Investigating the genetic determination of clutch traits in Chinese local chicken breed

Abstract

Background: Egg-laying rate is the trait with the highest economic weight in breeding programs for laying hens. Egg-laying rate is associated with a clutch, which is defined as consecutive days of oviposition. Clutch traits can be used to describe the individual laying pattern and has been considered as a trait for selection. However, little is known about the uniformity of clutch traits. Methods: In this study, after estimating the genetic parameters for age at first egg (afe), body weight at first egg (bwfe), longest clutch until 52 week of age (maxC), the first week when the longest clutch starts (fwlCs), the last week of longest clutch ends (lwlCe), number of clutches (numC), the longest number of days without egg-laying until 52 week of age (lndwel), we identified single nucleotide polymorphisms (SNPs) and potential candidate genes associated with clutch traits in Laiwu Black chicken (a native Chinese breed). The restricted maximum likelihood (REML)method was employed for estimation of genetic parameters of clutch pattern in 399 Laiwu Black hens, using the GCTA software. Results: The results showed that SNP-based heritability estimates of clutch traits ranged from 0.06 to 0.59. A genome-wide association study (GWAS) was performed based on a mixed linear model (MLM) implemented in the EMMAX software. Genotyping data were obtained from whole genome re-sequencing data (399 individuals were re-sequenced at 7× coverage). After quality control, a total of 10,810,544 SNPs remained to be analyzed. The GWAS results revealed that 401 significant SNPs responsible for clutch traits were scattered on chicken chromosomes 1-14, 17-19, 21-25, 28 and Z. Among the annotated genes, neural EGFL like 2 (NELL2), SET And MYND domain containing 3 (SMYD3), and phospholipase D1 (PLCL1)were the most promising candidates for clutch traits in Laiwu Black chicken. Conclusion: The clutch traits showed moderate to high heritability, and the GWAS results identified an array of genes associated with the clutch traits. The findings of this study provide critical insight into the genetic basis of clutch traits.