Inbreeding estimations based on runs of homozygosity revealed genes associated with local adaptation and dairy traits in Iranian water buffaloes, Bubalus bubalis

Abstract Background Consecutive homozygous fragments of the genome that inherited from a common ancestor to offspring are known as runs of homozygosity (ROH). The ROH stretches can be used to estimate the genomic inbreeding and also for identifying genomic regions under extensive selection pressure. The aims of this study were (i) to estimate inbreeding based on ROH (FROH); (ii) to compare FROH with FHOM (excess of homozygosity), FUNI (correlation between uniting gametes), and FGRM (genomic relationship matrix); and (iii) to identify frequently occurred ROH islands (i.e., shared by >20% of the population) for gene enrichment analyses. A dataset consisted of 396 buffalo including Azeri (N = 281) and Khuzestani (N = 115) breeds genotyped for ~65000 SNP were used. Results In total, 10,245 ROH were identified with an average number of 23.3±14.1 and 33.2±15.9 segments per animal for Azeri (AZ) and Khuzestani (KHZ) breeds, respectively. Our results showed that on average 4.71% (117.9±120.7 Mb) and 5.96% (149.15±107.7 Mb) of the genome of AZ and KHZ is autozygous, respectively. The amount of FHOM, FUNI and FGRM were 0.03, 0.03 and 0.03 in Azeri breed and 0.02, 0.02 and 0.02 in Khuzestani breed, respectively. Strong correlations between FROH-FHOM (0.93) and between FROH-FUNI (0.98 and 0.94) and moderate to strong correlations between FROH-FGRM (0.86 and 0.78) were obtained. Overall, we identified 13 frequently occurred ROH regions. The GO analyses revealed numerous enriched terms for the ROH gene list in KHZ breed. Genes associated with adaptation to hot and arid climate (BMP2), immune response (CYP27B1), milk production, protein, and fat percentage (MARS and ADRA1A, KCTD16), coat color and pigmentation (PMEL and MYO1A), reproductive traits (INHBE and INHBC, STAT6, PCNA), and bone development (SUOX) were identified. Conclusion Genes within common ROH spots present a modest phenotypic selection for milk production traits in Khuzestani buffalo. Further, our results suggest that natural selection may have a role in forming the genome of Iranian buffaloes in order to adapt them to the harsh environment of the country.