Genome-wide association analysis reveals genetic architecture of fertility traits in Sahiwal heifers and cows.

Abstract

Fertility traits are pivotal to the productivity and sustainability of dairy production systems; however, their genetic improvement remains constrained due to complex polygenic control and low heritability. Genome-wide association studies (GWAS) offer a powerful approach to identify genomic regions underlying reproductive traits, particularly in tropically adapted indigenous breeds like Sahiwal cattle, which exhibit resilience to environmental stress. This study aimed to elucidate the genetic basis of 8 fertility traits in 303 Sahiwal animals using 50 K SNP genotyping. Animals were genotyped with the Illumina BovineSNP50 BeadChip, and 26,267 high-quality SNPs were retained post quality control. Fertility traits analyzed in heifers included age at first calving (HAFC), interval between first and last insemination (HIFL), and number of services per conception (HNSPC); in cows, traits included cow pregnancy rate (CPR), number of services per conception (CNSPC), interval between first and last insemination (CIFL), service period (CSP), and calving-to-first insemination interval (CICAI). Phenotypic records were pre-adjusted for non-genetic factors such as year and season of birth or calving, and population structure was corrected using principal components. A total of 31 single-nucleotide polymorphisms (SNPs) were identified as significantly associated with these fertility traits, 13 in heifers and 18 in cows. Gene annotation of associated loci revealed several biologically relevant candidates, including DMXL2, SCG3, SIX2, CELSR1, and TRNAE-UUC for heifers, and PLA2G7, ADGRF5, RSRC1, TBC1D21, SPRED1, and FAM98B for cows. Evidence of shared SNPs across various traits indicates pleiotropic genetic control of fertility, with CNSPC-associated genes (SPRED1, RASGRP1, FAM98B), implicating Ras-MAPK-ERK signaling, immune regulation, and RNA processing in conception efficiency. These genes are involved in neuroendocrine regulation, gametogenesis, lipid metabolism, and early embryonic development. These findings provide candidate genomic regions for further validation and potential incorporation into fertility-focused genomic selection programs in tropical dairy cattle.