Genome-wide association analysis for heat tolerance at flowering detected a large set of genes involved in adaptation to thermal and other stresses
Fertilization sensitivity to heat in rice is a major issue within climate change scenarios in the tropics. A panel of 167 indica landraces and improved varieties was phenotyped for spikelet sterility (SPKST) under 38°C during anthesis and for several secondary traits potentially affecting panicle mi...
| Autores principales: | , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Public Library of Science
2017
|
| Acceso en línea: | https://hdl.handle.net/10568/165105 |
| _version_ | 1855521151498846208 |
|---|---|
| author | Lafarge, Tanguy Bueno, Crisanta Frouin, Julien Jacquin, Laval Courtois, Brigitte Ahmadi, Nourollah |
| author_browse | Ahmadi, Nourollah Bueno, Crisanta Courtois, Brigitte Frouin, Julien Jacquin, Laval Lafarge, Tanguy |
| author_facet | Lafarge, Tanguy Bueno, Crisanta Frouin, Julien Jacquin, Laval Courtois, Brigitte Ahmadi, Nourollah |
| author_sort | Lafarge, Tanguy |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Fertilization sensitivity to heat in rice is a major issue within climate change scenarios in the tropics. A panel of 167 indica landraces and improved varieties was phenotyped for spikelet sterility (SPKST) under 38°C during anthesis and for several secondary traits potentially affecting panicle micro-climate and thus the fertilization process. The panel was genotyped with an average density of one marker per 29 kb using genotyping by sequencing. Genome-wide association analyses (GWAS) were conducted using three methods based on single marker regression, haplotype regression and simultaneous fitting of all markers, respectively. Fourteen loci significantly associated with SPKST under at least two GWAS methods were detected. A large number of associations was also detected for the secondary traits. Analysis of co-localization of SPKST associated loci with QTLs detected in progenies of bi-parental crosses reported in the literature allowed to narrow -down the position of eight of those QTLs, including the most documented one, qHTSF4.1. Gene families underlying loci associated with SPKST corresponded to functions ranging from sensing abiotic stresses and regulating plant response, such as wall-associated kinases and heat shock proteins, to cell division and gametophyte development. Analysis of diversity at the vicinity of loci associated with SPKST within the rice three thousand genomes, revealed widespread distribution of the favourable alleles across O. sativa genetic groups. However, few accessions assembled the favourable alleles at all loci. Effective donors included the heat tolerant variety N22 and some Indian and Taiwanese varieties. These results provide a basis for breeding for heat tolerance during anthesis and for functional validation of major loci governing this trait |
| format | Journal Article |
| id | CGSpace165105 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| publisher | Public Library of Science |
| publisherStr | Public Library of Science |
| record_format | dspace |
| spelling | CGSpace1651052025-01-24T14:12:33Z Genome-wide association analysis for heat tolerance at flowering detected a large set of genes involved in adaptation to thermal and other stresses Lafarge, Tanguy Bueno, Crisanta Frouin, Julien Jacquin, Laval Courtois, Brigitte Ahmadi, Nourollah Fertilization sensitivity to heat in rice is a major issue within climate change scenarios in the tropics. A panel of 167 indica landraces and improved varieties was phenotyped for spikelet sterility (SPKST) under 38°C during anthesis and for several secondary traits potentially affecting panicle micro-climate and thus the fertilization process. The panel was genotyped with an average density of one marker per 29 kb using genotyping by sequencing. Genome-wide association analyses (GWAS) were conducted using three methods based on single marker regression, haplotype regression and simultaneous fitting of all markers, respectively. Fourteen loci significantly associated with SPKST under at least two GWAS methods were detected. A large number of associations was also detected for the secondary traits. Analysis of co-localization of SPKST associated loci with QTLs detected in progenies of bi-parental crosses reported in the literature allowed to narrow -down the position of eight of those QTLs, including the most documented one, qHTSF4.1. Gene families underlying loci associated with SPKST corresponded to functions ranging from sensing abiotic stresses and regulating plant response, such as wall-associated kinases and heat shock proteins, to cell division and gametophyte development. Analysis of diversity at the vicinity of loci associated with SPKST within the rice three thousand genomes, revealed widespread distribution of the favourable alleles across O. sativa genetic groups. However, few accessions assembled the favourable alleles at all loci. Effective donors included the heat tolerant variety N22 and some Indian and Taiwanese varieties. These results provide a basis for breeding for heat tolerance during anthesis and for functional validation of major loci governing this trait 2017-02-02 2024-12-19T12:54:43Z 2024-12-19T12:54:43Z Journal Article https://hdl.handle.net/10568/165105 en Open Access Public Library of Science Lafarge, Tanguy; Bueno, Crisanta; Frouin, Julien; Jacquin, Laval; Courtois, Brigitte and Ahmadi, Nourollah. 2017. Genome-wide association analysis for heat tolerance at flowering detected a large set of genes involved in adaptation to thermal and other stresses. PLoS ONE, Volume 12 no. 2 p. e0171254 |
| spellingShingle | Lafarge, Tanguy Bueno, Crisanta Frouin, Julien Jacquin, Laval Courtois, Brigitte Ahmadi, Nourollah Genome-wide association analysis for heat tolerance at flowering detected a large set of genes involved in adaptation to thermal and other stresses |
| title | Genome-wide association analysis for heat tolerance at flowering detected a large set of genes involved in adaptation to thermal and other stresses |
| title_full | Genome-wide association analysis for heat tolerance at flowering detected a large set of genes involved in adaptation to thermal and other stresses |
| title_fullStr | Genome-wide association analysis for heat tolerance at flowering detected a large set of genes involved in adaptation to thermal and other stresses |
| title_full_unstemmed | Genome-wide association analysis for heat tolerance at flowering detected a large set of genes involved in adaptation to thermal and other stresses |
| title_short | Genome-wide association analysis for heat tolerance at flowering detected a large set of genes involved in adaptation to thermal and other stresses |
| title_sort | genome wide association analysis for heat tolerance at flowering detected a large set of genes involved in adaptation to thermal and other stresses |
| url | https://hdl.handle.net/10568/165105 |
| work_keys_str_mv | AT lafargetanguy genomewideassociationanalysisforheattoleranceatfloweringdetectedalargesetofgenesinvolvedinadaptationtothermalandotherstresses AT buenocrisanta genomewideassociationanalysisforheattoleranceatfloweringdetectedalargesetofgenesinvolvedinadaptationtothermalandotherstresses AT frouinjulien genomewideassociationanalysisforheattoleranceatfloweringdetectedalargesetofgenesinvolvedinadaptationtothermalandotherstresses AT jacquinlaval genomewideassociationanalysisforheattoleranceatfloweringdetectedalargesetofgenesinvolvedinadaptationtothermalandotherstresses AT courtoisbrigitte genomewideassociationanalysisforheattoleranceatfloweringdetectedalargesetofgenesinvolvedinadaptationtothermalandotherstresses AT ahmadinourollah genomewideassociationanalysisforheattoleranceatfloweringdetectedalargesetofgenesinvolvedinadaptationtothermalandotherstresses |