goat_genotype
This study investigates the genomic determinants of post-thaw sperm quality in goats using multi-locus mixed-model (MLMM) genome-wide association analyses. Semen from 24 goats was cryopreserved in five replicates. Post-thaw semen quality was assessed using computer-assisted sperm analysis (CASA) for motility and kinematic traits, and flow cytometry for plasma membrane integrity, acrosome integrity, viability, mitochondrial membrane potential, oxidative stress, and capacitation status. MLMM-GWAS identified 48 SNPs associated with post-thaw traits, including 37 genome-wide significant and 11 suggestive associations. The strongest signals were detected for VAP (snp16934-scaffold177-165682, chr1; p = 1.34 × 10-29) and LIN (snp18232-scaffold185-18205520, chr10; p = 1.58 × 10-29). Motility-associated SNPs clustered on chromosomes 1 and 10, affecting VAP, VCL, ALH, BCF, STR, LIN, and WOB. Eleven SNPs were linked to functional traits, notably high mitochondrial membrane potential (snp16390-scaffold1728-6620, chr5; p = 7.53 × 10-16) and F-pattern capacitation (snp50870-scaffold737-440335, chr3; p = 3.42 × 10-20). Gene annotation within ±100 kb of significant SNPs identified 72 candidates, with enrichment highlighting meiotic recombination, chromatin organization, PON-mediated antioxidant systems, and membrane lipid metabolism. These findings provide insight into the molecular architecture of post-thaw sperm quality and suggest targets for genomic-assisted selection, although validation in larger independent populations is required to confirm robustness and applicability.