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

Abstract

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.