Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

Abstract

Background: Consecutive homozygous fragments of the genome inherited from a common ancestor to offspring are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identifying genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~65000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results: In this study, 9102 ROH were identified, with an average number of 21.2±13.1 and 33.2±15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8±120.3 Mb), and in KHZ, 5.96% (149.1±107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P<0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion: The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial and/or natural selection.

Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds

“…Body size and shape vary among breeds [ 2 , 81 ]. Whereas most bovine breeds from temperate regions with access to a good supply of high-quality nutrients have a larger body size, breeds that live in high altitude areas with a limited amount of feed often have a smaller body size.…”

“…Another gene, CSMD3, which encodes a transmembrane protein [79] was reported to be associated with body measurements in cattle [80]. Body size and shape vary among breeds [2,81]. Whereas most bovine breeds from temperate regions with access to a good supply of high-quality nutrients have a larger body size, breeds that live in high altitude areas with a limited amount of feed often have a smaller body size.…”

“…Similarly, different statistical tests have been conceptualized to detect signatures of selection and pinpoint the causal variants by using various models. The rationale behind selection signature theory is that the frequency of alleles that are under selection can vary in opposite directions (low or high), and thus results in stretches of consecutive homozygous genotypes [2], or in modifying the length and frequency of haplotypes around the region. Several statistical tests have been proposed to detect selection signals e.g.…”

Selection signatures of Fuzhong Buffalo based on whole-genome sequences

“…To date, there have been several studies using the highthroughput sequencing and genotyping technologies to search for candidate genes associated with milk production, growth traits, immune and nervous system of buffaloes [6][7][8][9]. However, most of these studies were performed for the dairy river buffalo.…”

“…[6]. Another study detected genes associated with the body size, immunity and coat color by analyzing the ROH of the Azeri and Khuzestani buffalo breeds using the same dataset [7]. The same chip has also been used for the GWAS analysis of water buffalo, revealing a set of candidate genes associated with milk traits (e.g., MFSD14A, SLC35A3, PALMD, RGS22) [8].…”