Identification of Promising Mutants Associated with Egg Production Traits Revealed by Genome-Wide Association Study

Abstract

Egg number (EN), egg laying rate (LR) and age at first egg (AFE) are important production traits related to egg production in poultry industry. To better understand the knowledge of genetic architecture of dynamic EN during the whole laying cycle and provide the precise positions of associated variants for EN, LR and AFE, laying records from 21 to 72 weeks of age were collected individually for 1,534 F2 hens produced by reciprocal crosses between White Leghorn and Dongxiang Blue-shelled chicken, and their genotypes were assayed by chicken 600 K Affymetrix high density genotyping arrays. Subsequently, pedigree and SNP-based genetic parameters were estimated and a genome-wide association study (GWAS) was conducted on EN, LR and AFE. The heritability estimates were similar between pedigree and SNP-based estimates varying from 0.17 to 0.36. In the GWA analysis, we identified nine genome-wide significant loci associated with EN of the laying periods from 21 to 26 weeks, 27 to 36 weeks and 37 to 72 weeks. Analysis of GTF2A1 and CLSPN suggested that they influenced the function of ovary and uterus, and may be considered as relevant candidates. The identified SNP rs314448799 for accumulative EN from 21 to 40 weeks on chromosome 5 created phenotypic differences of 6.86 eggs between two homozygous genotypes, which could be potentially applied to the molecular breeding for EN selection. Moreover, our finding showed that LR was a moderate polygenic trait. The suggestive significant region on chromosome 16 for AFE suggested the relationship between sex maturity and immune in the current population. The present study comprehensively evaluates the role of genetic variants in the development of egg laying. The findings will be helpful to investigation of causative genes function and future marker-assisted selection and genomic selection in chickens.

Genome-Wide Detection of Selective Signatures in Chicken through High Density SNPs

“…In our previous GWAS studies [37, 38, 39], 37 genes played a key role in egg production and feed efficiency in chicken such as egg weight (EW), egg number (EN), feed intake (FI), feed conversion ratio (FCR) and residual feed intake(RFI). Twenty-two genes overlapped with core regions had been demonstrated to be associated with economic traits.…”

“…Twenty-two genes overlapped with core regions had been demonstrated to be associated with economic traits. For instance, the NCAPG gene locating on chromosome 4 had been identified influencing both egg weight and body weight simultaneously in a pleiotropic manner [37]; the CLSPN gene on chromosome 23 displayed significant haplotype [38], may related with egg number via affecting the function of ovary and uterus[40,41]. These results could effectively elucidate that some important economic traits like egg production had undergone selection.…”

Identification of 19 loci for reproductive traits in a local Chinese chicken by genome-wide study

“…PPARGC1A may affect egg weight by regulating energy and cholesterol metabolism. Yuan et al (2015) detected nine genome-wide loci that significantly affected egg number during the laying phases of 21-26, 27-36, and 37-72 weeks using GWAS technology. Liao et al (2016) found a genome-wide significant locus (ss1985401199) located on the sex chromosome Z, which was associated with egg number in hens at 25-45 weeks.…”

Genotype frequency distributions of 28 SNP markers in two commercial lines and five Chinese native chicken populations

“…To characterize the genetic variations and genetic relationships among different populations using DNA markers, a total of 28 identified SNP markers, including 14 growth or carcass traits associated loci and 14 egg laying related genome positions, were selected from the previous reports [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33]. By using the MassArray technology, an Agena Bioscience MassARRAY System which is capable of efficiently genotyping tens to hundreds of SNPs with high accuracy, we detected the genotype frequency distributions of the 28 SNP markers in seven populations including four lowly selected as well as one moderately selected Sichuan native chicken populations, one commercial broiler line and one commercial layer line [34,35].…”