Genomic Dissection of Growth Traits and Spatial Independence from Breed-Defining Loci in Jining Grey Goats

Abstract

Simple Summary The Jining Grey goat is a Chinese indigenous goat breed valued for its gray coat, high prolificacy, and adaptation to local production systems, but its growth performance still requires genetic improvement. This study used growth records and low-depth whole-genome sequencing from 70 performance-graded goats to search for candidate genomic regions associated with growth traits. We also examined 47 seven-day-old goats from the same project to explore whether prioritized markers showed early-life trait trends. To reduce reliance on any single analysis in a small population, we combined phenotype comparisons, population-structure analysis, selective-sweep scans, genome-wide association analysis, superior-genotype screening, positional annotation, and exploratory genomic prediction. The results identified a 99-SNP candidate marker panel and showed limited physical overlap between growth-associated candidate regions and major selective-sweep regions related to breed background. However, the findings should be interpreted as preliminary because the cohort was small, sequencing depth was low, imputation was performed within the cohort, and the seven-day analysis did not provide independent validation. Overall, this study provides a conservative candidate-marker resource for future validation and for balanced improvement of growth traits while conserving key characteristics of Jining Grey goats.