Genomic Prediction and Genome-wide Association Study for Production Traits in Taiwan Country Chicken

報告時間：2025-4-25
報告地點：Room 407
指導老師：Chih-Feng Chen
學生：Tsung-Che Tu
摘要

Taiwan Country chicken plays a significant role in Taiwan's poultry industry and culture. However, its breeding program focuses on body weight selection within a "like-pure" bred population, facing challenges in balancing growth and egg production traits. Due to the niche market, the high genotyping cost limits the implementation of genomic selection (GS). Establishing a high-performing dam line in a crossbreeding system while preserving growth traits and applying GS to improve market competitiveness and selection efficiency remains a key challenge. This study focused on the NCHU-G101 chickens. Breeding value accuracy was estimated using pedigree-based BLUP (PBLUP), GBLUP, and single-step GBLUP (ssGBLUP) models, combined with GWAS (SNP-GWAS, GBLUP-GWAS, and ssGWAS) to identify SNPs and genes associated with growth-related and egg production traits. Results showed that compared to the PBLUP model, ssGBLUP model improved accuracy by 4.3% to 16.4% for growth-related and by an average of 3.41% for egg production traits, while the GBLUP model had the lowest accuracy across most traits. GWAS identified 312 SNPs, with 194 reaching 5% Bonferroni genome-wide significance and seven missense SNPs. These findings confirm that integrating the ssGBLUP model with identified SNPs can enhance genetic gain and selection efficiency. Further research is needed to explore mechanisms and assess the feasibility of GS and marker-assisted selection in Taiwan Country chicken breeding programs.

Keywords: Taiwan Country chicken, single-step GBLUP, GWAS, marker-assisted selection
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