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 Sunio, Frouin Julien, Jacquin Laval, Courtois Brigitte, 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, 12 (2):e0171254, 27 p.

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Lafarge 2017 GWAS for heat tolerance at flowering - PlosOne.pdf

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Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie; Staps

Additional Information : Accès aux jeux de données : Phenotypic and genotypic data files are available from: http:// tropgened pgene/JSP/inte rface.jsp? module=RICE . (Choose Tab Studies) as ™ORYTAGE _indica_Heat- tolerance_167- accessions _21-traits∫, and ™ORYTAGE _indica_GBS -genotype_167 - accessions _13160-S NP

Abstract : 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. (Résumé d'auteur)

Mots-clés Agrovoc : Oryza sativa, Amélioration des plantes, Tolérance à la chaleur, Fertilité, Phénotype, Variation génétique, Locus des caractères quantitatifs, Génotype, Stress, Résistance génétique, Marqueur génétique, Floraison, Changement climatique, adaptation aux changements climatiques

Mots-clés géographiques Agrovoc : Philippines

Mots-clés complémentaires : QTL, Séquencage

Classification Agris : F30 - Plant genetics and breeding
F63 - Plant physiology - Reproduction
H50 - Miscellaneous plant disorders
P40 - Meteorology and climatology
U30 - Research methods

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Lafarge Tanguy, CIRAD-BIOS-UMR AGAP (FRA)
  • Bueno Crisanta Sunio, IRRI (PHL)
  • Frouin Julien, CIRAD-BIOS-UMR AGAP (FRA)
  • Jacquin Laval, CIRAD-BIOS-UMR AGAP (FRA)
  • Courtois Brigitte, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-2118-7102
  • Ahmadi Nourollah, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-0072-6285

Source : Cirad-Agritrop (

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