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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 #397688
Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes

Author
item LI, RAN - Northwest A&f University
item GONG, MIAN - Northwest A&f University
item ZHANG, XINMIAO - Northwest A&f University
item WANG, FEI - Northwest A&f University
item LIU, ZHENYU - Northwest A&f University
item ZHANG, LEI - Northwest A&f University
item YANG, QIMENG - Northwest A&f University
item XU, YUAN - Northwest A&f University
item XU, MENGSI - Xinjiang Academy Of Agricultural And Reclamation Science
item ZHANG, HUANHUAN - Northwest A&f University
item ZHANG, YUNFENG - Xinjiang Academy Of Agricultural And Reclamation Science
item DAI, XUELEI - Northwest A&f University
item ZHANG, ZHUANGBIAO - Northwest A&f University
item FANG, WENWEN - Northwest A&f University
item YANG, YUTA - Northwest A&f University
item FU, WEIWEI - Northwest A&f University
item CAO, CHUNNA - Northwest A&f University
item YANG, PENG - Xinjiang Academy Of Agricultural And Reclamation Science
item GHANATSAMAN, ZEINAB - Agricultural Research, Education And Extension Organization (AREEO)
item NEGARI, NILOUFAR - University Of Kerman
item NANAEI, HOJJAT - Northwest A&f University
item YUE, XIANGPENG - Lanzhou University
item SONG, YUXUAN - Northwest A&f University
item LAN, XIANYONG - Northwest A&f University
item DENG, WEIDONG - Yunnan Agricultural University
item WANG, XIHONG - Northwest A&f University
item PAN, CHUANYING - Northwest A&f University
item XIANG, RUIDONG - University Of Melbourne
item IBEAGHA-AWEMU, EVELINE - Collaborator
item HESLOP-HARRISON, PAT - University Of Leicester
item Rosen, Benjamin - Ben
item LENSTRA, JOHANNES - Utrecht University
item GAN, SHANGQUAN - Xinjiang Academy Of Agricultural And Reclamation Science
item JIANG, YU - Northwest A&f University

Submitted to: Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/21/2023
Publication Date: 3/27/2023
Citation: Li, R., Gong, M., Zhang, X., Wang, F., Liu, Z., Zhang, L., Yang, Q., Xu, Y., Xu, M., Zhang, H., Zhang, Y., Dai, X., Zhang, Z., Fang, W., Yang, Y., Fu, W., Cao, C., Yang, P., Ghanatsaman, Z.A., Negari, N.J., Nanaei, H.A., Yue, X., Song, Y., Lan, X., Deng, W., Wang, X., Pan, C., Xiang, R., Ibeagha-Awemu, E.M., Heslop-Harrison, P.J., Rosen, B.D., Lenstra, J.A., Gan, S., Jiang, Y. 2023. A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes. Genome Research. 33:463-477. https://doi.org/10.1101/gr.277372.122.
DOI: https://doi.org/10.1101/gr.277372.122

Interpretive Summary: Genetic analysis and advanced animal breeding techniques rely upon accurate knowledge of the content and arrangement of a species genetic information. A high-quality reference assembly serves as a guidebook for the genome. However, a reference genome is just the representation of a single individual’s genetic information. Some types of genetic variation such as structural variation where regions have been duplicated, lost, or rearranged, are difficult to identify using reference genomes. A pangenome attempts to represent the genetic information of a whole species. Here we build a pangenome from 13 sheep breeds which provides a fundamental resource for understanding trait biology and mining genetic diversity in sheep.

Technical Abstract: Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here, we assembled 26 haplotype-resolved genome assemblies from 13 genetically diverse sheep using PacBio HiFi sequencing. We constructed a graph-based ovine pangenome and discovered 142,422 biallelic insertions and deletions, 7,028 divergent alleles and 13,419 multiallelic variations. We then used a graph-based approach to genotype the biallelic SVs in 684 individuals from 45 domestic breeds and two wild species. Integration with RNA-seq data allows to identify candidate expression-associated SVs. We demonstrate a direct link of SVs and phenotypes by localizing the putative causative insertion in HOXB13 gene responsible for the long-tail trait and identifying multiple large SVs associated with the fat-tail. Beyond generating a benchmark resource for ovine structural variants, our study highlights that animal genetic research will greatly benefit from using a pangenome graph rather than a single reference genome.