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...
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| Format: | Article |
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Frontiers Media S.A.
2022-09-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.983525/full |
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| author | Changmin Hu Changmin Hu Jianhua Jiang Yulong Li Shaojie Song Yu Zou Chunyu Jing Ying Zhang Dezheng Wang Qiang He Xiaojing Dang |
| author_facet | Changmin Hu Changmin Hu Jianhua Jiang Yulong Li Shaojie Song Yu Zou Chunyu Jing Ying Zhang Dezheng Wang Qiang He Xiaojing Dang |
| author_sort | Changmin Hu |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-11T20:35:45Z |
| format | Article |
| id | doaj.art-0b2b26b5613740cb83e7993cbe2b7158 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-11T20:35:45Z |
| publishDate | 2022-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-0b2b26b5613740cb83e7993cbe2b71582022-12-22T04:04:22ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-09-011310.3389/fgene.2022.983525983525QTL mapping and identification of candidate genes using a genome-wide association study for heat tolerance at anthesis in rice (Oryza sativa L.)Changmin Hu0Changmin Hu1Jianhua Jiang2Yulong Li3Shaojie Song4Yu Zou5Chunyu Jing6Ying Zhang7Dezheng Wang8Qiang He9Xiaojing Dang10Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei, ChinaInstitute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, ChinaInstitute of Crop Research, Anhui Academy of Agricultural Sciences, Hefei, ChinaInstitute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, ChinaInstitute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, ChinaInstitute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, ChinaInstitute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, ChinaInstitute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, ChinaState Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, ChinaInstitute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, ChinaHeat 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.https://www.frontiersin.org/articles/10.3389/fgene.2022.983525/fullanthesisheat tolerancegenome-wide association studyqRSF9.2high and stable yield |
| spellingShingle | Changmin Hu Changmin Hu Jianhua Jiang Yulong Li Shaojie Song Yu Zou Chunyu Jing Ying Zhang Dezheng Wang Qiang He Xiaojing Dang QTL mapping and identification of candidate genes using a genome-wide association study for heat tolerance at anthesis in rice (Oryza sativa L.) Frontiers in Genetics anthesis heat tolerance genome-wide association study qRSF9.2 high and stable yield |
| 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 | anthesis heat tolerance genome-wide association study qRSF9.2 high and stable yield |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.983525/full |
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