基于低深度全基因组重测序技术对太行鸡保种群体产蛋性状遗传参数估计OA

The study aimed to comprehensively assess the egg-production genetic potential of the Taihang chicken,a unique local breed from Hebei Province,under two distinct conservation breeding strategies and to validate the effectiveness of low-coverage whole-genome resequencing technology in constructing genomic relationship matrices and estimating genetic parameters for traits with low-heritability.A total of 956 Taihang chickens from two conservation populations were selected:the Tian-Kai(TK)population(family-based equal-contribution conservation)and the Ning-Jin(NJ)population(random retention conservation).After quality control,924 individuals were remained(382 from TK,542 from NJ).Seven key reproductive traits were recorded:age at first egg(AFE),early egg production(EN1),peak egg production(EN2),late egg production(EN3),total eggs to 300 days(EN300),total eggs to 400 days(EN400),and broodiness.Genomic DNA libraries were constructed using a Tn5 transposase-based protocol and sequenced on a next-generation platform,sequencing data with an average depth of 1.21× per individual was obtained.Base-Var(v0.0.1.3)was employed to identify polymorphic loci from the aligned low-coverage whole-genome resequencing data and infer allele frequencies for SNP genotyping.Genotype imputation was performed with STITCH to obtain high-density genome-wide SNP data.Based on these high-density genome-wide SNP data,a genomic relationship matrix(GRM)was constructed,and the heritability and genetic/phenotypic correlations between traits were estimated using bivariate animal model in BLUPF90 software.The results indicated that the heritabilities of egg production traits in both conservation populattions were generally low to moderate(ranging from 0.08±0.14 to 0.31±0.16),but significant differences existed between the two populations:The TK population exhibited a significantly higher heritability for AFE(0.32±0.15)compared with NJ population(0.16±0.15),whereas NJ population displayed a significantly higher heritability for broodiness(0.30±0.19)than TK population(0.08±0.16),indicating that conservation strategy may shift allele-frequency distributions.Correlation analyses revealed significant negative associations between egg numbers and both AFE and broodiness,with distinct correlation patterns between the two populations.Notably,total egg production during the early laying period(up to 30 weeks)was highly correlated with total egg production up to 400 days,suggesting its utility as an early selection index.The study also confirmed that GRMs constructed from low-coverage whole-genome resequencing effectively overcome the lack of pedigree information in conservation populations and provide reliable genetic parameter estimates.In summary,first,low-coverage whole-genome resequencing technology has significant advantages for estimating genetic parameters of traits with low heritability.Second,different conservation strategies markedly influence the genetic structure and trait performance of Taihang chickens:the family-based equal-contribution strategy preserves genetic variations more favorable for egg production,while the random retention strategy retains more genetic variations associated with broodiness.Finally,early egg-production traits reliably predict overall laying performance in both populations.Consequently,for genetic improvement programs based on these two conservation populations,it is recommended to advance breeding value estimation and selection decisions to the early laying stage(approximately 30 weeks)and to tailor selection emphasis according to the genetic structure of each population,thereby achieving both protective utilization of genetic resources and efficient breeding objectives.