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

## TL;DR

This study analyzed the genome of Sumba Ongole cattle to identify homozygous regions and estimate inbreeding levels using SNP data.

## Contribution

The study provides new insights into genomic inbreeding and candidate genes in Sumba Ongole cattle using ROH analysis.

## Key findings

- The average ROH length in SO cattle was 486.13 ± 156.11 Mb with segments classified into 1–4 Mb and 4–8 Mb.
- Significant homozygous segments were found on BTA1, BTA6, and BTA14, containing 13 candidate genes.
- The average FROH was 0.20 ± 0.06, indicating historical inbreeding in the population.

## Abstract

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.

GenomeStudio 2.0 software was used to generate the BovineSNP50K BeadChip output. The ROH and ROH-based inbreeding coefficients (FROH) 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 FROH analyses.

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 FROH in pool animals was 0.20 ± 0.06.

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.