Disentangling group specific QTL allele effects from genetic background epistasis using admixed individuals in GWAS: An application to maize flowering

Autoři: Simon Rio aff001;  Tristan Mary-Huard aff001;  Laurence Moreau aff001;  Cyril Bauland aff001;  Carine Palaffre aff003;  Delphine Madur aff001;  Valérie Combes aff001;  Alain Charcosset aff001
Působiště autorů: Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France aff001;  MIA, INRAE, AgroParisTech, Université Paris-Saclay, 75005, Paris, France aff002;  UE 0394 SMH, INRAE, 2297 Route de l’INRA, 40390, Saint-Martin-de-Hinx, France aff003
Vyšlo v časopise: Disentangling group specific QTL allele effects from genetic background epistasis using admixed individuals in GWAS: An application to maize flowering. PLoS Genet 16(3): e1008241. doi:10.1371/journal.pgen.1008241
Kategorie: Research Article
doi: 10.1371/journal.pgen.1008241


When handling a structured population in association mapping, group-specific allele effects may be observed at quantitative trait loci (QTLs) for several reasons: (i) a different linkage disequilibrium (LD) between SNPs and QTLs across groups, (ii) group-specific genetic mutations in QTL regions, and/or (iii) epistatic interactions between QTLs and other loci that have differentiated allele frequencies between groups. We present here a new genome-wide association (GWAS) approach to identify QTLs exhibiting such group-specific allele effects. We developed genetic materials including admixed progeny from different genetic groups with known genome-wide ancestries (local admixture). A dedicated statistical methodology was developed to analyze pure and admixed individuals jointly, allowing one to disentangle the factors causing the heterogeneity of allele effects across groups. This approach was applied to maize by developing an inbred “Flint-Dent” panel including admixed individuals that was evaluated for flowering time. Several associations were detected revealing a wide range of configurations of allele effects, both at known flowering QTLs (Vgt1, Vgt2 and Vgt3) and new loci. We found several QTLs whose effect depended on the group ancestry of alleles while others interacted with the genetic background. Our GWAS approach provides useful information on the stability of QTL effects across genetic groups and can be applied to a wide range of species.

Klíčová slova:

Alleles – Genetic loci – Genome-wide association studies – Maize – Molecular genetics – Plant genomics – Population genetics – Quantitative trait loci


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