GWAS analyses reveal QTL in egg layers that differ in response to diet differences

Abstract

BackgroundThe genetic architecture of egg production and egg quality traits, i.e. the quantitative trait loci (QTL) that influence these traits, is still poorly known. To date, 33 studies have focused on the detection of QTL for laying traits in chickens, but less than 10 genes have been identified. The availability of a high-density SNP (single nucleotide polymorphism) chicken array developed by Affymetrix, i.e. the 600K Affymetrix® Axiom® HD genotyping array offers the possibility to narrow down the localization of previously detected QTL and to detect new QTL. This high-density array is also anticipated to take research beyond the classical hypothesis of additivity of QTL effects or of QTL and environmental effects. The aim of our study was to search for QTL that influence laying traits using the 600K SNP chip and to investigate whether the effects of these QTL differed between diets and age at egg collection.ResultsOne hundred and thirty-one QTL were detected for 16 laying traits and were spread across all marked chromosomes, except chromosomes 16 and 25. The percentage of variance explained by a QTL varied from 2 to 10 % for the various traits, depending on diet and age at egg collection. Chromosomes 3, 9, 10 and Z were overrepresented, with more than eight QTL on each one. Among the 131 QTL, 60 had a significantly different effect, depending on diet or age at egg collection. For egg production traits, when the QTL × environment interaction was significant, numerous inversions of sign of the SNP effects were observed, whereas for egg quality traits, the QTL × environment interaction was mostly due to a difference of magnitude of the SNP effects.ConclusionsOur results show that numerous QTL influence egg production and egg quality traits and that the genomic regions, which are involved in shaping the ability of layer chickens to adapt to their environment for egg production, vary depending on the environmental conditions. The next question will be to address what the impact of these genotype × environment interactions is on selection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0160-2) contains supplementary material, which is available to authorized users.

Developing a 670k genotyping array to tag ∼2M SNPs across 24 horse breeds

“…High-density ~670k genotyping arrays were used in domestic cattle to identify structural variation [39,40]. Other studies have leveraged this technology to discover and refine loci associated with production traits [41][42][43]. Based on reports from other domestic animals, coupled with preliminary analyses performed here, we anticipate similar performance and increased power for map-based studies to soon follow in the horse.…”

Relevance of genomic evaluation for egg quality traits in layers

“…In both CC and IC, the reliability of genetic evaluation or of genomic evaluation varied greatly depending on the trait. This heterogeneousness in the impact on the evaluation can be explained by the differences found in the genetic architecture of the traits [16].…”

“…Blood samples were collected from the brachial veins of the animals and DNA was extracted. For the first two generations, all male candidates were genotyped by Ark-Genomics (Edinburgh, UK) during the research project UtopIGe [16]. From the G2 generation onward, male and female reproducers were genotyped at the high-throughput genotyping platform Gentyane (Clermont-Ferrand, France) (cf figure 1).…”

Quelles performances pour les animaux de demain ? Objectifs et méthodes de sélection

“…C'est l'hypothèse la plus cohérente avec la démarche agroécologique évoquée précédemment. Il existe dans la littérature de nombreux exemples la corroborant, en particulier montrant une variation des effets de gènes « majeurs » en fonction de l'environnement : voir par exemple l'effet du gène « cou nu » chez la poule en fonction de la température (Monnet et al, 1980) ou des interactions QTL x environnement (Romé et al, 2015). Enfin, la troisième hypothèse suppose Encadré 2.…”

“…Un protocole expérimental a été mis en place afin de disposer de poules pondeuses, issues d'un même père, mais élevées dans des environnements différents (Romé et al, 2015). Chaque père avait 40 filles nourries ad libitum avec un aliment dit « Basse Énergie » (BE) et 40 filles avec un aliment dit « Haute Énergie » (HE).…”