Genetic Parameters and Genome-Wide Association Analysis of Reproductive Traits in Egyptian Buffalo

Reproductive efficiency is a crucial factor in the sustainability and profitability of buffalo production systems. However, genetic improvement of reproductive traits is challenging due to low heritability, environmental sensitivity, limited recording, and shrinking reference populations caused by crossbreeding. This study aimed to estimate genetic parameters and detect the genomic architecture of key reproductive traits in Egyptian buffalo using pedigree-based analyses and genome-wide association studies (GWAS). Over a 44-year period (1980-2024), reproductive records from five Egyptian experimental herds were analysed. The dataset comprised 2843 buffalo cows, sired by 140 bulls and out of 1328 dams. In total, 2359 records were available for age at first calving (AFC), 10,478 for gestation length (GL), 7966 for calving interval (CI), 6705 for days open (DO), and 12,909 for calving ease (CE) and stillbirth (SB). For genome-wide association analysis, 275 Egyptian buffaloes were genotyped using the Affymetrix Buffalo 90 K array, and 66,295 high-quality SNPs were retained after quality control. De-regressed proofs derived from pedigree-based genetic evaluations were used as response variables in a mixed linear model implemented in the rMVP package. Genome-wide association analysis identified putative genomic regions associated with GL, CI, CE, and SB, whereas no genome-wide significant associations were detected for AFC and DO. Functional annotation and QTL enrichment analyses were subsequently used to provide exploratory biological context for the identified genomic regions. Heritability estimates were generally low: 0.16 for AFC, 0.06 for GL, 0.02 for CI, 0.02 for DO, 0.18 for CE, and 0.06 for SB. Manhattan plots revealed that 15 genomic regions containing significant SNPs were identified on chromosomes 2, 4, 10, 12, 13, 15, 19, 20, and 25 for the reproductive traits of GL, CI, CE, and SB. These findings provide preliminary evidence of genomic regions potentially contributing to variation in reproductive traits in Egyptian buffalo, although the relatively small number of genotyped animals limits the power to detect and validate small effect loci. Seven significant genomic regions on chromosomes 10, 13, 15, 20, and 25 were associated with the GL trait. Additionally, three suggestive SNPs mapped to chromosomes 2 and 19 were associated with the CE trait, and three suggestive SNPs mapped on chromosome 12 were significantly associated with the SB trait. The results of KEGG enrichment analyses and QTL classification analyses for reproductive traits in Egyptian buffalo suggest that candidate genes within known QTL may be involved in complex biological networks involving immune competence, cellular homeostasis, and systemic physiological resilience. Among the enriched pathways, Fc gamma R-mediated phagocytosis, protein export, viral myocarditis, and arrhythmogenic right ventricular cardiomyopathy (ARVC) were highlighted. Most annotated genomic regions (QTL) were related to reproductive traits (63.4%), followed by 17.3% for milk production traits, 9.95% for general production traits, 3.47% for meat and carcass traits, 3.71% for body conformation and robustness exterior traits, and 2.08% for health traits.