Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle

Abstract

Background: 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.

Results: We 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.

Conclusions: Our 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.

Keywords: Association analysis; Chinese Simmental beef cattle; Consensus ROH; Production traits; Runs of homozygosity.

Fig. 1

(A) The distribution of the total number of ROH across chromosomes. (B) The total number and length (Mb) of ROH belonging to three size classes including Small (0.5 to 1 Mb), Medium (1 to 5 Mb), and Large (> 5 Mb) size. (C) Evaluation of the number of ROH and ROH total length. The number of ROH found for each individual genome (y-axis) is plotted against ROH total length (i.e. the length of Mb covered by ROH in each genome, x-axis). (D) Distribution characteristics of ROH on chromosomes in Chinese Simmental beef cattle. The horizontal axis is the single nucleotide polymorphism (SNP) position, which is ordered by the physical location of the genome; the vertical axis is the ROH rate. The horizontal line in the graph is where the ROH frequency equals 20 %

Fig. 2

Scatter plot of total homozygosity per individual against four corrected carcass traits (NMW, CW, ADG, LW). (A) Net meat weight (NMW), (B) Carcass weight (CW), (C) Average daily gain (ADG); (D) Live weight (LW)

Fig. 3

Correlation between runs of homozygosity and four carcass traits (NMW, CW, ADG, LW). (A) Histogram showing the distribution of NMW for Chinese Simmental beef cattle. (B) Distribution of total homozygosity, calculated as the sum of all runs of homozygosity in the high group and low group for NMW. (C). Histogram showing the distribution of CW. (D). Distribution of total of runs of homozygosity in the high group and low for CW. (E). Histogram showing the distribution of ADG. (F). Distribution of total of runs of homozygosity in the high group and low group for ADG. (G). Histogram showing the distribution of LW. (H). Distribution of total of runs of homozygosity in the high group and low group for LW

Fig. 4

(A). The boxplot of the adjusted ADG for ROH and non ROH; (B). The boxplot of the pre-adjusted LW for ROH and non ROH; (C). Haplotype LD analyses nearby the ROH (chr1:95,450,372–95,517,810) on candidate gene ECT2

Fig. 5

(A). The rate of ROH plot at BTA6. (B). The number of ROH based on the region extracted from BTA6. (C). The length of ROH is based on the region extracted from BTA6. (D). Haplotype LD analyses nearby the 1.2 Mb region with three consensus ROH were overlapped with three genes (LAP3, NCAPG, and LCOLR)