Abstract
BackgroundGenomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle.ResultsWe detected a total of 116,953 homozygous segments with 2.47Gb across the genome in the studied population. The average number of ROH per individual was 99.03 and the average length was 117.29 Mb. Notably, we detected 42 regions with a frequency of more than 0.2. We obtained 17 candidate genes related to body size, meat quality, and reproductive traits. Furthermore, using Fisher’s exact test, we found 101 regions were associated with production traits by comparing high groups with low groups in terms of production traits. Of those, we identified several significant regions for production traits (P < 0.05) by association analysis, within which candidate genes including ECT2, GABRA4, and GABRB1 have been previously reported for those traits in beef cattle.ConclusionsOur study explored ROH patterns and their potential associations with production traits in beef cattle. These results may help to better understand the association between production traits and genome homozygosity and offer valuable insights into managing inbreeding by designing reasonable breeding programs in farm animals.
Highlights
Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals
Assessment of runs of homozygosity In this study, we identified a total of 116,953 ROH with 2.47Gb across the genome in 1181 Chinese Simmental beef cattle
We found the total length of ROH was significantly different between high and low groups for production traits using Wilcoxon Rank Sum Tests (CW, P = 1.85e-05; live weight (LW), P = 3.25e-06; net meat weight (NMW), P = 1.56e-03; average daily gain (ADG), P = 5.05e-05)
Summary
Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle. Many studies revealed the negative impact of high homozygosity on fertility traits including bull semen quality [4], calving rate [5], stillbirths, and dystocia [6]. A previous study evaluated the association between ROH and reproduction traits using whole-genome homozygosity mapping and revealed candidate regions affecting bull fertility in US Holstein cattle [13]. A recent study identified ROH that unfavorably affects female fertility and milk production traits in the Finnish Ayrshire population [14]
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