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Presence/absence variations and SNPs equally contribute to the variations of protein and metabolite abundance

hal.structure.identifierGénétique Quantitative et Evolution - Le Moulon (Génétique Végétale) [GQE-Le Moulon]
dc.contributor.authorDJABALI, Yacine
hal.structure.identifierGénétique Quantitative et Evolution - Le Moulon (Génétique Végétale) [GQE-Le Moulon]
dc.contributor.authorBLEIN-NICOLAS, Melisande
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorMOING, Annick
hal.structure.identifierNational Severe Storms Laboratory [NSSL]
dc.contributor.authorDUARTE, Jorge
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorBERNILLON, Stéphane
hal.structure.identifierBiologie du fruit et pathologie [BFP]
hal.structure.identifierPlateforme Bordeaux Metabolome
dc.contributor.authorPRIGENT, Sylvain
hal.structure.identifierGénétique Quantitative et Evolution - Le Moulon (Génétique Végétale) [GQE-Le Moulon]
dc.contributor.authorMABIRE, Clément
hal.structure.identifierGénétique Quantitative et Evolution - Le Moulon (Génétique Végétale) [GQE-Le Moulon]
dc.contributor.authorMADUR, Delphine
hal.structure.identifierÉcophysiologie des Plantes sous Stress environnementaux [LEPSE]
dc.contributor.authorCABRERA-BOSQUET, Llorenç
hal.structure.identifierÉcophysiologie des Plantes sous Stress environnementaux [LEPSE]
dc.contributor.authorWELCKER, Claude
hal.structure.identifierÉcophysiologie des Plantes sous Stress environnementaux [LEPSE]
dc.contributor.authorTARDIEU, Francois
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorGIBON, Yves
hal.structure.identifierGénétique Quantitative et Evolution - Le Moulon (Génétique Végétale) [GQE-Le Moulon]
dc.contributor.authorZIVY, Michel
hal.structure.identifierGénétique Quantitative et Evolution - Le Moulon (Génétique Végétale) [GQE-Le Moulon]
dc.contributor.authorCHARCOSSET, Alain
hal.structure.identifierGénétique Quantitative et Evolution - Le Moulon (Génétique Végétale) [GQE-Le Moulon]
dc.contributor.authorNICOLAS, Stephane
dc.date.conference2022-09-05
dc.description.abstractEnUnderstanding the mechanisms of adaptation to the environment in cultivated plants is a promising way to meet the challenge of maintaining food security in the context of global warming. In the case of maize, high-throughput sequencing has revealed that structural variations represent a large part of the genome and could have huge phenotypic effects. Among these, Presence Absence Variants (PAVs, which include insertion/deletion of large DNA sequences) may be involved in adaptation of maize to its environment, but their contribution to the genetic determinism of traits and genotype by environment interactions remains largely unknown. To address this issue, we performed a genome-wide association study between two types of polymorphisms, SNPs and InDels, and molecular traits obtained from proteomics and metabolomics analyses to detect quantitative trait loci (QTLs). The genetic panel used for this study was composed of 254 dent inbred lines genotyped with 978,134 SNPs and 72,041 InDels. The latter encompassed from 37 to 129,700 pb, including thousands of PAVs that are not present in the B73 reference genome. Proteins and metabolites were quantified by mass spectrometry in leaf samples from F1 hybrids obtained by crossing the inbred lines with one flint tester line. Hybrid plants were grown under two watering conditions (well-watered and water deficit) in greenhouse. In total, we detected 61,225 QTLs associated with proteome or metabolome variations. Among these, 4,766 QTLs were exclusively detected by InDels. To take into account the difference of marker density between InDels and SNPs, we used a re-sampling approach which showed that there was no difference between InDels and SNPs regarding the number and effect of the QTLs detected . Additionally, the QTLs detected by the two types of polymorphism were equally distributed in the two watering conditions. These preliminary results show that InDels are worse considering to detect new genetic regions of interest. They also suggest that InDels and SNPs equally contribute to molecular trait variation and response to drought stress.
dc.language.isoen
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.title.enPresence/absence variations and SNPs equally contribute to the variations of protein and metabolite abundance
dc.typeAutre communication scientifique (congrès sans actes - poster - séminaire...)
dc.subject.halSciences du Vivant [q-bio]/Biochimie, Biologie Moléculaire/Génomique, Transcriptomique et Protéomique [q-bio.GN]
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biochimie, Biologie Moléculaire/Réseaux moléculaires [q-bio.MN]
dc.subject.halSciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale/Amélioration des plantes
dc.subject.halSciences du Vivant [q-bio]/Génétique/Génétique des plantes
bordeaux.conference.titleAnalytics 2022
bordeaux.countryFR
bordeaux.conference.cityNantes
bordeaux.peerReviewedoui
hal.identifierhal-03879730
hal.version1
hal.invitednon
hal.proceedingsnon
hal.conference.end2022-09-08
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03879730v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.au=DJABALI,%20Yacine&BLEIN-NICOLAS,%20Melisande&MOING,%20Annick&DUARTE,%20Jorge&BERNILLON,%20St%C3%A9phane&rft.genre=conference


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