Genome-wide runs of homozygosity in Indian goat breeds reared under small holder production system

Abstract

Small holder goat production system is often constrained by high inbreeding due to small herd size and uncontrolled breeding. Runs of homozygosity (ROH), the long stretches of homozygous genomic DNA is the most reliable measure of autozygosity. The objective of present study was to investigate the number and coverage of ROH in the genome and to estimate the genomic inbreeding coefficient (FROH) in two divergent Indian goat breeds viz; Attappady Black and Malabari goats farmed under small holder production system. The genome-wide single nucleotide polymorphism (SNP) marker data obtained by Illumina SNP50 goat BeadChip genotyping of 48 goats (24 each of Attappady Black and Malabari goats) sampled from farmers flock in their respective breeding tract was utilised for ROH detection. The ROH of > 1 Mb was defined as tracts of homozygous genotypes with at least 15 SNPs and less than five missing SNPs. The ROH detection was carried out with PLINK 1.9 version. The proportion of goats lacking ROH (per cent) was 66.67 in Attappady Black and 39.13 in Malabari goats. The mean number and length of ROH of 1 Mb or more was higher in Malabari goats (2.1304 ± 0.6369 and 6.0016 ± 0.5271 Mb) compared to Attappady Black goats (0.4583 ± 0.1343 and 4.0197 ± 0.3755 Mb). Mean ± S.E of sum of ROH coverage of genome per individual (SROH) was 1.8423 ± 0.05976 and 8.8236 ± 1.2785 Mb in Attappady Black and Malabari goats, respectively and differed among the two breeds significantly (p ≤ 0.05). Analysis of the distribution of ROH according to their length showed that majority of the detected ROH were < 8 Mb in length in both breeds with no ROH of > 8 Mb in Attappady Black goats. Mean ± S.E of genomic inbreeding coefficient (FROH≥1 Mb) in per cent was 0.519 ± 0.19 and 0.07480 ± 0.0243 in Malabari goats and Attappady Black goats, respectively. The pattern of ROH estimated in the present analysis indicates the inbreeding history of the goats farmed under small holder production system. Results of present study indicate that both breeds are less consanguineous and showed no evidence of recent inbreeding.