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.

Fig 1. Manhattan and Q-Q plot of genome wide association study for egg number.

Each dot represents a SNP in the dataset. Manhattan plot (left). EN1, egg numbers in pre-peak laying stage from 21 to 26 weeks of age. SNPs showing association with EN1 are mapped to one signal in chromosome 5 and a singleton in chromosome 23; EN2, egg numbers in peak laying stage from 27 to 36 weeks of age. SNPs showing association with EN2 are mapped to a singleton in chromosome 9; EN3, egg numbers in persistent laying stage from 37 to 72 weeks of age. SNPs showing association with EN3 are mapped to a singleton in chromosome 1. The horizontal gray line and gray dashed line indicate the genome-wise significance threshold (P-value = 8.43e-7) and genome-wise suggestive significance threshold (P-value = 1.69e-5), respectively. GIF represents genomic inflation factor.

Fig 2. Linkage disequilibrium (r²) plot of associations (P-value < 1.69e-5) with egg number.

(a) and (b) indicate haplotype block on GGA5 and GGA23 for markers showing associations with egg number in the pre-peak laying period, respectively. Haplotype block on for markers showing associations with egg number in the pre-peak laying period. (c) indicates haplotype block on GGA1 for markers showing associations with egg number in the persistent laying period. Solid lines mark the identified blocks.

Fig 3. Box plot for effect of sentinel SNPs showing associations with egg number.

EN1, egg numbers in pre-peak laying stage from 21 to 26 weeks of age. EN2, egg numbers in peak laying stage from 27 to 36 weeks of age. EN3, egg numbers in persistent laying stage from 37 to 72 weeks of age.

Fig 4. Manhattan and Q-Q plot of genome wide association study for accumulative egg number.

Each dot represents a SNP in the dataset. Manhattan plot (left). EN21-40, egg numbers from 21 to 40 weeks of age. SNPs showing association with EN21-40 are mapped to one signal in chromosome 5 and a singleton in chromosome 23; EN21-56, egg numbers from 21 to 56 weeks of age. EN21-72, egg numbers from 21 to 72 weeks of age. The horizontal gray line and gray dashed line indicate the genome-wise significance threshold (P-value = 8.43e-7) and genome-wise suggestive significance threshold (P-value = 1.69e-5), respectively. GIF represents genomic inflation factor.

Fig 5. Linkage disequilibrium (r2) plot for associations with egg number betwwen 21 and 40 weeks.

Solid lines mark the identified blocks.

Fig 6. Manhattan and Q-Q plot of genome wide association study for egg laying rate.

Each dot represents a SNP in the dataset. Manhattan plot (left). LR, egg laying rate between 25 and 40 weeks of age. The horizontal gray line and gray dashed line indicate the genome-wise significance threshold (P-value = 8.43e-7) and genome-wise suggestive significance threshold (P-value = 1.69e-5), respectively. GIF represents genomic inflation factor.

Fig 7. Manhattan and Q-Q plot of genome wide association study for age at first egg.

Each dot represents a SNP in the dataset. Manhattan plot (left). AFE, age at first egg. The horizontal gray line and gray dashed line indicate the genome-wise significance threshold (P-value = 8.43e-7) and genome-wise suggestive significance threshold (P-value = 1.69e-5), respectively. GIF represents genomic inflation factor.