Genome-wide association studies for sperm traits in Assaf sheep breed

Area of Science:

• Animal Genetics
• Reproductive Biology
• Genomic Selection

Background:

• Sperm quality in rams is vital for artificial insemination (AI) success and economic viability of AI centers.
• Low heritability of sperm traits limits traditional genetic selection for improvement.
• Identifying genetic variants influencing sperm quality is essential for efficient breeding programs.

Purpose of the Study:

• To conduct a genome-wide association study (GWAS) to identify single-nucleotide polymorphisms (SNPs) associated with sperm quality traits in Assaf rams.
• To explore the potential of these identified SNPs for marker-assisted selection (MAS) to enhance ram fertility and AI efficiency.

Main Methods:

• A GWAS was performed using phenotype data for sperm concentration, volume, number, and mass motility from 429 Assaf rams.
• Genotyping data from a 50K Affymetrix custom chip were used, with imputation to HD genotypes for all rams.
• A linear regression model was applied to obtain pseudo-phenotypes for GWAS analysis, controlling for environmental and fixed effects.

Main Results:

• Significant associations (chromosome-wise, FDR 10%) were found for 76 SNPs (ejaculate concentration), 20 SNPs (ejaculate volume), 32 SNPs (spermatozoa number), and 23 SNPs (spermatozoa mass motility).
• Only SNPs associated with spermatozoa mass motility reached genome-wide significance.
• Candidate genes for sperm traits variability were identified, including SLC9C1, TSN, FUT10, DOCK2, CPLANE1, SPEF2, RAI14, SCAPER, PSMA4, PARM1, and LOC101110593.

Conclusions:

• Identified SNPs associated with sperm quality traits in Assaf rams can be utilized for marker-assisted selection.
• These genetic markers offer a promising strategy to improve ram sperm characteristics and increase the efficiency of AI centers.
• No correlation was found between sperm trait SNPs and milk production genetics, allowing for independent selection for both traits.