TY - JOUR T1 - The first sheep graph-based pan-genome reveals the spectrum of structural variations and their effects on tail phenotypes JF - bioRxiv DO - 10.1101/2021.12.22.472709 SP - 2021.12.22.472709 AU - Ran Li AU - Mian Gong AU - Xinmiao Zhang AU - Fei Wang AU - Zhenyu Liu AU - Lei Zhang AU - Mengsi Xu AU - Yunfeng Zhang AU - Xuelei Dai AU - Zhuangbiao Zhang AU - Wenwen Fang AU - Yuta Yang AU - Huanhuan Zhang AU - Weiwei Fu AU - Chunna Cao AU - Peng Yang AU - Zeinab Amiri Ghanatsaman AU - Niloufar Jafarpour Negari AU - Hojjat Asadollahpour Nanaei AU - Xiangpeng Yue AU - Yuxuan Song AU - Xianyong Lan AU - Weidong Deng AU - Xihong Wang AU - Ruidong Xiang AU - Eveline M. Ibeagha-Awemu AU - Pat (J.S.) Heslop-Harrison AU - Johannes A. Lenstra AU - Shangquan Gan AU - Yu Jiang Y1 - 2022/01/01 UR - http://biorxiv.org/content/early/2022/01/04/2021.12.22.472709.abstract N2 - 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 pan-genome 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 pan-genome graph rather than a single reference genome.Competing Interest StatementThe authors have declared no competing interest. ER -