Abstract
BackgroundAs a major economic trait in chickens, egg weight (EW) receives widespread interests in breeding, production and consumption. However, limited information is available for underlying genetic architecture of longitudinal trend in EW. Herein, we measured EWs at nine time points from onset of laying to 60 week of age, and conducted comprehensive genome-wide association studies (GWAS) in 1,534 F2 hens derived from reciprocal crosses between White Leghorn and Dongxiang chickens.ResultsEgg weights at all ages except the first egg weight (FEW) exhibited high SNP-based heritability estimates (0.47 ~ 0.60). Strong pair-wise genetic correlations (0.77 ~ 1.00) were found among all EWs. Nine separate univariate genome-wide screens suggested 73 signals showing significant associations with longitudinal EWs. After multivariate and conditional analyses, four variants on three chromosomes remained independent contributions. The minor alleles at two loci exerted consistent and positive substitution effects on EWs, and other two were negative. The four loci together accounted for 3.84 % of the phenotypic variance for FEW and 7.29 ~ 11.06 % for EWs from 32 to 60 week of age. We obtained five candidate genes, of which NCAPG harbors a non-synonymous SNP (rs14491030) causing a valine-to-alanine amino-acid substitution. Genome partitioning analysis indicated a strong linear correlation between the variance explained by each chromosome and its length, which provided evidence that EW follows a highly polygenic nature of inheritance.ConclusionsIdentification of significant genetic causes that together implicate EWs at different ages will greatly advance our understanding of the genetic basis behind longitudinal EWs, and would be helpful to illuminate the future breeding direction on how to select desired egg size.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1945-y) contains supplementary material, which is available to authorized users.
Highlights
As a major economic trait in chickens, egg weight (EW) receives widespread interests in breeding, production and consumption
The main goals of our current work were to assess the feasibility of longitudinal data as an intriguing resource in genome-wide association studies (GWAS), pinpoint associated loci and genes that contribute to the phenotypic variability and longitudinal trend in egg weight, and provide valuable insights into the genetic basis of longitudinal egg weights
Univariate GCTA analyses revealed that all egg weight traits, except first egg weight (FEW), had highly heritable patterns (Table 2), and the highest Single nucleotide polymorphism (SNP)-based heritability estimate was found in EW36
Summary
As a major economic trait in chickens, egg weight (EW) receives widespread interests in breeding, production and consumption. A majority of reported QTLs are mapped with wide confidence intervals by low-density linkage analysis in the past [12]. It is very difficult to identify potential causal variants in QTL mapping studies, mainly due to the relatively small number of recombinants generated from two original parents in a limited number of generations [13]. To improve the precision of gene-level mapping, genome-wide association study (GWAS) based on linkage disequilibrium (LD) between SNPs and causal QTLs/genes is proposed as a more powerful approach identifying genetic links between phenotypes and genotypes [14, 15]. The availability of 600 K Affymetrix Chicken SNP array could contribute to narrowing down candidate genomic segments and pinpointing several dominating causal variants
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