Estimation of Genomic Breeding Values for Economic Traits in Alxa-Type Cashmere Goats Using Bayesian Methods

Conventional breeding has a long generation interval; genomic selection can enable early selection and shorten the breeding process in cashmere goats. This study aimed to estimate genomic breeding values for economic traits in Inner Mongolia (Alxa-type) cashmere goats using Bayesian methods. Whole-genome resequencing at 1× depth was performed on 491 Alxa-type cashmere goats (40 males and 451 females), and genotypes were imputed to 10× using a reference panel with an average imputation accuracy of 97.90%. Fixed effects were determined by analysis of variance, and breeding values for body weight, cashmere fiber diameter, and cashmere yield were estimated using Bayes A, Bayes B, and Bayes C; prediction accuracy and unbiasedness were evaluated by five-fold cross-validation. Measurement year and group affected all three traits highly significantly (p < 0.01); sex affected body weight and cashmere yield highly significantly (p < 0.01) but no significant effect on cashmere fiber diameter (p > 0.05); and maternal age had a significant effect on body weight (p < 0.05), but no significant effect on cashmere fiber diameter or cashmere yield (p > 0.05); group had a highly significant effect on all three traits (p < 0.01). Breeding values were estimated using Bayes A, Bayes B, and Bayes C, with five-fold cross-validation, and the three methods performed comparably overall in this population.