Runs of homozygosity analysis and genomic inbreeding estimation in Sumba Ongole cattle ( Bos indicus ) using a BovineSNP50K BeadChip.

Background and Aim: Runs of homozygosity (ROH) is a biocomputational technique for identifying homozygous regions in the genomics of livestock. This study aimed to determine the ROH in Sumba Ongole (SO) bulls (n = 48) using the BovineSNP50K BeadChip.
Materials and Methods: GenomeStudio 2.0 software was used to generate the BovineSNP50K BeadChip output. The ROH and ROH-based inbreeding coefficients (F _ROH ) were determined using the detect RUNS R v4.1.0 package. Using the following filtering criteria, PLINK v1.90 software was used to perform genotype quality control: (1) Individuals and single-nucleotide polymorphism (SNPs) had call rates >0.95; (2) more than 0.05 was the minor allele frequency; (3) the list contained only SNPs linked to autosomes; and (4) SNPs that strongly deviated (p < 1e-6) from Hardy-Weinberg equilibrium were removed. Subsequently, 25,252 autosomal SNP markers were included in the ROH and F _ROH analyses.
Results: In general, the number and length of ROH segments in pool animals were 149.77 ± 16.02 Mb and 486.13 ± 156.11 Mb, respectively. Furthermore, the ROH segments in the animals under study can be discriminated into two classes of 1-4 Mb (83.33%) and 4-8 Mb (16.67%). Subsequently, Bos taurus autosomes (BTA) 1, BTA6, and BTA14 had significant homozygous segments comprising 13 genes. Despite this, the average F _ROH in pool animals was 0.20 ± 0.06.
Conclusion: These findings indicate that a recent inbreeding event in SO cattle occurred many generations ago. Furthermore, the candidate genes identified from the ROH analysis indicate phenotypic attributes associated with environmental adaptation and economic traits.
Competing Interests: The authors declare that they have no competing interests.
(Copyright: © Putra, et al.)