Elucidation of the genetic determination of clutch traits in Chinese local chickens of the Laiwu Black breed

Abstract

Background: Egg laying rate (LR) is associated with a clutch, which is defined as consecutive days of oviposition. The clutch trait can be used as a selection indicator to improve egg production in poultry breeding. However, little is known about the genetic basis of clutch traits. In this study, our aim was to estimate genetic parameters and identify quantitative trait single nucleotide polymorphisms for clutch traits in 399 purebred Laiwu Black chickens (a native Chinese breed) using a genome-wide association study (GWAS).

Methods: In this work, after estimating the genetic parameters of age at first egg, body weight at first egg, LR, longest clutch until 52 week of age, first week when the longest clutch starts, last week when the longest clutch ends, number of clutches, and longest number of days without egg-laying until 52 week of age, we identified single nucleotide polymorphisms (SNPs) and potential candidate genes associated with clutch traits in Laiwu Black chickens. The restricted maximum likelihood method was used to estimate 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. Genotyping data were obtained from whole genome re-sequencing data. After quality control, a total of 10,810,544 SNPs remained to be analyzed. The GWAS revealed that 421 significant SNPs responsible for clutch traits were scattered on chicken chromosomes 1-14, 17-19, 21-25, 28 and Z. Among the annotated genes, NELL2, SMYD9, SPTLC2, SMYD3 and PLCL1 were the most promising candidates for clutch traits in Laiwu Black chickens.

Conclusion: The findings of this research provide critical insight into the genetic basis of clutch traits. These results contribute to the identification of candidate genes and variants. Genes and SNPs potentially provide new avenues for further research and would help to establish a framework for new methods of genomic prediction, and increase the accuracy of estimated genetic merit for egg production and clutch traits.

Keywords: Chicken; Clutch traits; GWAS; Genome; Laying rate.

Fig. 1

Laiwu Black chickens are a dual-purpose breed for both egg-laying and meat production. The average bodyweight of 8-week-old roosters is 581 g, while the average weight of hens is 512 g. The onset of laying occurs at approximately 145 days, with an average bodyweight of 1,848 g for roosters and 1,399 g for hens. The annual egg production is around 175 eggs

Fig. 2

Manhattan plot derived from GWAS for the AFE. Each dot on this figure corresponds to a SNP within the dataset, and the horizontal red and blue lines denote the genome-wide significance (3.42E-8) and suggestive significance thresholds (6.84E-7), respectively. The Manhattan plot contains -log10 observed P-values for genome-wide SNPs (y-axis) plotted against their corresponding position on each chromosome (x-axis). The horizontal axis represents the chromosome length in Mb. Different colors correspond to SNP density

Fig. 3

Manhattan plot derived from GWAS for the BWFE. Each dot on this figure corresponds to a SNP within the dataset, and the horizontal red and blue lines denote the genome-wide significance (3.42E-8) and suggestive significance thresholds (6.84E-7), respectively. The Manhattan plot contains -log10 observed P-values for genome-wide SNPs (y-axis) plotted against their corresponding position on each chromosome (x-axis). The horizontal axis represents the chromosome length in Mb. Different colors correspond to SNP density

Fig. 4

Manhattan plot derived from GWASs for the LR. Each dot on this figure corresponds to a SNP within the dataset, and the horizontal red and blue lines denote the genome-wide significance (3.42E-8) and suggestive significance thresholds (6.84E-7), respectively. The Manhattan plot contains -log10 observed P-values for genome-wide SNPs (y-axis) plotted against their corresponding position on each chromosome (x-axis). The horizontal axis represents the chromosome length in Mb. Different colors correspond to SNP density

Fig. 5

Circle-Manhattan plot derived from GWAS for clutch traits. Each dot on this figure corresponds to a SNP within the dataset, and the horizontal red and blue lines denote the genome-wide significance (3.42E-8) and suggestive significance thresholds (6.84E-7), respectively. The Manhattan plot contains -log10 observed P-values for genome-wide SNPs (y-axis) plotted against their corresponding position on each chromosome (x-axis). The horizontal axis represents the chromosome length in Mb. Different colors correspond to SNP density. The circle from outside to inside are LC, FWLCS, LNDWEL, LWLCE, NUMC traits

Fig. 6

Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and GO enrichment analysis