Genome-wide scan for runs of homozygosity identifies potential candidate regions associated with growth traits in beef cattle
Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms. Identifications of regions of the genome lead to reduction in performance can provide valuable insight into the genetic architecture of complex traits. Here, we evaluated genome-wide patterns of homozygosity and their association with growth traits in a commercial beef cattle population. Results: We identified a total of 29,271 ROH segments with an average number of 63.36
... nd an average length of 0.98 Mb in this commercial beef cattle population, representing 2.53% (~63.36Mb) of the genome. To evaluate the enrichment of ROH across genomes, we initially identified 280 ROH regions by merging ROH events identified across all individuals. Of these, nine regions were significantly associated with six growth phenotype traits (body height, chest circumference, fat coverage, backfat thickness, ribeye area, carcass length; P<0.01), which contain 187 candidate genes. Furthermore, we found 26 consensus ROH regions with frequencies exceeding 10%, and several of these consensus overlapped with QTLs which are associated with weight gain, calving difficulty and stillbirth. To precisely locate locus within each ROH for every studied trait, we further utilized loci-based methods for association analysis among these identified regions. Totally, we obtained 9,360 loci within ROH, and 1,631 loci displaying significant association (P<0.01) for eight traits. In addition, we found that 67 genes embedded with homozygous loci. Several identified candidate genes, including EBF2, SLC20A2, SH3BGRL2, HMGA1 and ACSL1, were related to growth traits. Conclusions: This study assessed genome-wide autozygosity pattern and inbreeding level in a commercial beef cattle population. Our study identified many candidate regions and genes with ROH for growth traits in beef cattle, which can provide important insights into investigating homozygosity across genome in other farm animals. Our findings may further Results Genomic ROH distribution We identified a total of 29271 ROHs in 462 Chinese commercial beef cattle population. ROH were identified with an average number of 63.36 segments and an average length of 0.98 Mb. We found most ROH lengths are relatively short, and most of ROH with lengths ranging from 0.5 Mb to 5 Mb, which accounting for 98.50% of total number, while the proportion of the genome covered by them was relatively small (Fig. 1a) . The size of ROH autosomes; MAF:Minor allele frequency; QTL:Quantitative trait loci; Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape. PLoS Genet 2012, 8(11):e1003100. 7. Purfield DC, Berry DP, McParland S, Bradley DG: Runs of homozygosity and population history in cattle. BMC genetics 2012, 13(1):70. 8.