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QTL mapping and identification of candidate genes using a genome-wide association study for heat tolerance at anthesis in rice (Oryza sativa L.)
Heat tolerance (HT) of rice at anthesis is a key trait that ensures high and stable yields under heat stress. Finding the quantitative trait loci (QTLs) and gene loci controlling HT is crucial. We used relative spikelet fertility (RSF) as a measure of HT. The phenotypic values of RSF in 173 rice acc...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9520461/ https://www.ncbi.nlm.nih.gov/pubmed/36186421 http://dx.doi.org/10.3389/fgene.2022.983525 |
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author | Hu, Changmin Jiang, Jianhua Li, Yulong Song, Shaojie Zou, Yu Jing, Chunyu Zhang, Ying Wang, Dezheng He, Qiang Dang, Xiaojing |
author_facet | Hu, Changmin Jiang, Jianhua Li, Yulong Song, Shaojie Zou, Yu Jing, Chunyu Zhang, Ying Wang, Dezheng He, Qiang Dang, Xiaojing |
author_sort | Hu, Changmin |
collection | PubMed |
description | Heat tolerance (HT) of rice at anthesis is a key trait that ensures high and stable yields under heat stress. Finding the quantitative trait loci (QTLs) and gene loci controlling HT is crucial. We used relative spikelet fertility (RSF) as a measure of HT. The phenotypic values of RSF in 173 rice accessions were investigated in two environments and showed abundant variations. We performed a genome-wide association study on RSF using 1.2 million single nucleotide polymorphisms (SNPs). Five QTLs were significantly associated with RSF were identified, four were found in previously reported QTLs/genes, and one was novel. The novel QTL qRSF9.2 was mapped into the 22,059,984-22,259,984 bp region, which had 38 positional candidate genes. By combining the linkage disequilibrium analysis, the QTL region was narrowed to 22,110,508–22,187,677 bp, which contained 16 candidate genes. Among them, only gene LOC_Os09g38500 contained nonsynonymous SNPs that were significantly associated with RSF. In addition, accessions with large and small RSF values had corresponding respective high and low gene expression levels. Furthermore, the RSF of the CC allele was significantly higher than that of the TT allele. Hap 2 and Hap 3 can increase heat tolerance by 7.9 and 11.3%, respectively. Our results provide useful information that recommends further cloning of qRSF9.2 and breeding heat-tolerant rice varieties by marker-assisted selection. |
format | Online Article Text |
id | pubmed-9520461 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-95204612022-09-30 QTL mapping and identification of candidate genes using a genome-wide association study for heat tolerance at anthesis in rice (Oryza sativa L.) Hu, Changmin Jiang, Jianhua Li, Yulong Song, Shaojie Zou, Yu Jing, Chunyu Zhang, Ying Wang, Dezheng He, Qiang Dang, Xiaojing Front Genet Genetics Heat tolerance (HT) of rice at anthesis is a key trait that ensures high and stable yields under heat stress. Finding the quantitative trait loci (QTLs) and gene loci controlling HT is crucial. We used relative spikelet fertility (RSF) as a measure of HT. The phenotypic values of RSF in 173 rice accessions were investigated in two environments and showed abundant variations. We performed a genome-wide association study on RSF using 1.2 million single nucleotide polymorphisms (SNPs). Five QTLs were significantly associated with RSF were identified, four were found in previously reported QTLs/genes, and one was novel. The novel QTL qRSF9.2 was mapped into the 22,059,984-22,259,984 bp region, which had 38 positional candidate genes. By combining the linkage disequilibrium analysis, the QTL region was narrowed to 22,110,508–22,187,677 bp, which contained 16 candidate genes. Among them, only gene LOC_Os09g38500 contained nonsynonymous SNPs that were significantly associated with RSF. In addition, accessions with large and small RSF values had corresponding respective high and low gene expression levels. Furthermore, the RSF of the CC allele was significantly higher than that of the TT allele. Hap 2 and Hap 3 can increase heat tolerance by 7.9 and 11.3%, respectively. Our results provide useful information that recommends further cloning of qRSF9.2 and breeding heat-tolerant rice varieties by marker-assisted selection. Frontiers Media S.A. 2022-09-15 /pmc/articles/PMC9520461/ /pubmed/36186421 http://dx.doi.org/10.3389/fgene.2022.983525 Text en Copyright © 2022 Hu, Jiang, Li, Song, Zou, Jing, Zhang, Wang, He and Dang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Hu, Changmin Jiang, Jianhua Li, Yulong Song, Shaojie Zou, Yu Jing, Chunyu Zhang, Ying Wang, Dezheng He, Qiang Dang, Xiaojing QTL mapping and identification of candidate genes using a genome-wide association study for heat tolerance at anthesis in rice (Oryza sativa L.) |
title | QTL mapping and identification of candidate genes using a genome-wide association study for heat tolerance at anthesis in rice (Oryza sativa L.) |
title_full | QTL mapping and identification of candidate genes using a genome-wide association study for heat tolerance at anthesis in rice (Oryza sativa L.) |
title_fullStr | QTL mapping and identification of candidate genes using a genome-wide association study for heat tolerance at anthesis in rice (Oryza sativa L.) |
title_full_unstemmed | QTL mapping and identification of candidate genes using a genome-wide association study for heat tolerance at anthesis in rice (Oryza sativa L.) |
title_short | QTL mapping and identification of candidate genes using a genome-wide association study for heat tolerance at anthesis in rice (Oryza sativa L.) |
title_sort | qtl mapping and identification of candidate genes using a genome-wide association study for heat tolerance at anthesis in rice (oryza sativa l.) |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9520461/ https://www.ncbi.nlm.nih.gov/pubmed/36186421 http://dx.doi.org/10.3389/fgene.2022.983525 |
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