Identifying QTLs for Grain Size in a Colossal Grain Rice (<i>Oryza sativa</i> L.) Line, and Analysis of Additive Effects of QTLs
Grain size is an important component of quality and harvest traits in the field of rice breeding. Although numerous quantitative trait loci (QTLs) of grain size in rice have been reported, the molecular mechanisms of these QTLs remain poorly understood, and further research on QTL observation and ca...
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MDPI AG
2022-03-01
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| Series: | International Journal of Molecular Sciences |
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| author | Xuanxuan Hou Moxian Chen Yinke Chen Xin Hou Zichang Jia Xue Yang Jianhua Zhang Yinggao Liu Nenghui Ye |
| author_facet | Xuanxuan Hou Moxian Chen Yinke Chen Xin Hou Zichang Jia Xue Yang Jianhua Zhang Yinggao Liu Nenghui Ye |
| author_sort | Xuanxuan Hou |
| collection | DOAJ |
| description | Grain size is an important component of quality and harvest traits in the field of rice breeding. Although numerous quantitative trait loci (QTLs) of grain size in rice have been reported, the molecular mechanisms of these QTLs remain poorly understood, and further research on QTL observation and candidate gene identification is warranted. In our research, we developed a suite of F<sub>2</sub> intercross populations from a cross of 9311 and CG. These primary populations were used to map QTLs conferring grain size, evaluated across three environments, and then subjected to bulked-segregant analysis-seq (BSA-seq). In total, 4, 11, 12 and 14 QTLs for grain length (GL), grain width (GW), 1000-grain weight (TGW), and length/width ratio (LWR), respectively, were detected on the basis of a single-environment analysis. In particular, over 200 splicing-related sites were identified by whole-genome sequencing, including one splicing-site mutation with G>A at the beginning of intron 4 on <i>Os03g0841800</i> (<i>qGL3.3</i>), producing a smaller open reading frame, without the third and fourth exons. A previous study revealed that the loss-of-function allele caused by this splicing site can negatively regulate rice grain length. Furthermore, <i>qTGW2.1</i> and <i>qGW2.3</i> were new QTLs for grain width. We used the near-isogenic lines (NILs) of these GW QTLs to study their genetic effects on individuals and pyramiding, and found that they have additive effects on GW. In summary, these discoveries provide a valuable genetic resource, which will facilitate further study of the genetic polymorphism of new rice varieties in rice breeding. |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-37a28b7be2aa4e6d9f627298b273ad362023-11-30T23:18:12ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-03-01237352610.3390/ijms23073526Identifying QTLs for Grain Size in a Colossal Grain Rice (<i>Oryza sativa</i> L.) Line, and Analysis of Additive Effects of QTLsXuanxuan Hou0Moxian Chen1Yinke Chen2Xin Hou3Zichang Jia4Xue Yang5Jianhua Zhang6Yinggao Liu7Nenghui Ye8College of Agriculture, Hunan Agricultural University, Changsha 410128, ChinaCo-Innovation Center for Sustainable Forestry in Southern China & Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, ChinaCollege of Agriculture, Hunan Agricultural University, Changsha 410128, ChinaState Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai’an 271018, ChinaState Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai’an 271018, ChinaState Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai’an 271018, ChinaDepartment of Biology, Hong Kong Baptist University, Hong Kong 999077, ChinaState Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai’an 271018, ChinaCollege of Agriculture, Hunan Agricultural University, Changsha 410128, ChinaGrain size is an important component of quality and harvest traits in the field of rice breeding. Although numerous quantitative trait loci (QTLs) of grain size in rice have been reported, the molecular mechanisms of these QTLs remain poorly understood, and further research on QTL observation and candidate gene identification is warranted. In our research, we developed a suite of F<sub>2</sub> intercross populations from a cross of 9311 and CG. These primary populations were used to map QTLs conferring grain size, evaluated across three environments, and then subjected to bulked-segregant analysis-seq (BSA-seq). In total, 4, 11, 12 and 14 QTLs for grain length (GL), grain width (GW), 1000-grain weight (TGW), and length/width ratio (LWR), respectively, were detected on the basis of a single-environment analysis. In particular, over 200 splicing-related sites were identified by whole-genome sequencing, including one splicing-site mutation with G>A at the beginning of intron 4 on <i>Os03g0841800</i> (<i>qGL3.3</i>), producing a smaller open reading frame, without the third and fourth exons. A previous study revealed that the loss-of-function allele caused by this splicing site can negatively regulate rice grain length. Furthermore, <i>qTGW2.1</i> and <i>qGW2.3</i> were new QTLs for grain width. We used the near-isogenic lines (NILs) of these GW QTLs to study their genetic effects on individuals and pyramiding, and found that they have additive effects on GW. In summary, these discoveries provide a valuable genetic resource, which will facilitate further study of the genetic polymorphism of new rice varieties in rice breeding.https://www.mdpi.com/1422-0067/23/7/3526ricegrain sizeQTLBSA-seqsplicingadditive effects |
| spellingShingle | Xuanxuan Hou Moxian Chen Yinke Chen Xin Hou Zichang Jia Xue Yang Jianhua Zhang Yinggao Liu Nenghui Ye Identifying QTLs for Grain Size in a Colossal Grain Rice (<i>Oryza sativa</i> L.) Line, and Analysis of Additive Effects of QTLs International Journal of Molecular Sciences rice grain size QTL BSA-seq splicing additive effects |
| title | Identifying QTLs for Grain Size in a Colossal Grain Rice (<i>Oryza sativa</i> L.) Line, and Analysis of Additive Effects of QTLs |
| title_full | Identifying QTLs for Grain Size in a Colossal Grain Rice (<i>Oryza sativa</i> L.) Line, and Analysis of Additive Effects of QTLs |
| title_fullStr | Identifying QTLs for Grain Size in a Colossal Grain Rice (<i>Oryza sativa</i> L.) Line, and Analysis of Additive Effects of QTLs |
| title_full_unstemmed | Identifying QTLs for Grain Size in a Colossal Grain Rice (<i>Oryza sativa</i> L.) Line, and Analysis of Additive Effects of QTLs |
| title_short | Identifying QTLs for Grain Size in a Colossal Grain Rice (<i>Oryza sativa</i> L.) Line, and Analysis of Additive Effects of QTLs |
| title_sort | identifying qtls for grain size in a colossal grain rice i oryza sativa i l line and analysis of additive effects of qtls |
| topic | rice grain size QTL BSA-seq splicing additive effects |
| url | https://www.mdpi.com/1422-0067/23/7/3526 |
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