Dissecting the genetic basis of computer-assisted fresh semen traits in goats using multi-locus genome-wide association methods

Background Improving sperm quality through genetic selection is a critical strategy for enhancing reproductive efficiency in farm animals. Dissecting the molecular basis of complex reproductive traits requires identifying genetic variants linked to key semen characteristics. Genome-wide association studies (GWAS) provide a robust framework for exploring the genetic architecture of economically significant traits, including fertility. In this study, both conventional sperm parameters—semen volume (mL), mass activity (scale 1–4), sperm concentration (×10 ⁹ /mL), and total sperm count per ejaculation (×10 ⁹ )—and CASA-derived motility traits—total motility (%), progressive motility (%), average path velocity (VAP, µm/s), straight-line velocity (VSL, µm/s), curvilinear velocity (VCL, µm/s), amplitude of lateral head displacement (ALH, µm), beat cross frequency (BCF, Hz), straightness (STR, %), linearity (LIN, %), and wobble (WOB, %)—were evaluated in 24 bucks from three breeds (Boer, n = 11; Anglo-Nubian, n = 8; Murcia-Granada, n = 5) during the breeding season. To investigate the genetic basis of these traits, three advanced multi-locus GWAS models—BLINK, FarmCPU, and MLMM—were applied. Subsequent gene annotation, functional enrichment, and network analyses were performed for candidate genes located within ± 100 Kb of the associated SNPs, offering novel insights into the molecular mechanisms underlying spermatological characteristics. Results A total of 98 SNPs were found to be significantly associated with various semen parameters. Of these, 12 SNPs exhibited high statistical significance, with p-values ranging from 1 × 10⁻ ⁶ to 1 × 10⁻ ¹⁵ . Noteworthy SNPs included rs268240712 (upstream of TLE4 ) and rs268235538 (upstream of SOX5 ), significantly associated with mass activity and sperm concentration, respectively. Additionally, rs268283792 (downstream of STIM2 ), rs268247301 (downstream of TPCN2 ), and rs268257690 (located within an intronic region of PIDD1 ) were significantly linked to total motility. Gene annotation within ± 100 Kb of each SNP identified 49 candidate genes. Enrichment and network analyses suggested that sperm structural and functional development plays a pivotal role in determining semen quality. Conclusion This study reveals candidate genomic regions influencing CASA-derived sperm traits in goats, offering potential for marker-assisted selection. However, further validation in larger and independent populations is warranted to confirm these associations and to assess their practical utility in genetic improvement programs.