Genomic Diversity and Genome-Wide Association Analysis of Growth Traits in a Chongming White Goat Conservation Population

Background/Objectives: This study characterized genetic diversity in a Chongming white goat conservation population and identified loci associated with growth and body conformation. Methods: Whole-genome resequencing of 350 goats was used to assess genetic diversity, runs of homozygosity (ROH), genomic relationships, and population structure. Genome-wide association analyses examined body weight at 180 days (T8), body weight at 360 days (T13), and chest circumference at 180 days (T11). Results: Effective population size was estimated at 49.1, and the mean ROH-based inbreeding coefficient was 0.034 (range: 0–0.2112). Fourteen family groups were inferred. Three, 16, and eight variants were associated with T8, T13, and T11, respectively. A PRP1 variant was shared between the two weight traits, whereas a FOXJ2 variant was shared between 360-day weight and 180-day chest circumference. Chest circumference associations clustered in a 186.6-kb chromosome 5 interval containing CLEC4D, CLEC6A, and CLEC4E. Exploratory enrichment included nutrient-response, developmental, and immune recognition terms. Conclusions: These findings inform conservation mating and genetic diversity management and prioritize growth-associated candidates for independent validation.