Genomic patterns of homozygosity in Chinese local cattle

Authors: XU, LINGYANG - Chinese Academy Of Agricultural Sciences; ZHAO, GUOYAO - Chinese Academy Of Agricultural Sciences; XU, LEI - Chinese Academy Of Agricultural Sciences; WANG, ZEZHAO - Chinese Academy Of Agricultural Sciences; YANG, LIU - Chinese Academy Of Agricultural Sciences; ZHANG, LUPEI - Chinese Academy Of Agricultural Sciences; GAO, XUE - Chinese Academy Of Agricultural Sciences; GAO, HUIJIANG - Chinese Academy Of Agricultural Sciences; Liu, Ge - George; LI, JUNYA - Chinese Academy Of Agricultural Sciences

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/21/2019
Publication Date: 8/28/2019
Citation: Xu, L., Zhao, G., Xu, L., Wang, Z., Yang, L., Zhang, L., Gao, X., Gao, H., Liu, G., Li, J. 2019. Genomic patterns of homozygosity in Chinese local cattle. Scientific Reports. 9(1):16977. https://doi.org/10.1038/s41598-019-53274-3.
DOI: https://doi.org/10.1038/s41598-019-53274-3

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 native 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: Background: Genome wide single nucleotide polymorphisms arrays are suitable to investigate region of homozygosity (ROH) segments where the two haplotypes inherited from the parents are identical. Here, we investigated the occurrence and distribution of ROH and characterize ROH pattern and its island hotspots using a high-dense SNP array in diverse Chinese native cattle. Results: We identified a total of 27,358 ROHs with an average 153 ROH per animal in Chinese native cattle. The lengths of ROH varied considerably ranging from 0.5 to 66 Mb, while an average ROH length was 1.22 Mb across all autosomes. We observed the highest average proportion of the genome covered by ROHs (323.1Mb, ~11.54% of cattle genome) in NDC from South China, whereas the lowest average proportion was found in YHC (86.7Mb, ~3.1%). The average FROH values ranged from 0.03 in YHC to 0.12 in NDC cattle. For each of three ROH classes (small 0.5-1 Mb, medium 1-5 Mb and large >5 Mb), the numbers and total lengths of ROH per individual showed considerable changes across both individuals and populations. Our results suggested the ROH frequencies across the genome were related to local genomic variables such as recombination rate, as well as with signals of recent positive selection. By investigating the occurrence of ROHs across genome, we observed a list of hotspots ranged from 993 to 3603 for top 1% in eight cattle breeds, respectively. According to gene ontology annotation, most of these genes were involved in multiple signaling and signal transduction pathways for a wide variety of cellular and biochemical processes. We also revealed the presence of ROH islands in genomic regions that harbor several candidate genes for selection in response to environmental stress and local adaptation. Conclusion: We generated baselines for homozygosity patterns in diverse Chinese cattle populations. Our results imply that natural selection has, at least partially, played a role in shaping the genomes of Chinese native cattle and that breed-specific ROH pattern may provide valuable insights about traits under selection. These findings further made it possible to explore the mechanism of homozygosity and can be further utilized to study genetic diversity and evolutionary history.