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Meng QL, Qiang CG, Li JL, Geng MF, Ren NN, Cai Z, Wang MX, Jiao ZH, Zhang FM, Song XJ, Ge S. Genetic architecture of ecological divergence between Oryza rufipogon and Oryza nivara. Mol Ecol 2024; 33:e17268. [PMID: 38230514 DOI: 10.1111/mec.17268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/18/2024]
Abstract
Ecological divergence due to habitat difference plays a prominent role in the formation of new species, but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild ancestors of rice (Oryza rufipogon and Oryza nivara) are a progenitor-derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolution linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two Oryza species. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots) on 11 chromosomes, significantly more than that expected by chance, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v-test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and help effective manipulation of specific genes or gene cluster in rice breeding.
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Affiliation(s)
- Qing-Lin Meng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Gen Qiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ji-Long Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mu-Fan Geng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ning-Ning Ren
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhe Cai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Mei-Xia Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zi-Hui Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fu-Min Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xian-Jun Song
- Key Laboratory of Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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Ashraf H, Ghouri F, Baloch FS, Nadeem MA, Fu X, Shahid MQ. Hybrid Rice Production: A Worldwide Review of Floral Traits and Breeding Technology, with Special Emphasis on China. PLANTS (BASEL, SWITZERLAND) 2024; 13:578. [PMID: 38475425 DOI: 10.3390/plants13050578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/26/2024] [Accepted: 02/08/2024] [Indexed: 03/14/2024]
Abstract
Rice is an important diet source for the majority of the world's population, and meeting the growing need for rice requires significant improvements at the production level. Hybrid rice production has been a significant breakthrough in this regard, and the floral traits play a major role in the development of hybrid rice. In grass species, rice has structural units called florets and spikelets and contains different floret organs such as lemma, palea, style length, anther, and stigma exsertion. These floral organs are crucial in enhancing rice production and uplifting rice cultivation at a broader level. Recent advances in breeding techniques also provide knowledge about different floral organs and how they can be improved by using biotechnological techniques for better production of rice. The rice flower holds immense significance and is the primary focal point for researchers working on rice molecular biology. Furthermore, the unique genetics of rice play a significant role in maintaining its floral structure. However, to improve rice varieties further, we need to identify the genomic regions through mapping of QTLs (quantitative trait loci) or by using GWAS (genome-wide association studies) and their validation should be performed by developing user-friendly molecular markers, such as Kompetitive allele-specific PCR (KASP). This review outlines the role of different floral traits and the benefits of using modern biotechnological approaches to improve hybrid rice production. It focuses on how floral traits are interrelated and their possible contribution to hybrid rice production to satisfy future rice demand. We discuss the significance of different floral traits, techniques, and breeding approaches in hybrid rice production. We provide a historical perspective of hybrid rice production and its current status and outline the challenges and opportunities in this field.
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Affiliation(s)
- Humera Ashraf
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Fozia Ghouri
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, Mersin 33100, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye
| | - Xuelin Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
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Zhu X, Gou Y, Heng Y, Ding W, Li Y, Zhou D, Li X, Liang C, Wu C, Wang H, Shen R. Targeted manipulation of grain shape genes effectively improves outcrossing rate and hybrid seed production in rice. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:381-390. [PMID: 36342212 PMCID: PMC9884017 DOI: 10.1111/pbi.13959] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/09/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Stigma exsertion rate (SER) of the male sterile line is a key limiting factor for hybrid seed production in rice. Although a large number of quantitative trait loci associated with SER have been reported, few genes have been molecularly cloned and functionally characterized, severely hindering the genetic improvement of SER of the male sterile line and the breeding efficiency of hybrid rice. In this study, we identified three grain shape regulatory genes, GS3, GW8 and GS9, as potential candidate genes for targeted manipulation of grain shape and SER. We show that simultaneously knocking out these three genes could effectively increase SER by increasing the ratio of spikelet length/spikelet width and length of stigma and style, without negative impacts on other agronomic traits. Cellular examination and transcriptomic analyses revealed a role of these genes in coordinated regulation of transverse and longitudinal cell division in the pistils. Moreover, we demonstrate that targeted manipulation of these grain shape genes could significantly improve the outcrossing rate in both the ZH11 (a japonica variety) and Zhu6S (an indica male sterile line) backgrounds. Our results provide new insights into the mechanisms of rice SER regulation and develop an effective strategy to improve SER and out-crossing rate in rice, thus facilitating hybrid rice production.
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Affiliation(s)
- Xinyu Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhou510642China
| | - Yajun Gou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhou510642China
| | - Yueqin Heng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhou510642China
| | - Wenyan Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhou510642China
| | - Yajing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhou510642China
| | - Degui Zhou
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou510640China
| | - Xiaoqing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhou510642China
| | - Churong Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhou510642China
| | - Chuanyin Wu
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhou510642China
| | - Rongxin Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhou510642China
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4
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Tan Q, Chen S, Gan Z, Lu Q, Yan Z, Chen G, Lin S, Yang W, Zhao J, Ba Y, Zhu H, Bu S, Liu G, Liu Z, Wang S, Zhang G. Grain shape is a factor affecting the stigma exsertion rate in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1087285. [PMID: 36798706 PMCID: PMC9927237 DOI: 10.3389/fpls.2023.1087285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Stigma exsertion rate (SER) is an index of outcrossing ability in rice and is a key trait of male sterile lines (MSLs) in hybrid rice. In this study, it was found that the maintainer lines carrying gs3 and gs3/gw8 showed higher SER. Single-segment substitution lines (SSSLs) carrying gs3, gw5, GW7 or gw8 genes for grain shape and gene pyramiding lines were used to reveal the relationship between grain shape and SER. The results showed that the grain shape regulatory genes had pleiotropic effects on SER. The SERs were affected by grain shapes including grain length, grain width and the ratio of length to width (RLW) not only in low SER background, but also in high SER background. The coefficients of determination (R2) between grain length and SER, grain width and SER, and grain RLW and SER were 0.78, 0.72, and 0.91 respectively. The grain RLW was the most important parameter affecting SER, and a larger grain RLW was beneficial to stigma exsertion. The pyramiding line PL-gs3/GW7/gw8 showed the largest grain RLW and the highest SER, which will be a fine breeding resource. Further research showed that the grain shape regulatory genes had pleiotropic effects on stigma shape, although the R2 values between grain shape and stigma shape, and stigma shape and SER were lower. Our results demonstrate that grain shape is a factor affecting SER in rice, in part by affecting stigma shape. This finding will be helpful for breeding MSLs with high SER in hybrid rice.
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Affiliation(s)
- Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Songliang Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Zhenpeng Gan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Qimiao Lu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Zhenguang Yan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guodong Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Shaojun Lin
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Jiao Zhao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Yuanyuan Ba
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Suhong Bu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
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5
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Liu Y, Fu D, Kong D, Ma X, Zhang A, Wang F, Wang L, Xia H, Liu G, Yu X, Luo L. Linkage mapping and association analysis to identify a reliable QTL for stigma exsertion rate in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:982240. [PMID: 36082291 PMCID: PMC9445662 DOI: 10.3389/fpls.2022.982240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/04/2022] [Indexed: 05/25/2023]
Abstract
The commercialization of hybrid rice has greatly contributed to the increase in rice yield, with the improvement of its seed production capacity having played an important role. The stigma exsertion rate (SER) is a key factor for improving the outcrossing of the sterile line and the hybrid rice seed production. We used the Zhenshan 97B × IRAT109 recombinant inbred population comprising 163 lines and a natural population of 138 accessions to decipher the genetic foundation of SER over 2 years in three environments. Additionally, we detected eight QTLs for SER on chromosomes 1, 2, and 8 via linkage mapping. We also identified seven and 19 significant associations for SER using genome-wide association study in 2016 and 2017, respectively. Interestingly, we located two lead SNPs (sf0803343504 and sf083344610) on chromosome 8 in the qTSE8 QTL region that were significantly associated with total SER. After transcriptomic analysis, quantitative real-time PCR, and haplotype analysis, we found 13 genes within this reliable region as important candidate genes. Our study results will be beneficial to molecular marker-assisted selection of rice lines with high outcrossing rate, thereby improving the efficiency of hybrid seed production.
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Affiliation(s)
- Yi Liu
- Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Dong Fu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Deyan Kong
- Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Xiaosong Ma
- Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Anning Zhang
- Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Feiming Wang
- Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Lei Wang
- Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Hui Xia
- Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Guolan Liu
- Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Xinqiao Yu
- Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
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6
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Tan Q, Bu S, Chen G, Yan Z, Chang Z, Zhu H, Yang W, Zhan P, Lin S, Xiong L, Chen S, Liu G, Liu Z, Wang S, Zhang G. Reconstruction of the High Stigma Exsertion Rate Trait in Rice by Pyramiding Multiple QTLs. FRONTIERS IN PLANT SCIENCE 2022; 13:921700. [PMID: 35747883 PMCID: PMC9209754 DOI: 10.3389/fpls.2022.921700] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/05/2022] [Indexed: 05/25/2023]
Abstract
Asian cultivated rice is a self-pollinating crop, which has already lost some traits of natural outcrossing in the process of domestication. However, male sterility lines (MSLs) need to have a strong outcrossing ability to produce hybrid seeds by outcrossing with restorer lines of male parents in hybrid rice seed production. Stigma exsertion rate (SER) is a trait related to outcrossing ability. Reconstruction of the high-SER trait is essential in the MSL breeding of rice. In previous studies, we detected eighteen quantitative trait loci (QTLs) for SER from Oryza sativa, Oryza glaberrima, and Oryza glumaepatula using single-segment substitution lines (SSSLs) in the genetic background of Huajingxian 74 (HJX74). In this study, eleven of the QTLs were used to develop pyramiding lines. A total of 29 pyramiding lines with 2-6 QTLs were developed from 10 SSSLs carrying QTLs for SER in the HJX74 genetic background. The results showed that the SER increased with increasing QTLs in the pyramiding lines. The SER in the lines with 5-6 QTLs was as high as wild rice with strong outcrossing ability. The epistasis of additive by additive interaction between QTLs in the pyramiding lines was less-than-additive or negative effect. One QTL, qSER3a-sat, showed minor-effect epistasis and increased higher SER than other QTLs in pyramiding lines. The detection of epistasis of QTLs on SER uncovered the genetic architecture of SER, which provides a basis for using these QTLs to improve SER levels in MSL breeding. The reconstruction of the high-SER trait will help to develop the MSLs with strong outcrossing ability in rice.
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Affiliation(s)
- Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Suhong Bu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guodong Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Zhenguang Yan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Zengyuan Chang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Penglin Zhan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Shaojun Lin
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Liang Xiong
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Songliang Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
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7
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Guo N, Wang Y, Chen W, Tang S, An R, Wei X, Hu S, Tang S, Shao G, Jiao G, Xie L, Wang L, Sheng Z, Hu P. Fine mapping and target gene identification of qSE4, a QTL for stigma exsertion rate in rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:959859. [PMID: 35923872 PMCID: PMC9341389 DOI: 10.3389/fpls.2022.959859] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/27/2022] [Indexed: 05/11/2023]
Abstract
The stigma exsertion rate (SER) is a complex agronomy phenotype controlled by multiple genes and climate and a key trait affecting the efficiency of hybrid rice seed production. Using a japonica two-line male sterile line (DaS) with a high SER as the donor and a tropical japonica rice (D50) with a low SER as the acceptor to construct a near-isogenic line [NIL (qSE4 DaS)]. Populations were segregated into 2,143 individuals of BC3F2 and BC4F2, and the stigma exsertion quantitative trait locus (QTL) qSE4 was determined to be located within 410.4 Kb between markers RM17157 and RM17227 on chromosome 4. Bioinformatic analysis revealed 13 candidate genes in this region. Sequencing and haplotype analysis indicated that the promoter region of LOC_Os04g43910 (ARF10) had a one-base substitution between the two parents. Further Reverse Transcription-Polymerase Chain Reaction (RT-PCR) analysis showed that the expression level of ARF10 in DaS was significantly higher than in D50. After knocking out ARF10 in the DaS background, it was found that the SER of arf10 (the total SER of the arf10-1 and the arf10-2 were 62.54 and 66.68%, respectively) was significantly lower than that of the wild type (the total SER was 80.97%). Transcriptome and hormone assay analysis showed that arf10 had significantly higher auxin synthesis genes and contents than the wild type and the expression of auxin signaling-related genes was significantly different, Similar results were observed for abscisic acid and jasmonic acid. These results indicate that LOC_Os04g43910 is mostly likely the target gene of qSE4, and the study of its gene function is of great significance for understanding the molecular mechanisms of SER and improving the efficiency of hybrid seed production.
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Affiliation(s)
- Naihui Guo
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
- Rice Research Institute, Shengyang Agricultural University, Shenyang, China
| | - Yakun Wang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Wei Chen
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Shengjia Tang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Ruihu An
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Shikai Hu
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Lihong Xie
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Ling Wang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
- Zhonghua Sheng,
| | - Peisong Hu
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou, China
- Rice Research Institute, Shengyang Agricultural University, Shenyang, China
- *Correspondence: Peisong Hu,
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8
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Dang X, Zhang Y, Li Y, Chen S, Liu E, Fang B, Liu Q, She D, Dong Z, Fan Z, Li D, Wang H, Zhu S, Hu X, Li Y, Jiang J, Hong D. SYL3-k increases style length and yield of F 1 seeds via enhancement of endogenous GA 4 content in Oryza sativa L. pistils. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:321-336. [PMID: 34657161 PMCID: PMC8741667 DOI: 10.1007/s00122-021-03968-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
SYL3-k allele increases the outcrossing rate of male sterile line and the yield of hybrid F1 seeds via enhancement of endogenous GA4 content in Oryza sativa L. pistils. The change in style length might be an adaptation of rice cultivation from south to north in the northern hemisphere. The style length (SYL) in rice is one of the major factors influencing the stigma exertion, which affects the outcross rate of male sterile line and the yield of hybrid F1 seeds. However, the biological mechanisms underlying SYL elongation remain elusive. Here, we report a map-based cloning and characterisation of the allele qSYL3-k. The qSYL3-k allele encodes a MADS-box family transcription factor, and it is expressed in various rice organs. The qSYL3-k allele increases SYL via the elongation of cell length in the style, which is associated with a higher GA4 content in the pistil. The expression level of OsGA3ox2 in pistils with qSYL3-k alleles is significantly higher than that in pistils with qSYL3-n allele on the same genome background of Nipponbare. The yield of F1 seeds harvested from plants with 7001SSYL3-k alleles was 16% higher than that from plants with 7001SSYL3-n allele. The sequence data at the qSYL3 locus in 136 accessions showed that alleles containing the haplotypes qSYL3AA, qSYL3AG, and qSYL3GA increased SYL, whereas those containing the haplotype qSYL3GG decreased it. The frequency of the haplotype qSYL3GG increases gradually from the south to north in the northern hemisphere. These findings will facilitate improvement in SYL and yield of F1 seeds henceforward.
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Affiliation(s)
- Xiaojing Dang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Yuanqing Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yulong Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Siqi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Erbao Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bingjie Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qiangming Liu
- Special Crop Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing, 402160, China
| | - Dong She
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhiyao Dong
- Department of Student Affairs, Jilin Normal University, Siping, 136000, Jilin, China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Dalu Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hui Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shangshang Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoxiao Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanhui Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianhua Jiang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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9
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Prahalada GD, Marathi B, Vinarao R, Kim SR, Diocton R, Ramos J, Jena KK. QTL Mapping of a Novel Genomic Region Associated with High Out-Crossing Rate Derived from Oryza longistaminata and Development of New CMS Lines in Rice, O. sativa L. RICE (NEW YORK, N.Y.) 2021; 14:80. [PMID: 34529158 PMCID: PMC8446144 DOI: 10.1186/s12284-021-00521-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/30/2021] [Indexed: 05/27/2023]
Abstract
High seed cost due to poor seed yield severely limits the adoption of hybrid rice by farmers. Increasing the out-crossing rate is one of the key strategies to increase hybrid seed production. Out-crossing rate is highly influenced by the size of female floral traits, which capture pollen grains from male donor plants. In the current study, we identified 14 QTLs derived from the perennial wild rice Oryza longistaminata by composite interval mapping for five key floral traits: stigma length (five), style length (three), stigma breadth (two), stigma area (one), and pistil length (three). QTL analysis and correlation studies revealed that these stigma traits were positively correlated and pleiotropic to the stigma length trait. We selected the major-effect QTL qSTGL8.0 conferring long stigma phenotype for further fine mapping and marker-assisted selection. The qSTGL8.0 (~ 3.9 Mb) was fine mapped using newly developed internal markers and was narrowed down to ~ 2.9 Mb size (RM7356-RM256 markers). Further, the flanking markers were validated in a segregating population and in progenies from different genetic backgrounds. The markers PA08-03 and PA08-18 showed the highest co-segregation with the stigma traits. The qSTGL8.0 was introgressed into two cytoplasmic male sterile (CMS) lines, IR58025A and IR68897A, by foreground, background, and trait selection approaches. The qSTGL8.0 introgression lines in CMS backgrounds showed a significantly higher seed setting rate (2.5-3.0-fold) than the original CMS lines in test crosses with their corresponding maintainer lines. The newly identified QTLs especially qSTGL8.0, will be quite useful for increasing out-crossing rate and this will contribute to increase seed production and decrease seed cost.
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Affiliation(s)
- G D Prahalada
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Balram Marathi
- PJ Telangana State Agricultural University, Hyderabad, Telangana, 500030, India
| | - Ricky Vinarao
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Sung-Ryul Kim
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Reynaldo Diocton
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Joie Ramos
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Kshirod K Jena
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India.
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10
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Tan Q, Wang C, Luan X, Zheng L, Ni Y, Yang W, Yang Z, Zhu H, Zeng R, Liu G, Wang S, Zhang G. Dissection of closely linked QTLs controlling stigma exsertion rate in rice by substitution mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1253-1262. [PMID: 33492412 PMCID: PMC7973394 DOI: 10.1007/s00122-021-03771-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/09/2021] [Indexed: 05/18/2023]
Abstract
Through substitution mapping strategy, two pairs of closely linked QTLs controlling stigma exsertion rate were dissected from chromosomes 2 and 3 and the four QTLs were fine mapped. Stigma exsertion rate (SER) is an important trait affecting the outcrossing ability of male sterility lines in hybrid rice. This complex trait was controlled by multiple QTLs and affected by environment condition. Here, we dissected, respectively, two pairs of tightly linked QTLs for SER on chromosomes 2 and 3 by substitution mapping. On chromosome 2, two linkage QTLs, qSER-2a and qSER-2b, were located in the region of 1288.0 kb, and were, respectively, delimited to the intervals of 234.9 kb and 214.3 kb. On chromosome 3, two QTLs, qSER-3a and qSER-3b, were detected in the region of 3575.5 kb and were narrowed down to 319.1 kb and 637.3 kb, respectively. The additive effects of four QTLs ranged from 7.9 to 9.0%. The epistatic effect produced by the interaction of qSER-2a and qSER-2b was much greater than that of qSER-3a and qSER-3b. The open reading frames were identified within the maximum intervals of qSER-2a, qSER-2b and qSER-3a, respectively. These results revealed that there are potential QTL clusters for SER in the two regions of chromosome 2 and chromosome 3. Fine mapping of the QTLs laid a foundation for cloning of the genes of SER.
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Affiliation(s)
- Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Chengshu Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Xin Luan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Lingjie Zheng
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Yuerong Ni
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Ruizhen Zeng
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
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11
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Abebrese SO, Amoah NKA, Dartey PKA, Bimpong IK, Akromah R, Gracen VE, Offei SK, Danquah EY. Mapping chromosomal regions associated with anther indehiscence with exerted stigmas in CRI-48 and Jasmine 85 cross of rice ( Oryza sativa L). Heliyon 2021; 7:e06483. [PMID: 33763616 PMCID: PMC7973294 DOI: 10.1016/j.heliyon.2021.e06483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/07/2020] [Accepted: 03/08/2021] [Indexed: 11/18/2022] Open
Abstract
Anther indehiscence in certain wide crosses combines male sterility with stigma exertion, a phenomenon that is desirable for hybrid rice seed production. This study sought to identify chromosomal region(s) that combine anther indehiscence with exerted stigmas. A mapping population consisting of 189 BC1F1 plants was derived from a cross between CRI-48 and Jasmine 85 and backcrossing the resulting F1 to Jasmine 85. Contrary to the three complementary genes mode of inheritance reported earlier, a single locus (AI6-1) was mapped on chromosome 6 at 27.4 cM for anther indehiscence with exerted stigmas through a mixed model-based composite interval mapping (MCIM). This locus was flanked by two single nucleotide polymorphism (SNP) markers, K_ID6002884 and K_ID6003341 within a range of 23.1-28.9 cM. The allele at the locus was contributed by the CRI-48 parent which has Oryza glaberrima ancestry. This locus is suggested to control anther indehiscence and stigma exertion through pleiotropic gene action or cluster of genes.
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Affiliation(s)
| | - Nana Kofi Abaka Amoah
- Africa Rice Centre, Headquarters, M'bé Research Station. 01 B.P 2551, Bouaké o1, Cote d’Ivoire
| | | | - Isaac Kofi Bimpong
- Africa Rice Centre, Headquarters, M'bé Research Station. 01 B.P 2551, Bouaké o1, Cote d’Ivoire
| | | | | | - Samuel Kwame Offei
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
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12
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Dang X, Yang Y, Zhang Y, Chen X, Fan Z, Liu Q, Ji J, Li D, Li Y, Fang B, Wu Z, Liu E, Hu X, Zhu S, She D, Wang H, Li Y, Chen S, Wu Y, Hong D. OsSYL2 AA , an allele identified by gene-based association, increases style length in rice (Oryza sativa L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1491-1503. [PMID: 33031564 PMCID: PMC7821000 DOI: 10.1111/tpj.15013] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/10/2020] [Accepted: 09/18/2020] [Indexed: 06/01/2023]
Abstract
Stigma characteristics are important factors affecting the seed yield of hybrid rice per unit area. Natural variation of stigma characteristics has been reported in rice, but the genetic basis for this variation is largely unknown. We performed a genome-wide association study on three stigma characteristics in six environments using 1.3 million single-nucleotide polymorphism (SNPs) characterized in 353 diverse accessions of Oryza sativa. An abundance of phenotypic variation was present in the three stigma characteristics of these collections. We identified four significant SNPs associated with stigma length, 20 SNPs with style length (SYL), and 17 SNPs with the sum of stigma and style length, which were detected repeatedly in more than four environments. Of these SNPs, 28 were novel. We identified two causal gene loci for SYL, OsSYL3 and OsSYL2; OsSYL3 was co-localized with the grain size gene GS3. The SYL of accessions carrying allele OsSYL3AA was significantly longer than that of those carrying allele OsSYL3CC . We also demonstrated that the outcrossing rate of female parents carrying allele OsSYL2AA increased by 5.71% compared with that of the isogenic line carrying allele OsSYL2CC in an F1 hybrid seed production field. The allele frequencies of OsSYL3AA and OsSYL2AA decreased gradually with an increase in latitude in the Northern Hemisphere. Our results should facilitate the improvement in stigma characteristics of parents of hybrid rice.
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Affiliation(s)
- Xiaojing Dang
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Yang Yang
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Yuanqing Zhang
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Xiangong Chen
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Zhilan Fan
- Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou510640China
| | - Qiangming Liu
- Special Crop Research InstituteChongqing Academy of Agricultural SciencesChongqing402160China
| | - Jie Ji
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Dalu Li
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai200240China
| | - Yanhui Li
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Bingjie Fang
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Zexu Wu
- Key Laboratory of Crop Germplasm of Zhejiang ProvinceInstitute of Crop ScienceZhejiang UniversityHangzhou310058China
| | - Erbao Liu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Xiaoxiao Hu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Shangshang Zhu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Dong She
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Hui Wang
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Yulong Li
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Siqi Chen
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Yufeng Wu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
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13
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Lin Y, Laosatit K, Chen J, Yuan X, Wu R, Amkul K, Chen X, Somta P. Mapping and Functional Characterization of Stigma Exposed 1, a DUF1005 Gene Controlling Petal and Stigma Cells in Mungbean ( Vigna radiata). FRONTIERS IN PLANT SCIENCE 2020; 11:575922. [PMID: 33329637 PMCID: PMC7710877 DOI: 10.3389/fpls.2020.575922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/22/2020] [Indexed: 05/23/2023]
Abstract
Flowers with exposed stigma increase the outcrossing rate and are useful in developing improved hybrid crop cultivars. This exposure results mainly from the cellular morphology of the petal and pistil, but what affects the formation of the petal and pistil in the late developmental stages is less understood. Here, we characterized a novel floral mutant in mungbean (Vigna radiata), stigma exposed 1 (se1), which displays irregular petals and pistils. Floral organ initiation in the se1 mutant was normal, but petal and pistil growth malfunctioned during late development. A histological analysis revealed that the se1 mutant had wrinkled petals with knotted structures and elongated styles. The cellular morphology of the epidermal layers of the se1 petals was deformed, while the cell lengths in the styles increased. A genetic analysis indicated that the se1 phenotype is controlled by a single recessive gene, and it was mapped to chromosome 11. A sequence analysis suggested that a DUF1005-encoding gene, LOC106777793, is the gene controlling the se1 phenotype. The se1 mutant possessed a single-nucleotide polymorphism that resulted in an amino acid change in VrDUF1005. Overexpression of VrDUF1005 in Arabidopsis resulted in rolling leaves and reduced floral size. Consequently, we proposed that VrSE1 functions to modulate cell division in petals and cell expansion in styles during the late developmental stages in mungbean. The se1 mutant is a new genetic resource for mung bean hybrid breeding.
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Affiliation(s)
- Yun Lin
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Jingbin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ranran Wu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Kitiya Amkul
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, Thailand
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14
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Tan Q, Zou T, Zheng M, Ni Y, Luan X, Li X, Yang W, Yang Z, Zhu H, Zeng R, Liu G, Wang S, Fu X, Zhang G. Substitution Mapping of the Major Quantitative Trait Loci Controlling Stigma Exsertion Rate from Oryza glumaepatula. RICE (NEW YORK, N.Y.) 2020; 13:37. [PMID: 32519122 PMCID: PMC7283377 DOI: 10.1186/s12284-020-00397-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/27/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Stigma exsertion rate (SER) is a key determinant for the outcrossing ability of male sterility lines (MSLs) in hybrid rice seed production. In the process of domestication, the outcrossing ability of cultivated rice varieties decreased, while that of wild Oryza species kept strong. Here, we detected the quantitative trait loci (QTLs) controlling SER using a set of single-segment substitution lines (SSSLs) derived from O. glumaepatula, a wild Oryza species. RESULTS Seven QTLs for SER were located on 5 chromosomes. qSER-1a and qSER-1b were located on chromosome 1. qSER-3a and qSER-3b were mapped on chromosome 3, and qSER-3b was further located at an estimated interval of 898.8 kb by secondary substitution mapping. qSER-5, qSER-9 and qSER-10 were identified on chromosomes 5, 9 and 10, respectively, and qSER-9 was delimited to an estimated region of 551.9 kb by secondary substitution mapping. The additive effects of the 7 QTLs ranged from 10.6% to 14.8%, which were higher than those of most loci for SER reported previously. CONCLUSIONS qSER-1a and qSER-1b are novel loci for SER on chromosome 1. All of the 7 QTLs have major effects on SER. The major QTLs of SER will help to develop MSLs with strong outcrossing ability.
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Affiliation(s)
- Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Tuo Zou
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Mingmin Zheng
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Yuerong Ni
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Xin Luan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaohui Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Ruizhen Zeng
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Xuelin Fu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
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Liu Y, Zhang A, Wang F, Kong D, Li M, Bi J, Zhang F, Wang J, Luo X, Pan Z, Yu X, Liu G, Luo L. Fine mapping a quantitative trait locus, qSER-7, that controls stigma exsertion rate in rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2019; 12:46. [PMID: 31289958 PMCID: PMC6616572 DOI: 10.1186/s12284-019-0304-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/14/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Stigma exsertion rate (SER) is a key determinant of outcrossing in hybrid rice seed production. A quantitative trait locus (QTL) for stigma exsertion rate in rice, qSER-7, has previously been detected on chromosome 7 by using a F2 population derived from two indica cytoplasmic male sterility (CMS) maintainers, Huhan 1B and II-32B. RESULTS The chromosomal location of qSER-7 was precisely delimited by fine-scale mapping. Near-isogenic lines (NILs) were established, one of which isolated the locus in the qSER-7II-32B line, which contains an introgressed segment of II-32B in the Huhan 1B genetic background, and exhibits a significantly higher stigma exsertion rate than that of the recurrent parent. Using 3192 individuals from the BC4F2 segregation population, the QTL qSER-7 was narrowed down to a 28.4-kb region between the markers RM3859 and Indel4373 on chromosome 7. According to the rice genome annotation database, three genes were predicted within the target region. Real-time PCR analysis showed significantly higher expression levels of LOC_Os07g15370 and LOC_Os07g15390 in II-32B than in Huhan 1B. LOC_Os07g15370(OsNRAMP5) was a previously reported gene for Mn and Cd transporter. The stigma exertion rates of OsNRAMP5-overexpressing plants were significantly higher than that of wild type plants, in contrast, a T-DNA insertion mutant osnramp5 showed a lower stigma exertion rate. CONCLUSIONS In the present study, the QTL qSER-7 was isolated to a region between the markers RM3859 and Indel4373. Two candidate genes were selected based on the expression difference between the two parents, which can facilitate the further cloning of the gene underlying the quantitative trait associated with qSER-7 as well as the marker-assisted transfer of desirable genes for stigma exsertion rate improvement in rice.
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Affiliation(s)
- Yi Liu
- Huazhong agricultural university, Wuhan, 430070, People's Republic of China
- Shanghai agrobiological gene center, Shanghai, 201106, People's Republic of China
| | - Anning Zhang
- Huazhong agricultural university, Wuhan, 430070, People's Republic of China
- Shanghai agrobiological gene center, Shanghai, 201106, People's Republic of China
| | - Feiming Wang
- Shanghai agrobiological gene center, Shanghai, 201106, People's Republic of China
| | - Deyan Kong
- Shanghai agrobiological gene center, Shanghai, 201106, People's Republic of China
| | - Mingshou Li
- Shanghai agrobiological gene center, Shanghai, 201106, People's Republic of China
| | - Junguo Bi
- Shanghai agrobiological gene center, Shanghai, 201106, People's Republic of China
| | - Fenyun Zhang
- Shanghai agrobiological gene center, Shanghai, 201106, People's Republic of China
| | - Jiahong Wang
- Shanghai agrobiological gene center, Shanghai, 201106, People's Republic of China
| | - Xingxing Luo
- Shanghai agrobiological gene center, Shanghai, 201106, People's Republic of China
| | - Zhongquan Pan
- Shanghai agrobiological gene center, Shanghai, 201106, People's Republic of China
| | - Xinqiao Yu
- Shanghai agrobiological gene center, Shanghai, 201106, People's Republic of China
| | - Guolan Liu
- Shanghai agrobiological gene center, Shanghai, 201106, People's Republic of China.
| | - Lijun Luo
- Huazhong agricultural university, Wuhan, 430070, People's Republic of China.
- Shanghai agrobiological gene center, Shanghai, 201106, People's Republic of China.
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qSE7 is a major quantitative trait locus (QTL) influencing stigma exsertion rate in rice (Oryza sativa L.). Sci Rep 2018; 8:14523. [PMID: 30266907 PMCID: PMC6162257 DOI: 10.1038/s41598-018-32629-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 09/03/2018] [Indexed: 11/09/2022] Open
Abstract
Stigma exsertion is a key determinant to increase the efficiency of commercial hybrid rice seed production. The major quantitative trait locus (QTL) qSE7 for stigma exsertion rate was previously detected on the chromosome 7 using 75 Chromosome Segment Substitution Lines (CSSLs) derived from a cross between the high stigma exsertion indica maintainer XieqingzaoB (XQZB) and low stigma exsertion indica restorer Zhonghui9308 (ZH9308). The C51 line, a CSSL population with an introgression from XQZB, was backcrossed with ZH9308 to produce the secondary F2 (BC5F2) and F2:3 (BC5F2:3) populations. As a result, the Near Isogenic Line (NIL qSE7XB) was developed. Analysis indicated qSE7 acted as a single Mendelian factor and decreased the stigma exsertion. We hypothesized qSE7 regulates single, dual, and total stigma exsertion rate, provided experimental support. qSE7 was mapped and localized between RM5436 and RM5499 markers, within a physical distance of 1000-kb. With use of new insertion-deletion (InDel) markers and analysis of the heterozygous and phenotypic data, it was ultimately dissected to a 322.9-kb region between InDel SER4-1 and RM5436. The results are useful for additional identification and isolation of this candidate gene controlling stigma exsertion rate, and provide a basis for further fine mapping, gene cloning, and Marker Assisted Selection (MAS) breeding later.
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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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Zhou H, Li P, Xie W, Hussain S, Li Y, Xia D, Zhao H, Sun S, Chen J, Ye H, Hou J, Zhao D, Gao G, Zhang Q, Wang G, Lian X, Xiao J, Yu S, Li X, He Y. Genome-wide Association Analyses Reveal the Genetic Basis of Stigma Exsertion in Rice. MOLECULAR PLANT 2017; 10:634-644. [PMID: 28110091 DOI: 10.1016/j.molp.2017.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/27/2016] [Accepted: 01/05/2017] [Indexed: 05/11/2023]
Abstract
Stigma exsertion, a key determinant of the rice mating system, greatly contributes to the application of heterosis in rice. Although a few quantitative trait loci associated with stigma exsertion have been fine mapped or cloned, the underlying genetic architecture remains unclear. We performed a genome-wide association study on stigma exsertion and related floral traits using 6.5 million SNPs characterized in 533 diverse accessions of Oryza sativa. We identified 23 genomic loci that are significantly associated with stigma exsertion and related traits, three of which are co-localized with three major grain size genes GS3, GW5, and GW2. Further analyses indicated that these three genes affected the stigma exsertion by controlling the size and shape of the spikelet and stigma. Combinations of GS3 and GW5 largely defined the levels of stigma exsertion and related traits. Selections of these two genes resulted in specific distributions of floral traits among subpopulations of O. sativa. The low stigma exsertion combination gw5GS3 existed in half of the cultivated rice varieties; therefore, introducing the GW5gs3 combination into male sterile lines is of high potential for improving the seed production of hybrid rice.
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Affiliation(s)
- Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Pingbo Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Saddam Hussain
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yibo Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Duo Xia
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Shengyuan Sun
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Junxiao Chen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hong Ye
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Hou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Da Zhao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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Rahman MH, Zhang Y, Zhang K, Rahman MS, Barman HN, Riaz A, Chen Y, Wu W, Zhan X, Cao L, Cheng S. Genetic Dissection of the Major Quantitative Trait Locus (qSE11), and Its Validation As the Major Influence on the Rate of Stigma Exsertion in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1818. [PMID: 29163563 PMCID: PMC5666294 DOI: 10.3389/fpls.2017.01818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 10/06/2017] [Indexed: 05/11/2023]
Abstract
The rate of stigma exsertion (SE) is an important trait in rice breeding because the efficiency of hybrid rice seed production can be improved by increasing the percentage of stigmas that exsert. In this study, we developed a near isogenic line (NIL) from two parents, XieqingzaoB (XQZB) and Zhonghoi9308 (ZH9308), which have high and low SE rates in that order. In our previous study, we employed 75 chromosome segment substitution lines (CSSLs) and analyzed quantitative trait loci (QTLs) for their influence on SE rate. The single gene QTL (qSE11), which is located on chromosome 11, was responsible for this trait. In this study, we focused on one of the CSSLs (C65), namely, the NIL (qSE11XB). It contains an introgression segment of XQZB in the genetic background of ZH9308, and exhibits a significantly higher SE rate than that of the parents. We demonstrated that qSE11 regulated both the single and the dual SE rates. They both contribute to the total SE rate. Genetic analysis revealed that qSE11 acted as a single Mendelian factor and that the allele from XQZB increased the SE rate. The validity of our conclusions was established when C65 was used to develop secondary F2 (BC5F2) and F2:3 (BC5F2:3) populations by backcrossing to ZH9308, with subsequent selfing. We entered 3600 plants from the F2 population and 3200 from the F2:3 populations into a genetic dissection program and dissected the major QTL qSE11 to a 350.7-kb region located on chromosome 11. This study will contribute to the future isolation of candidate genes of SE and will play a vital role in future hybrid rice seed production programs.
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Affiliation(s)
- Md Habibur Rahman
- Crop Genetics and Breeding, China National Rice Research Institute, Hangzhou, China
- Department of Agricultural Extension, Ministry of Agriculture, Dhaka, Bangladesh
| | - Yingxing Zhang
- Crop Genetics and Breeding, China National Rice Research Institute, Hangzhou, China
| | - Keqin Zhang
- Crop Genetics and Breeding, China National Rice Research Institute, Hangzhou, China
| | - Md Sazzadur Rahman
- Plant Physiology Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - Hirendra N. Barman
- Crop Genetics and Breeding, China National Rice Research Institute, Hangzhou, China
- Plant Physiology Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - Aamir Riaz
- Crop Genetics and Breeding, China National Rice Research Institute, Hangzhou, China
| | - Yuyu Chen
- Crop Genetics and Breeding, China National Rice Research Institute, Hangzhou, China
| | - Weixun Wu
- Crop Genetics and Breeding, China National Rice Research Institute, Hangzhou, China
| | - Xiaodeng Zhan
- Crop Genetics and Breeding, China National Rice Research Institute, Hangzhou, China
| | - Liyong Cao
- Crop Genetics and Breeding, China National Rice Research Institute, Hangzhou, China
- *Correspondence: Liyong Cao, Shihua Cheng,
| | - Shihua Cheng
- Crop Genetics and Breeding, China National Rice Research Institute, Hangzhou, China
- *Correspondence: Liyong Cao, Shihua Cheng,
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20
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Zhang X, Guo B, Lan G, Li H, Lin S, Ma J, Lv C, Xu R. A Major QTL, Which Is Co-located with cly1, and Two Minor QTLs Are Associated with Glume Opening Angle in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2016; 7:1585. [PMID: 27822223 PMCID: PMC5075565 DOI: 10.3389/fpls.2016.01585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/07/2016] [Indexed: 05/25/2023]
Abstract
Cleistogamous and chasmogamous are two opposing phenomena for flowering in barley. Cleistogamy limits the rate of outcrossing, and increases the cost of producing hybrid barley seeds. Selecting chasmogamous lines with a large glume opening angle (GOA) is essential for the utilization of barley heterosis. In the current study, 247 DH lines derived from a cross between Yangnongpi7 and Yang0187 were used to identify and validate quantitative trait loci (QTLs) associated with the GOA in different environments using SSR markers. Three QTLs associated with barley GOA were mapped on chromosomes 2H and 7H. The major QTL QGOA-2H-2 was mapped on chromosome 2H with the flanking markers of KDH and GBM1498, explaining 63.92% of the phenotypic variation. The marker KDH was developed from the gene Cly1, which was the candidate gene for QGOA-2H-2. This new marker can be used to identify barley chasmogamous lines with a large GOA. The two minor QTLs were validated at all three locations across two seasons after removing DH lines carrying the candidate gene Cly1 of QGOA-2H-2.
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Affiliation(s)
- XinZhong Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou UniversityYangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
- Institute of Barley Research, Yangzhou UniversityYangzhou, China
| | - BaoJian Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou UniversityYangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
- Institute of Barley Research, Yangzhou UniversityYangzhou, China
| | - GuoFang Lan
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou UniversityYangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
- Institute of Barley Research, Yangzhou UniversityYangzhou, China
| | - HongTao Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou UniversityYangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
- Institute of Barley Research, Yangzhou UniversityYangzhou, China
| | - Shen Lin
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou UniversityYangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
- Institute of Barley Research, Yangzhou UniversityYangzhou, China
| | - Jun Ma
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou UniversityYangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
- Institute of Barley Research, Yangzhou UniversityYangzhou, China
| | - Chao Lv
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou UniversityYangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
- Institute of Barley Research, Yangzhou UniversityYangzhou, China
| | - RuGen Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou UniversityYangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
- Institute of Barley Research, Yangzhou UniversityYangzhou, China
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Dang X, Liu E, Liang Y, Liu Q, Breria CM, Hong D. QTL Detection and Elite Alleles Mining for Stigma Traits in Oryza sativa by Association Mapping. FRONTIERS IN PLANT SCIENCE 2016; 7:1188. [PMID: 27555858 PMCID: PMC4977947 DOI: 10.3389/fpls.2016.01188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/22/2016] [Indexed: 05/20/2023]
Abstract
Stigma traits are very important for hybrid seed production in Oryza sativa, which is a self-pollinated crop; however, the genetic mechanism controlling the traits is poorly understood. In this study, we investigated the phenotypic data of 227 accessions across 2 years and assessed their genotypic variation with 249 simple sequence repeat (SSR) markers. By combining phenotypic and genotypic data, a genome-wide association (GWA) map was generated. Large phenotypic variations in stigma length (STL), stigma brush-shaped part length (SBPL) and stigma non-brush-shaped part length (SNBPL) were found. Significant positive correlations were identified among stigma traits. In total, 2072 alleles were detected among 227 accessions, with an average of 8.3 alleles per SSR locus. GWA mapping detected 6 quantitative trait loci (QTLs) for the STL, 2 QTLs for the SBPL and 7 QTLs for the SNBPL. Eleven, 5, and 12 elite alleles were found for the STL, SBPL, and SNBPL, respectively. Optimal cross designs were predicted for improving the target traits. The detected genetic variation in stigma traits and QTLs provides helpful information for cloning candidate STL genes and breeding rice cultivars with longer STLs in the future.
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Affiliation(s)
- Xiaojing Dang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Erbao Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Yinfeng Liang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Qiangming Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural UniversityNanjing, China; Rice Research Institute, Chongqing Academy of Agricultural SciencesChongqing, China
| | - Caleb M Breria
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University Nanjing, China
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Liu Q, Qin J, Li T, Liu E, Fan D, Edzesi WM, Liu J, Jiang J, Liu X, Xiao L, Liu L, Hong D. Fine Mapping and Candidate Gene Analysis of qSTL3, a Stigma Length-Conditioning Locus in Rice (Oryza sativa L.). PLoS One 2015; 10:e0127938. [PMID: 26030903 PMCID: PMC4452489 DOI: 10.1371/journal.pone.0127938] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 04/21/2015] [Indexed: 11/19/2022] Open
Abstract
The efficiency of hybrid seed production can be improved by increasing the percentage of exserted stigma, which is closely related to the stigma length in rice. In the chromosome segment substitute line (CSSL) population derived from Nipponbare (recipient) and Kasalath (donor), a single CSSL (SSSL14) was found to show a longer stigma length than that of Nipponbare. The difference in stigma length between Nipponbare and SSSL14 was controlled by one locus (qSTL3). Using 7,917 individuals from the SSSL14/Nipponbare F2 population, the qSTL3 locus was delimited to a 19.8-kb region in the middle of the short arm of chromosome 3. Within the 19.8-kb chromosome region, three annotated genes (LOC_Os03g14850, LOC_Os03g14860 and LOC_Os03g14880) were found in the rice genome annotation database. According to gene sequence alignments in LOC_Os03g14850, a transition of G (Nipponbare) to A (Kasalath) was detected at the 474-bp site in CDS. The transition created a stop codon, leading to a deletion of 28 amino acids in the deduced peptide sequence in Kasalath. A T-DNA insertion mutant (05Z11CN28) of LOC_Os03g14850 showed a longer stigma length than that of wild type (Zhonghua 11), validating that LOC_Os03g14850 is the gene controlling stigma length. However, the Kasalath allele of LOC_Os03g14850 is unique because all of the alleles were the same as that of Nipponbare at the 474-bp site in the CDS of LOC_Os03g14850 among the investigated accessions with different stigma lengths. A gene-specific InDel marker LQ30 was developed for improving stigma length during rice hybrid breeding by marker-assisted selection.
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Affiliation(s)
- Qiangming Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiancai Qin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tianwei Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Erbao Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dejia Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wisdom Mawuli Edzesi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianhai Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianhua Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Xiaoli Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lianjie Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Linglong Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- * E-mail:
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23
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Iwata H, Ebana K, Uga Y, Hayashi T. Genomic prediction of biological shape: elliptic Fourier analysis and kernel partial least squares (PLS) regression applied to grain shape prediction in rice (Oryza sativa L.). PLoS One 2015; 10:e0120610. [PMID: 25825876 PMCID: PMC4380318 DOI: 10.1371/journal.pone.0120610] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/29/2015] [Indexed: 12/16/2022] Open
Abstract
Shape is an important morphological characteristic both in animals and plants. In the present study, we examined a method for predicting biological contour shapes based on genome-wide marker polymorphisms. The method is expected to contribute to the acceleration of genetic improvement of biological shape via genomic selection. Grain shape variation observed in rice (Oryza sativa L.) germplasms was delineated using elliptic Fourier descriptors (EFDs), and was predicted based on genome-wide single nucleotide polymorphism (SNP) genotypes. We applied four methods including kernel PLS (KPLS) regression for building a prediction model of grain shape, and compared the accuracy of the methods via cross-validation. We analyzed multiple datasets that differed in marker density and sample size. Datasets with larger sample size and higher marker density showed higher accuracy. Among the four methods, KPLS showed the highest accuracy. Although KPLS and ridge regression (RR) had equivalent accuracy in a single dataset, the result suggested the potential of KPLS for the prediction of high-dimensional EFDs. Ordinary PLS, however, was less accurate than RR in all datasets, suggesting that the use of a non-linear kernel was necessary for accurate prediction using the PLS method. Rice grain shape can be predicted accurately based on genome-wide SNP genotypes. The proposed method is expected to be useful for genomic selection in biological shape.
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Affiliation(s)
- Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
- * E-mail:
| | - Kaworu Ebana
- Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Yusaku Uga
- Agronomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Takeshi Hayashi
- Agroinformatics Division, National Agricultural Research Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
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Severa L. Shape and strength of Red Haven peaches at the different stages of their maturity. ACTA UNIVERSITATIS AGRICULTURAE ET SILVICULTURAE MENDELIANAE BRUNENSIS 2014. [DOI: 10.11118/actaun200856040161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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25
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Mano Y, Omori F. Flooding tolerance in interspecific introgression lines containing chromosome segments from teosinte (Zea nicaraguensis) in maize (Zea mays subsp. mays). ANNALS OF BOTANY 2013; 112:1125-39. [PMID: 23877074 PMCID: PMC3783227 DOI: 10.1093/aob/mct160] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 05/31/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Nicaraguan teosinte (Zea nicaraguensis), a species found in frequently flooded areas, provides useful germplasm for breeding flooding-tolerant maize (Z. mays subsp. mays). The objective of this study was to select flooding-tolerant lines using a library of introgression lines (ILs), each containing a chromosome segment from Z. nicaraguensis in the maize inbred line Mi29. METHODS To produce the ILs, a single F1 plant derived from a cross between maize Mi29 and Z. nicaraguensis was backcrossed to Mi29 three times, self-pollinated four times and genotyped using simple sequence repeat markers. Flooding tolerance was evaluated at the seedling stage under reducing soil conditions. KEY RESULTS By backcrossing and selfing, a series of 45 ILs were developed covering nearly the entire maize genome. Five flooding-tolerant lines were identified from among the ILs by evaluating leaf injury. Among these, line IL#18, containing a Z. nicaraguensis chromosome segment on the long arm of chromosome 4, showed the greatest tolerance to flooding, suggesting the presence of a major quantitative trait locus (QTL) in that region. The presence of the QTL was verified by examining flooding tolerance in a population segregating for the candidate region of chromosome 4. There was no significant relationship between the capacity to form constitutive aerenchyma and flooding tolerance in the ILs, indicating the presence of other factors related to flooding tolerance under reducing soil conditions. CONCLUSIONS A flooding-tolerant genotype, IL#18, was identified; this genotype should be useful for maize breeding. In addition, because the chromosome segments of Z. nicaraguensis in the ILs cover nearly the entire genome and Z. nicaraguensis possesses several unique traits related to flooding tolerance, the ILs should be valuable material for additional QTL detection and the development of flooding-tolerant maize lines.
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Affiliation(s)
- Y. Mano
- Forage Crop Research Division, NARO Institute of Livestock and Grassland Science, 768 Senbonmatsu, Nasushiobara, Tochigi 329-2793, Japan
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26
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Takano-Kai N, Doi K, Yoshimura A. GS3 participates in stigma exsertion as well as seed length in rice. BREEDING SCIENCE 2011; 61:244-250. [PMID: 0 DOI: 10.1270/jsbbs.61.244] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Affiliation(s)
- Noriko Takano-Kai
- Plant Breeding Laboratory, Faculty of Agriculture, Graduate School, Kyushu University
| | - Kazuyuki Doi
- Plant Breeding Laboratory, Faculty of Agriculture, Graduate School, Kyushu University
- Present address: Graduate School of Bioagricultural Sciences, Nagoya University
| | - Atsushi Yoshimura
- Plant Breeding Laboratory, Faculty of Agriculture, Graduate School, Kyushu University
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Dwivedi SL, Perotti E, Upadhyaya HD, Ortiz R. Sexual and apomictic plant reproduction in the genomics era: exploring the mechanisms potentially useful in crop plants. ACTA ACUST UNITED AC 2010; 23:265-79. [PMID: 20509033 DOI: 10.1007/s00497-010-0144-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Accepted: 05/11/2010] [Indexed: 11/26/2022]
Abstract
Arabidopsis, Mimulus and tomato have emerged as model plants in researching genetic and molecular basis of differences in mating systems. Variations in floral traits and loss of self-incompatibility have been associated with mating system differences in crops. Genomics research has advanced considerably, both in model and crop plants, which may provide opportunities to modify breeding systems as evidenced in Arabidopsis and tomato. Mating system, however, not recombination per se, has greater effect on the level of polymorphism. Generating targeted recombination remains one of the most important factors for crop genetic enhancement. Asexual reproduction through seeds or apomixis, by producing maternal clones, presents a tremendous potential for agriculture. Although believed to be under simple genetic control, recent research has revealed that apomixis results as a consequence of the deregulation of the timing of sexual events rather than being the product of specific apomixis genes. Further, forward genetic studies in Arabidopsis have permitted the isolation of novel genes reported to control meiosis I and II entry. Mutations in these genes trigger the production of unreduced or apomeiotic megagametes and are an important step toward understanding and engineering apomixis.
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Affiliation(s)
- Sangam L Dwivedi
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502324 AP, India.
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28
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Yan WG, Li Y, Agrama HA, Luo D, Gao F, Lu X, Ren G. Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2009; 24:277-292. [PMID: 20234878 PMCID: PMC2837221 DOI: 10.1007/s11032-009-9290-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2008] [Accepted: 04/27/2009] [Indexed: 05/20/2023]
Abstract
Stigma and spikelet characteristics play an essential role in hybrid seed production. A mini-core of 90 accessions developed from USDA rice core collection was phenotyped in field grown for nine traits of stigma and spikelet and genotyped with 109 DNA markers, 108 SSRs plus an indel. Three major clusters were built upon Rogers' genetic distance, indicative of indicas, and temperate and tropical japonicas. A mixed linear model combining PC-matrix and K-matrix was adapted for mapping marker-trait associations. Resulting associations were adjusted using false discovery rate technique. We identified 34 marker-trait associations involving 22 SSR markers for eight traits. Four markers were associated with single stigma exsertion (SStgE), six with dual exsertion (DStgE) and five with total exsertion. RM5_Chr1 played major role indicative of high regression with not only DStgE but also SStgE. Four markers were associated with spikelet length, three with width and seven with L/W ratio. Numerous markers were co-associated with multiple traits that were phenotypically correlated, i.e. RM12521_Chr2 associated with all three correlated spikelet traits. The co-association should improve breeding efficiency because single marker could be used to assist breeding for multiple traits. Indica entry 1032 (cultivar 50638) and japonica entry 671 (cultivar Linia 84 Icar) with 80.65 and 75.17% of TStgE, respectively are recommended to breeder for improving stigma exsertion. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-009-9290-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wen Gui Yan
- Dale Bumpers National Rice Research Center, United States Department of Agriculture, Agricultural Research Service, 2890 Highway 130 East, Stuttgart, AR 72160 USA
| | - Yong Li
- Sichuan Academy of Agricultural Sciences, No. 20 Jingjusi Road, 610066 Chengdu, Sichuan China
| | - Hesham A. Agrama
- Rice Research and Extension Center, University of Arkansas, 2890 Highway 130 East, Stuttgart, AR 72160 USA
| | - Dagang Luo
- Sichuan Academy of Agricultural Sciences, No. 20 Jingjusi Road, 610066 Chengdu, Sichuan China
| | - Fangyuan Gao
- Sichuan Academy of Agricultural Sciences, No. 20 Jingjusi Road, 610066 Chengdu, Sichuan China
| | - Xianjun Lu
- Sichuan Academy of Agricultural Sciences, No. 20 Jingjusi Road, 610066 Chengdu, Sichuan China
| | - Guangjun Ren
- Sichuan Academy of Agricultural Sciences, No. 20 Jingjusi Road, 610066 Chengdu, Sichuan China
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Yu XQ, Mei HW, Luo LJ, Liu GL, Liu HY, Zou GH, Hu SP, Li MS, Wu JH. Dissection of additive, epistatic effect and Q x E interaction of quantitative trait loci influencing stigma exsertion under water stress in rice. ACTA ACUST UNITED AC 2009; 33:542-50. [PMID: 16800385 DOI: 10.1016/s0379-4172(06)60083-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Four flowering related traits, spikelet number per panicle (SNP), percentage of single exserted stigma (PSES), dual exserted stigma (PDES) and total exserted stigma (PES) of a RI population with 185 lines under water stress and non-stress conditions for 2 years, were investigated in a drought tolerance screening facility. ANOVA results showed high significance between years, lines, and water stress treatments, together with interactions among them in pairs. Highest phenotypic correlation was found between PSES and PES (r = 0.9752***), followed by PDES and PES (r = 0.7150***), and PSES and PDES (r = 0.5424***). Based on a linkage map of 203 SSR markers, six main effect QTLs were detected for SNP and three or four main effect QTLs were associated with PSES, PDES and PES under stress or non-stress conditions. There were one to nine pairs of epistatic QTLs influencing SNP and stigma exsertion. The contribution rates of additive and epistatic effects seemed to be in a low magnitude for most cases (0.76%-9.92%) while a few QTLs or QTL pairs explained more than 10% of total variance. Some main effect QTL and epistasis were commonly detected among PSES, PDES and PES, explaining the high positive correlation between them. Few QTLs were detected under both water stress and non-stress condition, implying that drought had severe impact on the genetic behaviors of both spikelet number and stigma exsertion.
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QTL analysis of floral traits of rice (Oryza Sativa L.) under well-watered and drought stress conditions. Genes Genomics 2009. [DOI: 10.1007/bf03191150] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Sang T, Ge S. Genetics and phylogenetics of rice domestication. Curr Opin Genet Dev 2007; 17:533-8. [PMID: 17988855 DOI: 10.1016/j.gde.2007.09.005] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 09/07/2007] [Accepted: 09/20/2007] [Indexed: 11/19/2022]
Abstract
With genetically divergent cultivars and ecologically distinct wild progenitors, rice has posed a great challenge to the genetic and phylogenetic studies of the origin and evolution of crop species. A growing body of phylogenetic evidence suggested that the diverged genomic backgrounds of indica and japonica rice cultivars were derived independently from genetically distinct wild populations. However, a domestication gene, sh4, which was responsible for the reduction of grain shattering, seems to have originated only once, and it is now fixed in both cultivars. Two models have been proposed to reconcile these data. Whereas the 'combination model' emphasizes the importance of early introgression between independently domesticated cultivars, the 'snowballing model' emphasizes the importance of introgression from local populations of wild species into an ancestral domesticated population. In either case, the domestication of rice was a dynamic process.
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Affiliation(s)
- Tao Sang
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.
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New insights into the history of rice domestication. Trends Genet 2007; 23:578-87. [DOI: 10.1016/j.tig.2007.08.012] [Citation(s) in RCA: 357] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 08/16/2007] [Accepted: 08/21/2007] [Indexed: 11/18/2022]
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Goodwillie C, Ritland C, Ritland K. THE GENETIC BASIS OF FLORAL TRAITS ASSOCIATED WITH MATING SYSTEM EVOLUTION IN LEPTOSIPHON (POLEMONIACEAE): AN ANALYSIS OF QUANTITATIVE TRAIT LOCI. Evolution 2007. [DOI: 10.1111/j.0014-3820.2006.tb01131.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Carol Goodwillie
- Department of Biology, East Caroline University, Greenville, North Carolina 27858
| | - Carol Ritland
- Faculty of Forestry, The University of British Columbia, Vancounver, British Columbia V6T IZ4, Canada
| | - Kermit Ritland
- Faculty of Forestry, The University of British Columbia, Vancounver, British Columbia V6T IZ4, Canada
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Miyata M, Yamamoto T, Komori T, Nitta N. Marker-assisted selection and evaluation of the QTL for stigma exsertion under japonica rice genetic background. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:539-48. [PMID: 17131105 DOI: 10.1007/s00122-006-0454-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2006] [Accepted: 11/04/2006] [Indexed: 05/11/2023]
Abstract
Stigma exsertion is one of the important traits which contribute to the efficient improvement of commercial seed production in hybrid rice. In order to understand the genetic factors involved in the stigma exsertion of an indica variety--IR24--a QTL analysis was conducted using the F2 population between a japonica variety--Koshihikari--and a breeding line showing exserted stigma selected from the backcross population between IR24 as a donor and japonica varieties. As a result, a highly significant QTL (qES3), which had been predicted in the recombinant inbred population of IR24, was confirmed at the centromeric region on chromosome 3. qES3 increases about 20% of the frequency of the exserted stigmas at the IR24 allele and explains about 32% of the total phenotypic variance. A QTL near-isogenic line for qES3 increased the frequency of the exserted stigma by 36% compared to that of Koshihikari in a field evaluation, which suggests that qES3 is a promising QTL for the development of a maternal line for hybrid rice.
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Affiliation(s)
- Maiko Miyata
- Orynova K.K., 700 Higashibara, Iwata, Shizuoka, 438-0802, Japan
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35
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Goodwillie C, Ritland C, Ritland K. THE GENETIC BASIS OF FLORAL TRAITS ASSOCIATED WITH MATING SYSTEM EVOLUTION IN LEPTOSIPHON (POLEMONIACEAE): AN ANALYSIS OF QUANTITATIVE TRAIT LOCI. Evolution 2006. [DOI: 10.1554/05-471.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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36
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Goto S, Iwata H, Shibano S, Ohya K, Suzuki A, Ogawa H. Fruit shape variation in Fraxinus mandshurica var. japonica characterized using elliptic Fourier descriptors and the effect on flight duration. Ecol Res 2005. [DOI: 10.1007/s11284-005-0090-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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