Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Hu, Changmin, Jiang, Jianhua, Li, Yulong, Song, Shaojie, Zou, Yu, Jing, Chunyu, Zhang, Ying, Wang, Dezheng, He, Qiang, Dang, Xiaojing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
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
_version_ 1784799629579124736
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
work_keys_str_mv AT huchangmin qtlmappingandidentificationofcandidategenesusingagenomewideassociationstudyforheattoleranceatanthesisinriceoryzasatival
AT jiangjianhua qtlmappingandidentificationofcandidategenesusingagenomewideassociationstudyforheattoleranceatanthesisinriceoryzasatival
AT liyulong qtlmappingandidentificationofcandidategenesusingagenomewideassociationstudyforheattoleranceatanthesisinriceoryzasatival
AT songshaojie qtlmappingandidentificationofcandidategenesusingagenomewideassociationstudyforheattoleranceatanthesisinriceoryzasatival
AT zouyu qtlmappingandidentificationofcandidategenesusingagenomewideassociationstudyforheattoleranceatanthesisinriceoryzasatival
AT jingchunyu qtlmappingandidentificationofcandidategenesusingagenomewideassociationstudyforheattoleranceatanthesisinriceoryzasatival
AT zhangying qtlmappingandidentificationofcandidategenesusingagenomewideassociationstudyforheattoleranceatanthesisinriceoryzasatival
AT wangdezheng qtlmappingandidentificationofcandidategenesusingagenomewideassociationstudyforheattoleranceatanthesisinriceoryzasatival
AT heqiang qtlmappingandidentificationofcandidategenesusingagenomewideassociationstudyforheattoleranceatanthesisinriceoryzasatival
AT dangxiaojing qtlmappingandidentificationofcandidategenesusingagenomewideassociationstudyforheattoleranceatanthesisinriceoryzasatival