Yang Zhou1,6, Lv Yang1,6, Xiaotao Han1, Jiazheng Han1, Yan Hu1, Fan Li1, Han Xia1, Lingwei Peng1, Clarissa Boschiero2, Benjamin D. Rosen2, Derek M. Bickhart3, Shujun Zhang1, Aizhen Guo4, Curtis P. Van Tassell2, Timothy P.L. Smith5, Liguo Yang1 and George E. Liu2 1Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; 2Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA; 3Dairy Forage Research Center, ARS USDA, Madison, Wisconsin 53706, USA; 4The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; 5U.S. Meat Animal Research Center, ARS USDA, Clay Center, Nebraska 68933, USA

↵6 These authors contributed equally to this work.

Corresponding authors: George.Liuusda.gov, yangzhoumail.hzau.edu.cn, ylgmail.hzau.edu.cn Abstract

A cattle pangenome representation was created based on the genome sequences of 898 cattle representing 57 breeds. The pangenome identified 83 Mb of sequence not found in the cattle reference genome, representing 3.1% novel sequence compared with the 2.71-Gb reference. A catalog of structural variants developed from this cattle population identified 3.3 million deletions, 0.12 million inversions, and 0.18 million duplications. Estimates of breed ancestry and hybridization between cattle breeds using insertion/deletions as markers were similar to those produced by single nucleotide polymorphism–based analysis. Hundreds of deletions were observed to have stratification based on subspecies and breed. For example, an insertion of a Bov-tA1 repeat element was identified in the first intron of the APPL2 gene and correlated with cattle breed geographic distribution. This insertion falls within a segment overlapping predicted enhancer and promoter regions of the gene, and could affect important traits such as immune response, olfactory functions, cell proliferation, and glucose metabolism in muscle. The results indicate that pangenomes are a valuable resource for studying diversity and evolutionary history, and help to delineate how domestication, trait-based breeding, and adaptive introgression have shaped the cattle genome.

Received January 2, 2022. Accepted July 21, 2022.