya T, Hori K, Ogiso-Tanaka E, Yamanouchi U, Shu K, Kitazawa N, Shomura A, Ando T, Ebana K, Wu J, Yamazaki T, Yano M. Hd18, Encoding Histone Acetylase Related to Arabidopsis FLOWERING LOCUS D, is Involved in the Control of Flowering Time in Rice. PLANT & CELL PHYSIOLOGY 2016; 57:1828-38. [PMID: 27318280 DOI: 10.1093/pcp/pcw105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/06/2016] [Indexed: 05/04/2023]
Abstract
Flowering time is one of the most important agronomic traits in rice (Oryza sativa L.), because it defines harvest seasons and cultivation areas, and affects yields. We used a map-based strategy to clone Heading date 18 (Hd18). The difference in flowering time between the Japanese rice cultivars Koshihikari and Hayamasari was due to a single nucleotide polymorphism within the Hd18 gene, which encodes an amine oxidase domain-containing protein and is homologous to Arabidopsis FLOWERING LOCUS D (FLD). The Hayamasari Hd18 allele and knockdown of Hd18 gene expression delayed the flowering time of rice plants regardless of the day-length condition. Structural modeling of the Hd18 protein suggested that the non-synonymous substitution changed protein stability and function due to differences in interdomain hydrogen bond formation. Compared with those in Koshihikari, the expression levels of the flowering-time genes Early heading date 1 (Ehd1), Heading date 3a (Hd3a) and Rice flowering locus T1 (RFT1) were lower in a near-isogenic line with the Hayamasari Hd18 allele in a Koshihikari genetic background. We revealed that Hd18 acts as an accelerator in the rice flowering pathway under both short- and long-day conditions by elevating transcription levels of Ehd1 Gene expression analysis also suggested the involvement of MADS-box genes such as OsMADS50, OsMADS51 and OsMADS56 in the Hd18-associated regulation of Ehd1 These results suggest that, like FLD, its rice homolog accelerates flowering time but is involved in rice flowering pathways that differ from the autonomous pathways in Arabidopsis.
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Affiliation(s)
- Taeko Shibaya
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan These authors contributed equally to this work
| | - Kiyosumi Hori
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan These authors contributed equally to this work.
| | - Eri Ogiso-Tanaka
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Utako Yamanouchi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Koka Shu
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Noriyuki Kitazawa
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Ayahiko Shomura
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Tsuyu Ando
- 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
| | - Jianzhong Wu
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Toshimasa Yamazaki
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Masahiro Yano
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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Zhao J, Chen H, Ren D, Tang H, Qiu R, Feng J, Long Y, Niu B, Chen D, Zhong T, Liu YG, Guo J. Genetic interactions between diverged alleles of Early heading date 1 (Ehd1) and Heading date 3a (Hd3a)/ RICE FLOWERING LOCUS T1 (RFT1) control differential heading and contribute to regional adaptation in rice (Oryza sativa). THE NEW PHYTOLOGIST 2015; 208:936-48. [PMID: 26096631 DOI: 10.1111/nph.13503] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 05/06/2015] [Indexed: 05/03/2023]
Abstract
Initiation of flowering, also called heading, in rice (Oryza sativa) is determined by the florigens encoded by Heading date 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1). Early heading date 1 (Ehd1) regulates Hd3a and RFT1. However, different rice varieties have diverged alleles of Ehd1 and Hd3a/RFT1 and their genetic interactions remain largely unclear. Here we generated three segregating populations for different combinations of diverged Ehd1 and Hd3a/RFT1 alleles, and analyzed their genetic interactions between these alleles. We demonstrated that, in an ehd1 mutant background, Hd3a was silenced, but RFT1 was expressed (although at lower levels than in plants with a functional Ehd1) under short-day (SD) and long-day (LD) conditions. We identified a nonfunctional RFT1 allele (rft1); the lines carrying homozygous ehd1 and Hd3a/rft1 failed to induce the floral transition under SD and LD conditions. Like Hd3a, RFT1 also interacted with 14-3-3 proteins, the florigen receptors, but a nonfunctional RFT1 with a crucial E105K mutation failed to interact with 14-3-3 proteins. Furthermore, analyses of sequence variation and geographic distribution suggested that functional RFT1 alleles were selected during rice adaptation to high-latitude regions. Our results demonstrate the important roles of RFT1 in rice flowering and regional adaptation.
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Affiliation(s)
- Jing Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Hongyi Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Ding Ren
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Huiwu Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Rong Qiu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jinglei Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yunming Long
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Baixiao Niu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Danping Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Tianyu Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
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Hori K, Nonoue Y, Ono N, Shibaya T, Ebana K, Matsubara K, Ogiso-Tanaka E, Tanabata T, Sugimoto K, Taguchi-Shiobara F, Yonemaru JI, Mizobuchi R, Uga Y, Fukuda A, Ueda T, Yamamoto SI, Yamanouchi U, Takai T, Ikka T, Kondo K, Hoshino T, Yamamoto E, Adachi S, Nagasaki H, Shomura A, Shimizu T, Kono I, Ito S, Mizubayashi T, Kitazawa N, Nagata K, Ando T, Fukuoka S, Yamamoto T, Yano M. Genetic architecture of variation in heading date among Asian rice accessions. BMC PLANT BIOLOGY 2015; 15:115. [PMID: 25953146 PMCID: PMC4424449 DOI: 10.1186/s12870-015-0501-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/22/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND Heading date, a crucial factor determining regional and seasonal adaptation in rice (Oryza sativa L.), has been a major selection target in breeding programs. Although considerable progress has been made in our understanding of the molecular regulation of heading date in rice during last two decades, the previously isolated genes and identified quantitative trait loci (QTLs) cannot fully explain the natural variation for heading date in diverse rice accessions. RESULTS To genetically dissect naturally occurring variation in rice heading date, we collected QTLs in advanced-backcross populations derived from multiple crosses of the japonica rice accession Koshihikari (as a common parental line) with 11 diverse rice accessions (5 indica, 3 aus, and 3 japonica) that originate from various regions of Asia. QTL analyses of over 14,000 backcrossed individuals revealed 255 QTLs distributed widely across the rice genome. Among the detected QTLs, 128 QTLs corresponded to genomic positions of heading date genes identified by previous studies, such as Hd1, Hd6, Hd3a, Ghd7, DTH8, and RFT1. The other 127 QTLs were detected in different chromosomal regions than heading date genes. CONCLUSIONS Our results indicate that advanced-backcross progeny allowed us to detect and confirm QTLs with relatively small additive effects, and the natural variation in rice heading date could result from combinations of large- and small-effect QTLs. We also found differences in the genetic architecture of heading date (flowering time) among maize, Arabidopsis, and rice.
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Affiliation(s)
- Kiyosumi Hori
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Yasunori Nonoue
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Nozomi Ono
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Taeko Shibaya
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Kaworu Ebana
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Kazuki Matsubara
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Eri Ogiso-Tanaka
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Takanari Tanabata
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Kazuhiko Sugimoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Fumio Taguchi-Shiobara
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Jun-ichi Yonemaru
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Ritsuko Mizobuchi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Yusaku Uga
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Atsunori Fukuda
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Tadamasa Ueda
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Shin-ichi Yamamoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Utako Yamanouchi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Toshiyuki Takai
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Takashi Ikka
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Katsuhiko Kondo
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Tomoki Hoshino
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Eiji Yamamoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Shunsuke Adachi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Hideki Nagasaki
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Ayahiko Shomura
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Takehiko Shimizu
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Izumi Kono
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Sachie Ito
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Tatsumi Mizubayashi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Noriyuki Kitazawa
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Kazufumi Nagata
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Tsuyu Ando
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Shuichi Fukuoka
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Toshio Yamamoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Masahiro Yano
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
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10
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Kwon CT, Yoo SC, Koo BH, Cho SH, Park JW, Zhang Z, Li J, Li Z, Paek NC. Natural variation in Early flowering1 contributes to early flowering in japonica rice under long days. PLANT, CELL & ENVIRONMENT 2014; 37:101-12. [PMID: 23668360 DOI: 10.1111/pce.12134] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 03/26/2013] [Accepted: 05/06/2013] [Indexed: 05/04/2023]
Abstract
Natural variation in heading-date genes enables rice, a short-day (SD) plant, to flower early under long-day (LD) conditions at high latitudes. Through analysis of heading-date quantitative trait loci (QTL) with F7 recombinant inbred lines from the cross of early heading 'H143' and late heading 'Milyang23 (M23)', we found a minor-effect Early Heading3 (EH3) QTL in the Hd16 region on chromosome 3. We found that Early flowering1 (EL1), encoding casein kinase I (CKI), is likely to be responsible for the EH3/Hd16 QTL, because a missense mutation occurred in the highly conserved serine/threonine kinase domain of EL1 in H143. A different missense mutation was found in the EL1 kinase domain in Koshihikari. In vitro kinase assays revealed that EL1/CKI in H143 and Koshihikari are non-functional. In F7:9 heterogeneous inbred family-near isogenic lines (HNILs), HNIL(H143) flowered 13 days earlier than HNIL(M23) in LD, but not in SD, in which EL1 mainly acts as a LD-dependent flowering repressor, down-regulating Ehd1 expression. In the world rice collection, two types of non-functional EL1 variants were found in japonica rice generally cultivated at high latitudes. These results indicate that natural variation in EL1 contributes to early heading for rice adaptation to LD in temperate and cooler regions.
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Affiliation(s)
- Choon-Tak Kwon
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
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11
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Koo BH, Yoo SC, Park JW, Kwon CT, Lee BD, An G, Zhang Z, Li J, Li Z, Paek NC. Natural variation in OsPRR37 regulates heading date and contributes to rice cultivation at a wide range of latitudes. MOLECULAR PLANT 2013; 6:1877-88. [PMID: 23713079 DOI: 10.1093/mp/sst088] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Heading date and photoperiod sensitivity are fundamental traits that determine rice adaptation to a wide range of geographic environments. By quantitative trait locus (QTL) mapping and candidate gene analysis using whole-genome re-sequencing, we found that Oryza sativa Pseudo-Response Regulator37 (OsPRR37; hereafter PRR37) is responsible for the Early heading7-2 (EH7-2)/Heading date2 (Hd2) QTL which was identified from a cross of late-heading rice 'Milyang23 (M23)' and early-heading rice 'H143'. H143 contains a missense mutation of an invariantly conserved amino acid in the CCT (CONSTANS, CO-like, and TOC1) domain of PRR37 protein. In the world rice collection, different types of nonfunctional PRR37 alleles were found in many European and Asian rice cultivars. Notably, the japonica varieties harboring nonfunctional alleles of both Ghd7/Hd4 and PRR37/Hd2 flower extremely early under natural long-day conditions, and are adapted to the northernmost regions of rice cultivation, up to 53° N latitude. Genetic analysis revealed that the effects of PRR37 and Ghd7 alleles on heading date are additive, and PRR37 down-regulates Hd3a expression to suppress flowering under long-day conditions. Our results demonstrate that natural variations in PRR37/Hd2 and Ghd7/Hd4 have contributed to the expansion of rice cultivation to temperate and cooler regions.
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Affiliation(s)
- Bon-Hyuk Koo
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
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12
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Ogiso-Tanaka E, Matsubara K, Yamamoto SI, Nonoue Y, Wu J, Fujisawa H, Ishikubo H, Tanaka T, Ando T, Matsumoto T, Yano M. Natural variation of the RICE FLOWERING LOCUS T 1 contributes to flowering time divergence in rice. PLoS One 2013; 8:e75959. [PMID: 24098411 PMCID: PMC3788028 DOI: 10.1371/journal.pone.0075959] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 08/18/2013] [Indexed: 12/26/2022] Open
Abstract
In rice (Oryza sativa L.), there is a diversity in flowering time that is strictly genetically regulated. Some indica cultivars show extremely late flowering under long-day conditions, but little is known about the gene(s) involved. Here, we demonstrate that functional defects in the florigen gene RFT1 are the main cause of late flowering in an indica cultivar, Nona Bokra. Mapping and complementation studies revealed that sequence polymorphisms in the RFT1 regulatory and coding regions are likely to cause late flowering under long-day conditions. We detected polymorphisms in the promoter region that lead to reduced expression levels of RFT1. We also identified an amino acid substitution (E105K) that leads to a functional defect in Nona Bokra RFT1. Sequencing of the RFT1 region in rice accessions from a global collection showed that the E105K mutation is found only in indica, and indicated a strong association between the RFT1 haplotype and extremely late flowering in a functional Hd1 background. Furthermore, SNPs in the regulatory region of RFT1 and the E105K substitution in 1,397 accessions show strong linkage disequilibrium with a flowering time-associated SNP. Although the defective E105K allele of RFT1 (but not of another florigen gene, Hd3a) is found in many cultivars, relative rate tests revealed no evidence for differential rate of evolution of these genes. The ratios of nonsynonymous to synonymous substitutions suggest that the E105K mutation resulting in the defect in RFT1 occurred relatively recently. These findings indicate that natural mutations in RFT1 provide flowering time divergence under long-day conditions.
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Affiliation(s)
- Eri Ogiso-Tanaka
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai Tsukuba, Ibaraki, Japan
| | - Kazuki Matsubara
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai Tsukuba, Ibaraki, Japan
| | - Shin-ichi Yamamoto
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai Tsukuba, Ibaraki, Japan
| | - Yasunori Nonoue
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai Tsukuba, Ibaraki, Japan
| | - Jianzhong Wu
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai Tsukuba, Ibaraki, Japan
| | - Hiroko Fujisawa
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai Tsukuba, Ibaraki, Japan
| | - Harumi Ishikubo
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai Tsukuba, Ibaraki, Japan
| | - Tsuyoshi Tanaka
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai Tsukuba, Ibaraki, Japan
| | - Tsuyu Ando
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai Tsukuba, Ibaraki, Japan
| | - Takashi Matsumoto
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai Tsukuba, Ibaraki, Japan
| | - Masahiro Yano
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai Tsukuba, Ibaraki, Japan
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13
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Brachi B, Faure N, Bergelson J, Cuguen J, Roux F. Genome-wide association mapping of flowering time in Arabidopsis thaliana in nature: genetics for underlying components and reaction norms across two successive years. ACTA BOTANICA GALLICA : BULLETIN DE LA SOCIETE BOTANIQUE DE FRANCE 2013; 160:205-219. [PMID: 24470785 PMCID: PMC3901435 DOI: 10.1080/12538078.2013.807302] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Often used as a proxy for the transition to reproduction, flowering time (FT) is an integrative trait of two successive biological processes, i.e. bolting time (BT) and the interval between bolting and flowering time (INT). In this study, we aimed to identify candidate genes associated with these composite traits in Arabidopsis thaliana using a field experiment. Genome-wide association (GWA) mapping was performed on BT, INT and FT based on a sample of 179 worldwide natural accessions genotyped for 216,509 SNPs. The high resolution conferred by GWA mapping indicates that FT is an integrative trait at the genetic level, with distinct genetics for BT and INT. BT is shaped largely by genes involved in the circadian clock whereas INT is shaped by genes involved in both the hormone pathways and cold acclimation. Finally, the florigen TSF appears to be the main integrator of environmental and internal signals in ecologically realistic conditions. Based on FT scored in a previous field experiment, we also studied the genetics underlying reaction norms across two years. Only four genes were common to both years, emphasizing the need to repeat field experiments. The gene regulation model appeared as the main genetic model for genotype × year interactions.
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Affiliation(s)
- Benjamin Brachi
- Laboratoire Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université des Sciences et Technologies de Lille – Lille 1, F-59655 Villeneuve d'Ascq cedex France
| | - Nathalie Faure
- Laboratoire Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université des Sciences et Technologies de Lille – Lille 1, F-59655 Villeneuve d'Ascq cedex France
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57 Street, Chicago, IL 60637, USA
| | - Joël Cuguen
- Laboratoire Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université des Sciences et Technologies de Lille – Lille 1, F-59655 Villeneuve d'Ascq cedex France
| | - Fabrice Roux
- Laboratoire Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université des Sciences et Technologies de Lille – Lille 1, F-59655 Villeneuve d'Ascq cedex France
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14
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Fujino K, Yamanouchi U, Yano M. Roles of the Hd5 gene controlling heading date for adaptation to the northern limits of rice cultivation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:611-8. [PMID: 23090144 DOI: 10.1007/s00122-012-2005-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 10/06/2012] [Indexed: 05/04/2023]
Abstract
During the diversification of cultivated rice after domestication, rice was grown in diverse geographic regions using genetic variations attributed to the combination of alleles in loci for adaptability to various environmental conditions. To elucidate the key gene for adaptation in rice cultivars to the northern limit of rice cultivation, we conducted genetic analyses of heading date using extremely early-heading cultivars. The Hd5 gene controlling heading date (flowering time) generated variations in heading date among cultivars adapted to Hokkaido, where is the northernmost region of Japan and one of the northern limits of rice cultivation in the world. The association of the Hd5 genotype with heading date and genetical analysis clearly showed that the loss-of-function Hd5 has an important role in exhibiting earlier heading among a local population in Hokkaido. Distinct distribution of the loss-of-function Hd5 revealed that this mutation event of the 19-bp deletion occurred in a local landrace Bouzu and that this mutation may have been selected as an early-heading variety in rice breeding programs in Hokkaido in the early 1900s. The loss-of-function Hd5 was then introduced into the rice variety Fanny from France and contributed to its extremely early heading under the presence of functional Ghd7. These results demonstrated that Hd5 plays roles not only in generating early heading in variations of heading date among a local population in Hokkaido, but also in extremely early heading for adaptation to northern limits of rice cultivation.
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Affiliation(s)
- Kenji Fujino
- Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido, 067-1317, Japan.
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15
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Yonemaru JI, Yamamoto T, Ebana K, Yamamoto E, Nagasaki H, Shibaya T, Yano M. Genome-wide haplotype changes produced by artificial selection during modern rice breeding in Japan. PLoS One 2012; 7:e32982. [PMID: 22427922 PMCID: PMC3302797 DOI: 10.1371/journal.pone.0032982] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 02/05/2012] [Indexed: 11/18/2022] Open
Abstract
During the last 90 years, the breeding of rice has delivered cultivars with improved agronomic and economic characteristics. Crossing of different lines and successive artificial selection of progeny based on their phenotypes have changed the chromosomal constitution of the ancestors of modern rice; however, the nature of these changes is unclear. The recent accumulation of data for genome-wide single-nucleotide polymorphisms (SNPs) in rice has allowed us to investigate the change in haplotype structure and composition. To assess the impact of these changes during modern breeding, we studied 177 Japanese rice accessions, which were categorized into three groups: landraces, improved cultivars developed from 1931 to 1974 (the early breeding phase), and improved cultivars developed from 1975 to 2005 (the late breeding phase). Phylogenetic tree and structure analysis indicated genetic differentiation between non-irrigated (upland) and irrigated (lowland) rice groups as well as genetic structuring within the irrigated rice group that corresponded to the existence of three subgroups. Pedigree analysis revealed that a limited number of landraces and cultivars was used for breeding at the beginning of the period of systematic breeding and that 11 landraces accounted for 70% of the ancestors of the modern improved cultivars. The values for linkage disequilibrium estimated from SNP alleles and the haplotype diversity determined from consecutive alleles in five-SNP windows indicated that haplotype blocks became less diverse over time as a result of the breeding process. A decrease in haplotype diversity, caused by a reduced number of polymorphisms in the haplotype blocks, was observed in several chromosomal regions. However, our results also indicate that new haplotype polymorphisms have been generated across the genome during the breeding process. These findings will facilitate our understanding of the association between particular haplotypes and desirable phenotypes in modern Japanese rice cultivars.
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Affiliation(s)
- Jun-ichi Yonemaru
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai,Tsukuba, Ibaraki, Japan.
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16
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Marzougui S, Sugimoto K, Yamanouchi U, Shimono M, Hoshino T, Hori K, Kobayashi M, Ishiyama K, Yano M. Mapping and characterization of seed dormancy QTLs using chromosome segment substitution lines in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:893-902. [PMID: 22105913 DOI: 10.1007/s00122-011-1753-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 11/05/2011] [Indexed: 05/05/2023]
Abstract
Seed dormancy--the temporary failure of a viable seed to germinate under favorable conditions--is a complex characteristic influenced by many genes and environmental factors. To detect the genetic factors associated with seed dormancy in rice, we conducted a QTL analysis using chromosome segment substitution lines (CSSLs) derived from a cross between Nona Bokra (strong dormancy) and Koshihikari (weak dormancy). Comparison of the levels of seed dormancy of the CSSLs and their recurrent parent Koshihikari revealed that two chromosomal regions-on the short arms of chromosomes 1 and 6-were involved in the variation in seed dormancy. Further genetic analyses using an F(2) population derived from crosses between the CSSLs and Koshihikari confirmed the allelic differences and the chromosomal locations of three putative QTLs: Sdr6 on chromosome 1 and Sdr9 and Sdr10 on chromosome 6. The Nona Bokra alleles of the three QTLs were associated with decreased germination rate. We discuss the physiological features of the CSSLs and speculate on the possible mechanisms of dormancy in light of the newly detected QTLs.
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17
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Brachi B, Morris GP, Borevitz JO. Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol 2011; 12:232. [PMID: 22035733 PMCID: PMC3333769 DOI: 10.1186/gb-2011-12-10-232] [Citation(s) in RCA: 296] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Genome-wide association studies (GWAS) have been even more successful in plants than in humans. Mapping approaches can be extended to dissect adaptive genetic variation from structured background variation in an ecological context.
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Affiliation(s)
- Benjamin Brachi
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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18
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Miura K, Ashikari M, Matsuoka M. The role of QTLs in the breeding of high-yielding rice. TRENDS IN PLANT SCIENCE 2011; 16:319-26. [PMID: 21429786 DOI: 10.1016/j.tplants.2011.02.009] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 02/09/2011] [Accepted: 02/22/2011] [Indexed: 05/19/2023]
Abstract
Food shortages have once again become a serious problem, not only because of world population growth but also as a result of escalating demand for crops as a substrate for biofuels. The production of improved plant varieties, especially major crops such as rice, is urgently required to increase yield. The completion of the sequencing of the rice genome has made it possible to clone and analyze quantitative trait loci (QTLs). Furthermore, the development of high-throughput sequencing and genotyping technologies has improved spectacularly the accuracy of QTL analysis. In this review article, we focus on the potential roles of major QTLs in the selection for agronomic traits in rice and discuss the application of high-throughput technologies for high-resolution genetic analysis.
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Affiliation(s)
- Kotaro Miura
- Department of Bioscience, Fukui Prefectural University, 4-1-1 Matsuoka Kenjyojima, Eiheiji-cho, Yoshida-gun, Fukui, 910-1195, Japan
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19
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Abstract
In general, heterozygosity is considered to be advantageous, primarily because it masks the effects of deleterious recessive alleles. However, there is usually a reduction in fitness in individuals that are heterozygous due to the pairing of two species (heterospecific). Because the parental alleles arose along separate evolutionary paths, they may not function properly when brought together within an individual. The formation of these unfit interspecies hybrids is one of the mechanisms that maintains species isolation. Interestingly, it has been observed that later-generation individuals resulting from a backcross to one parent are more often sterile than those resulting from a backcross to the other parent, but the mechanism underlying this trend is unknown. Here, I show that one direction of backcross produces offspring with more heterospecific genome, and that this is correlated with the directionality seen in backcross hybrid sterility. Therefore, the directionality in sterility is likely due to the different amounts of heterospecific genome present in the two backcrosses. Surprisingly, in spite of the potential fitness consequences, I also find that interspecies laboratory backcrosses in general yield an excess of heterospecific individuals, and that this trend is consistent across multiple taxa.
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Affiliation(s)
- Amanda J Moehring
- Department of Biology, The University of Western Ontario, BGS 2080, London, ON, N6A 5B7, Canada.
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20
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Ebana K, Shibaya T, Wu J, Matsubara K, Kanamori H, Yamane H, Yamanouchi U, Mizubayashi T, Kono I, Shomura A, Ito S, Ando T, Hori K, Matsumoto T, Yano M. Uncovering of major genetic factors generating naturally occurring variation in heading date among Asian rice cultivars. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:1199-210. [PMID: 21229229 PMCID: PMC3057013 DOI: 10.1007/s00122-010-1524-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 12/11/2010] [Indexed: 05/04/2023]
Abstract
To dissect the genetic factors controlling naturally occurring variation of heading date in Asian rice cultivars, we performed QTL analyses using F(2) populations derived from crosses between a japonica cultivar, Koshihikari, and each of 12 cultivars originating from various regions in Asia. These 12 diverse cultivars varied in heading date under natural field conditions in Tsukuba, Japan. Transgressive segregation was observed in 10 F(2) combinations. QTL analyses using multiple crosses revealed a comprehensive series of loci involved in natural variation in flowering time. One to four QTLs were detected in each cross combination, and some QTLs were shared among combinations. The chromosomal locations of these QTLs corresponded well with those detected in other studies. The allelic effects of the QTLs varied among the cross combinations. Sequence analysis of several previously cloned genes controlling heading date, including Hd1, Hd3a, Hd6, RFT1, and Ghd7, identified several functional polymorphisms, indicating that allelic variation at these loci probably contributes to variation in heading date. Taken together, the QTL and sequencing results indicate that a large portion of the phenotypic variation in heading date in Asian rice cultivars could be generated by combinations of different alleles (possibly both loss- and gain-of-function) of the QTLs detected in this study.
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Affiliation(s)
- Kaworu Ebana
- QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Taeko Shibaya
- QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Jianzhong Wu
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Kazuki Matsubara
- QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
- Present Address: National Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518 Japan
| | - Hiroyuki Kanamori
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854 Japan
| | - Hiroko Yamane
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854 Japan
| | - Utako Yamanouchi
- QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Tatsumi Mizubayashi
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854 Japan
| | - Izumi Kono
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854 Japan
| | - Ayahiko Shomura
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854 Japan
| | - Sachie Ito
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854 Japan
| | - Tsuyu Ando
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854 Japan
| | - Kiyosumi Hori
- QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Takashi Matsumoto
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Masahiro Yano
- QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
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Fujino K, Wu J, Sekiguchi H, Ito T, Izawa T, Matsumoto T. Multiple introgression events surrounding the Hd1 flowering-time gene in cultivated rice, Oryza sativa L. Mol Genet Genomics 2010; 284:137-46. [PMID: 20607290 DOI: 10.1007/s00438-010-0555-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 06/22/2010] [Indexed: 12/18/2022]
Abstract
Flowering time is a major determinant for the local adaptation of crops. Hd1 is a key flowering-time gene in rice and is orthologous to the Arabidopsis CONSTANS gene. To elucidate the role of Hd1 in selection, we examined the Hd1 alleles of 60 landraces of Asian cultivated rice (Oryza sativa L.) originating from all regions of Asia, which comprised three cultivar groups, indica, japonica, and aus. The identified alleles were classified into four allele groups. The functional Hd1 alleles in allele groups I and II corresponded to indica and japonica, respectively. Non-functional alleles in these groups were not clearly associated with cultivar groups or locations. Allele groups III and IV corresponded to the aus cultivar group. The ancestry of each cultivar group was identified by the coalescent approach for Hd1 molecular evolution using the haplotype patterns of 14 regions over the 1.1 Mb chromosomal region surrounding Hd1 and the pSINE patterns of two loci, 1.4 and 4.4 Mb apart from Hd1. The haplotype patterns clearly revealed that Hd1 allele migration was caused by multiple and complex introgression events between cultivar groups. The Hd1 haplotypes among dozens of accessions of the wild species O. rufipogon were strongly divergent and only two of the haplotype clusters in O. rufipogon were closely related to those in cultivated rice. This strongly suggested that multiple introgression events have played an important role in the shaping and diversification of adaptation in addition to primary selection steps at the beginning of domestication.
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Affiliation(s)
- Kenji Fujino
- Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Higashi-5, Kita-15, Naganuma, Hokkaido 0691317, Japan.
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Brachi B, Faure N, Horton M, Flahauw E, Vazquez A, Nordborg M, Bergelson J, Cuguen J, Roux F. Linkage and association mapping of Arabidopsis thaliana flowering time in nature. PLoS Genet 2010; 6:e1000940. [PMID: 20463887 PMCID: PMC2865524 DOI: 10.1371/journal.pgen.1000940] [Citation(s) in RCA: 305] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 04/06/2010] [Indexed: 12/28/2022] Open
Abstract
Flowering time is a key life-history trait in the plant life cycle. Most studies to unravel the genetics of flowering time in Arabidopsis thaliana have been performed under greenhouse conditions. Here, we describe a study about the genetics of flowering time that differs from previous studies in two important ways: first, we measure flowering time in a more complex and ecologically realistic environment; and, second, we combine the advantages of genome-wide association (GWA) and traditional linkage (QTL) mapping. Our experiments involved phenotyping nearly 20,000 plants over 2 winters under field conditions, including 184 worldwide natural accessions genotyped for 216,509 SNPs and 4,366 RILs derived from 13 independent crosses chosen to maximize genetic and phenotypic diversity. Based on a photothermal time model, the flowering time variation scored in our field experiment was poorly correlated with the flowering time variation previously obtained under greenhouse conditions, reinforcing previous demonstrations of the importance of genotype by environment interactions in A. thaliana and the need to study adaptive variation under natural conditions. The use of 4,366 RILs provides great power for dissecting the genetic architecture of flowering time in A. thaliana under our specific field conditions. We describe more than 60 additive QTLs, all with relatively small to medium effects and organized in 5 major clusters. We show that QTL mapping increases our power to distinguish true from false associations in GWA mapping. QTL mapping also permits the identification of false negatives, that is, causative SNPs that are lost when applying GWA methods that control for population structure. Major genes underpinning flowering time in the greenhouse were not associated with flowering time in this study. Instead, we found a prevalence of genes involved in the regulation of the plant circadian clock. Furthermore, we identified new genomic regions lacking obvious candidate genes.
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Affiliation(s)
- Benjamin Brachi
- Laboratoire Génétique et Evolution des Populations Végétales, Unité Mixte de Recherche CNRS 8016, Université des Sciences et Technologies de Lille 1, Villeneuve d'Ascq, France
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23
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Yoshida T, Nishida H, Zhu J, Nitcher R, Distelfeld A, Akashi Y, Kato K, Dubcovsky J. Vrn-D4 is a vernalization gene located on the centromeric region of chromosome 5D in hexaploid wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:543-552. [PMID: 19847391 DOI: 10.1007/s00122-009-1174-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 09/27/2009] [Indexed: 05/28/2023]
Abstract
Natural variation in wheat requirement of long exposures to cold temperatures to accelerate flowering (vernalization) is mainly controlled by the Vrn-1, Vrn-2, Vrn-3, and Vrn-4 loci. The first three loci have been well characterized, but limited information is available for Vrn-4. So far, natural variation for Vrn-4 has been detected only in the D genome (Vrn-D4), and genetic stocks for this gene are available in Triple Dirk (TDF, hereafter). We detected heterogeneity in the Vrn-1 alleles present in different TDF stocks, which may explain inconsistencies among previous studies. A correct TDF seed stock from Japan carrying recessive vrn-A1, vrn-B1, and vrn-D1 alleles was crossed with three different winter cultivars to generate F(2) mapping populations. Most of the variation in flowering time in these three populations was controlled by a single locus, Vrn-D4, which was mapped within a 1.8 cM interval flanked by markers Xcfd78 and Xbarc205 in the centromeric region of chromosome 5D. A factorial ANOVA for heading time using Vrn-D4 alleles and vernalization as factors showed a significant interaction (P < 0.0001), which confirmed that the Vrn-D4 effect on flowering time is modulated by vernalization. Comparison of the different Triple Dirk stocks revealed that Vrn-B1, Vrn-D1, and Vrn-D4 all have a small residual response to vernalization, but Vrn-D4 differs from the other two in its response to short vernalization periods. The precise mapping and characterization of Vrn-D4 presented here represent a first step toward the positional cloning of this gene.
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Affiliation(s)
- Tetsuya Yoshida
- Graduate School of Natural Science and Technology, Okayama University, 1-1-1, Tsushima-Naka, Kita-Ku, Okayama 700-8530, Japan
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24
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Matsubara K, Kono I, Hori K, Nonoue Y, Ono N, Shomura A, Mizubayashi T, Yamamoto S, Yamanouchi U, Shirasawa K, Nishio T, Yano M. Novel QTLs for photoperiodic flowering revealed by using reciprocal backcross inbred lines from crosses between japonica rice cultivars. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:935-45. [PMID: 18726584 DOI: 10.1007/s00122-008-0833-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2008] [Accepted: 06/21/2008] [Indexed: 05/06/2023]
Abstract
The rice japonica cultivars Nipponbare and Koshihikari differ in heading date and response of heading to photoperiod (photoperiod sensitivity). Using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers, we conducted quantitative trait locus (QTL) analyses for heading date in a set of reciprocal backcross inbred lines (BILs) from crosses between Nipponbare and Koshihikari. Under natural-day conditions, transgressive segregation in days to heading (DTH) toward both early and late heading was observed in both BIL populations. QTL analyses revealed that two QTLs--on chromosomes 3 and 6--were involved in the difference in heading date between the parental cultivars. The Nipponbare allele at the QTLs on chromosomes 3 and 6 showed, respectively, increasing and decreasing effects on DTH in both BIL populations. The transgressive segregation observed in the BILs could be accounted for mainly by the complementary action of a set of alleles with opposing effects. Both QTLs were finely mapped as single Mendelian factors in secondary mapping populations (BC2F2 plants/BC2F3 lines). The QTL on chromosome 3 was mapped in the 1,140-kb interval between 94O03-4 (SSR) and OJ21G19-4 (SNP) and was designated Hd16. The QTL on chromosome 6 was mapped in the 328-kb interval between P548D347 (SSR) and 0007O20 (SSR) and was designated Hd17. Both Hd16 and Hd17 were involved in photoperiod sensitivity, as revealed by observation of the DTH of nearly isogenic lines of Nipponbare under short- and long-day conditions, suggesting that allelic differences in both Hd16 and Hd17 account for most of the difference in photoperiod sensitivity between the parental cultivars.
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Affiliation(s)
- K Matsubara
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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Nonoue Y, Fujino K, Hirayama Y, Yamanouchi U, Lin SY, Yano M. Detection of quantitative trait loci controlling extremely early heading in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:715-22. [PMID: 18193402 DOI: 10.1007/s00122-007-0704-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 12/13/2007] [Indexed: 05/08/2023]
Abstract
To clarify the genetic basis of extremely early heading in rice, we conducted quantitative trait locus (QTL) analyses using F2 populations from two genetically wide cross combinations, Hayamasari/Kasalath (HaF2) and Hoshinoyume/Kasalath (HoF2). Hayamasari and Hoshinoyume are extremely early-heading japonica cultivars. Photoperiod sensitivity is completely lost in Hayamasari and weak in Hoshinoyume. Three QTLs, QTL(chr6), QTL(chr7), and QTL(chr8), for days-to-heading (DTH) in HaF2 were detected on chromosomes 6, 7, and 8, respectively, and QTL(chr6) and QTL(chr7) were detected in HoF2. On the basis of the chromosomal locations, QTL(chr6), QTL(chr7), and QTL(chr8) may be likely to be Hd1, Hd4, and Hd5, respectively, which had been detected previously as QTLs for DTH in an F2 population of NipponbarexKasalath. Alleles of QTL(chr7) decreased DTH dramatically in both Hayamasari and Hoshinoyume, suggesting that QTL(chr7) has a major role in determining extremely early heading. In addition, allele-specific interactions were detected between QTL(chr6), QTL(chr7) and QTL(chr8). This result suggests that not only allelic differences but also epistatic interactions contribute to extremely early heading. QTL(chr8) was detected in HaF2, but not in HoF2, suggesting that it determines the difference in DTH between Hayamasari and Hoshinoyume. A major QTL was also detected in the region of QTL(chr8) in QTL analysis using an F2 population of HayamasarixHoshinoyume. This result supports the idea that QTL(chr8) is a major factor that determines the difference in DTH between Hayamasari and Hoshinoyume, and is involved in photoperiod sensitivity.
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Affiliation(s)
- Y Nonoue
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
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Takai T, Nonoue Y, Yamamoto SI, Yamanouchi U, Matsubara K, Liang ZW, Lin HX, Ono N, Uga Y, Yano M. Development of Chromosome Segment Substitution Lines Derived from Backcross between indica Donor Rice Cultivar 'Nona Bokra' and japonica Recipient Cultivar 'Koshihikari'. BREEDING SCIENCE 2007; 57:257-261. [PMID: 0 DOI: 10.1270/jsbbs.57.257] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
| | - Yasunori Nonoue
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries
| | | | | | | | - Zheng-Wei Liang
- National Institute of Agrobiological Sciences
- Present address: Northeast Institute of Geography and Agricultural Ecology, Chinese Academy of Sciences
| | - Hong-xuan Lin
- National Institute of Agrobiological Sciences
- Present address: Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences
| | - Nozomi Ono
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries
| | - Yusaku Uga
- National Institute of Agrobiological Sciences
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