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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #375353
Research Project: Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Genome-wide assessment of runs of homozygosity in Chinese Wagyu beef cattle

Author
item ZHAO, GUOYAO - Chinese Academy Of Agricultural Sciences
item ZHANG, TIANLIU - Chinese Academy Of Agricultural Sciences
item LIU, YUQIANG - Chinese Academy Of Agricultural Sciences
item WANG, ZEZHAO - Chinese Academy Of Agricultural Sciences
item XU, LEI - Chinese Academy Of Agricultural Sciences
item ZHU, BO - Chinese Academy Of Agricultural Sciences
item GAO, XUE - Chinese Academy Of Agricultural Sciences
item ZHANG, LUPEI - Chinese Academy Of Agricultural Sciences
item GAO, HUIJIANG - Chinese Academy Of Agricultural Sciences
item Liu, Ge - George
item LI, JUNYA - Chinese Academy Of Agricultural Sciences
item XU, LINGYANG - Chinese Academy Of Agricultural Sciences

Submitted to: Animals
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/10/2020
Publication Date: 8/14/2020
Citation: Zhao, G., Zhang, T., Liu, Y., Wang, Z., Xu, L., Zhu, B., Gao, X., Zhang, L., Gao, H., Liu, G., Li, J., Xu, L. 2020. Genome-wide assessment of runs of homozygosity in Chinese Wagyu beef cattle. Animals. 10(8):E1425. https://doi.org/10.3390/ani10081425.
DOI: https://doi.org/10.3390/ani10081425

Interpretive Summary: Region of homozygosity (ROH) are homozygous segments where the two haplotypes inherited from the parents are identical. Using high dense SNP arrays, we investigated its occurrence, distribution, and hotspots in Chinese Wagyu beef cattle. These results can be utilized to study the homozygosity mechanism, genetic diversity and evolutionary history. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enable animal selection will benefit from this study.

Technical Abstract: Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms. Identifications of regions of the genome lead 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 growth traits in Chinese Wagyu beef cattle. We identified a total of 29,271 ROH segments from 462 Chinese Wagyu animals. Within each animal, an average number of 63.36 ROH with an average length of 0.98 Mb, represent ~2.53% (~63.36Mb) of the genome. 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 growth phenotype traits (body height, chest circumference, fat coverage, backfat thickness, ribeye area, carcass length; P<0.01). Furthermore, we found 26 consensus ROH regions with frequencies exceeding 10%, and several of them overlapped with QTLs, which are associated with weight gain, calving difficulty and stillbirth. Among the detected 26 regions with ROH frequency exceeding 10%, we observed 41 reference 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 trait in cattle. In summary, this study assessed genome-wide autozygosity pattern and inbreeding level in Chinese Wagyu beef cattle. We study identified many candidate regions and genes with ROH for several important traits, which can be unitized to assist the design of selection mating strategy.