Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle.

Guoyao Zhao,Xue Gao,Junya Li,George E Liu,Lei Xu,Yuqiang Liu,Huijiang Gao,Bo Zhu,Lupei Zhang,Tianliu Zhang,Lingyang Xu,Zezhao Wang

doi:10.3390/ani10081425

Abstract

Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms. Identifications of ROH leading to reduction in performance can provide valuable insight into the genetic architecture of complex traits. Here, we evaluated genome-wide patterns of homozygosity and their association with important traits in Chinese Wagyu beef cattle. We identified a total of 29,271 ROH segments from 462 animals. Within each animal, an average number of ROH was 63.36 while an average length was 62.19 Mb. To evaluate the enrichment of ROH across genomes, we initially identified 280 ROH regions by merging ROH events across all individuals. Of these, nine regions containing 154 candidate genes, were significantly associated with six traits (body height, chest circumference, fat coverage, backfat thickness, ribeye area, and carcass length; p < 0.01). Moreover, we found 26 consensus ROH regions with frequencies exceeding 10%, and several regions overlapped with QTLs, which are associated with body weight, calving ease, and stillbirth. Among them, we observed 41 candidate genes, including BCKDHB, MAB21L1, SLC2A13, FGFR3, FGFRL1, CPLX1, CTNNA1, CORT, CTNNBIP1, and NMNAT1, which have been previously reported to be related to body conformation, meat quality, susceptibility, and reproductive traits. In summary, we assessed genome-wide autozygosity patterns and inbreeding levels in Chinese Wagyu beef cattle. Our study identified many candidate regions and genes overlapped with ROH for several important traits, which could be unitized to assist the design of a selection mating strategy in beef cattle.

Highlights

Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms [1]
We identified a total of 29,271 ROH in 462 Chinese Wagyu beef cattle
The longest ROH were identified on BTA10 (48.6 Mb with 10,015 singlenucleotide nucleotide polymorphism (SNP)), while the shortest ROH were detected on BTA3 (0.5 Mb with 130 SNPs)

Summary

Introduction

Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms [1]. Several studies have suggested that an individual inherits the chromosomal fragment from both parents, resulting in homozygous segments in the offspring’s genome [2,3]. With the development of high-density array and whole-genome sequencing technologies, they provided unprecedented opportunities to explore homozygosity segments in high resolution [6]. Jane et al further explored different distribution frequencies of ROH with various lengths using high-density SNP arrays, promoting the development for the ROH study in humans [1]. Additional analyses found that ROH can provide insights into the population structure and demography in humans [8,9,10] and genetic relationships [11,12,13,14,15,16]. The enrichment of ROH may increase the harmful recessive alleles, and reduce the survival ability of individuals [17]

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