Genomic insights into demographic history, structural variation landscape, and complex traits from 514 Hu sheep genomes

Kaiyu Chen; Yuelang Zhang; Yizhe Pan; Xin Xiang; Chen Peng; Jiayi He; Guiqing Huang; Zhengguang Wang; Pengju Zhao

doi:10.1016/j.jgg.2024.11.015

Volume 52 Issue 2

Feb. 2025

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Genomic insights into demographic history, structural variation landscape, and complex traits from 514 Hu sheep genomes

doi: 10.1016/j.jgg.2024.11.015

a. College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China;
b. Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China;
c. Agricultural Product Quality and Safety Research Center of Huzhou City, Huzhou, Zhejiang 313000, China

Received Date: 2024-08-28
Accepted Date: 2024-11-24
Rev Recd Date: 2024-11-21

Available Online: 2025-07-11

Publish Date: 2024-12-04

Abstract

Abstract

Hu sheep is an indigenous breed from the Taihu Lake Plain in China, known for its high fertility. Although Hu sheep belong to the Mongolian group, their demographic history and genetic architecture remain inconclusive. Here, we analyze 697 sheep genomes from representatives of Mongolian sheep breeds. Our study suggests that the ancestral Hu sheep first separated from the Mongolian group approximately 3000 years ago. As Hu sheep migrated from the north and flourished in the Taihu Lake Plain around 1000 years ago, they developed a unique genetic foundation and phenotypic characteristics, which are evident in the genomic footprints of selective sweeps and structural variation landscape. Genes associated with reproductive traits (BMPR1B and TDRD10) and horn phenotype (RXFP2) exhibit notable selective sweeps in the genome of Hu sheep. A genome-wide association analysis reveals that structural variations at LOC101110773, MAST2, and ZNF385B may significantly impact polledness, teat number, and early growth in Hu sheep, respectively. Our study offers insights into the evolutionary history of Hu sheep and may serve as a valuable genetic resource to enhance the understanding of complex traits in Hu sheep.
- Hu sheep,
- Population sequencing,
- Demographic history,
- Structural variation,
- Genome-wide association study

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References

Alexander, D.H., Novembre, J.,Lange, K., 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655-1664.

Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I.T., Novak, A.M., Deran, A., Fang, Q., Xie, D., Feng, S., Stiller, J., et al., 2020. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature 587, 246-251.

Audano, P.A., Sulovari, A., Graves-Lindsay, T.A., Cantsilieris, S., Sorensen, M., Welch, A.E., Dougherty, M.L., Nelson, B.J., Shah, A., Dutcher, S.K., et al., 2019. Characterizing the major structural variant alleles of the human genome. Cell 176, 663-675 e619.

Bao, J., Xiong, J., Huang, J., Yang, P., Shang, M.,Zhang, L., 2024. Genetic diversity, selection signatures, and genome-wide association study identify candidate genes related to litter size in Hu sheep. Int. J. Mol. Sci. 25, 9397.

Browning, B.L., Tian, X., Zhou, Y.,Browning, S.R., 2021. Fast two-stage phasing of large-scale sequence data. Am. J. Hum. Genet. 108, 1880-1890.

Bu, D., Luo, H., Huo, P., Wang, Z., Zhang, S., He, Z., Wu, Y., Zhao, L., Liu, J., Guo, J., et al., 2021. KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis. Nucleic Acids Res. 49, W317-W325.

Bushnell, B. 2014. BBMap: a fast, accurate, splice-aware aligner.

Cameron, D.L., Baber, J., Shale, C., Valle-Inclan, J.E., Besselink, N., van Hoeck, A., Janssen, R., Cuppen, E., Priestley, P.,Papenfuss, A.T., 2021. GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing. Genome Biol. 22, 202.

Chen, H., Patterson, N.,Reich, D., 2010. Population differentiation as a test for selective sweeps. Genome Res. 20, 393-402.

Chen, S.F., Zhou, Y.Q., Chen, Y.R.,Gu, J., 2018. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, 884-890.

Chen, T., Chen, X., Zhang, S., Zhu, J., Tang, B., Wang, A., Dong, L., Zhang, Z., Yu, C., Sun, Y., et al., 2021. The genome sequence archive family: toward explosive data growth and diverse data types. Genomics, Proteomics Bioinf. 19, 578-583.

Chen, X., Schulz-Trieglaff, O., Shaw, R., Barnes, B., Schlesinger, F., Kallberg, M., Cox, A.J., Kruglyak, S.,Saunders, C.T., 2016. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics 32, 1220-1222.

Chong, Y.Q., Jiang, X.P.,Liu, G.Q., 2022. An ancient positively selected BMPRIB missense variant increases litter size of Mongolian sheep populations following latitudinal gradient. Mol. Genet. Genomics 297, 155-167.

Clark, E.L., Bush, S.J., McCulloch, M.E.B., Farquhar, I.L., Young, R., Lefevre, L., Pridans, C., Tsang, H.G., Wu, C., Afrasiabi, C., et al., 2017. A high resolution atlas of gene expression in the domestic sheep (Ovis aries). PLoS Genet. 13, e1006997.

Clark, P.U., Dyke, A.S., Shakun, J.D., Carlson, A.E., Clark, J., Wohlfarth, B., Mitrovica, J.X., Hostetler, S.W.,McCabe, A.M., 2009. The last glacial maximum. Science 325, 710-714.

Clay, M.R., Varma, S.,West, R.B., 2013. MAST2 and NOTCH1 translocations in breast carcinoma and associated pre-invasive lesions. Hum. Pathol. 44, 2837-2844.

Cleal, K.,Baird, D.M., 2022. Dysgu: efficient structural variant calling using short or long reads. Nucleic Acids Res. 50, e53.

Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., et al., 2011. The variant call format and VCFtools. Bioinformatics 27, 2156-2158.

Deng, J., Xie, X.L., Wang, D.F., Zhao, C., Lv, F.H., Li, X., Yang, J., Yu, J.L., Shen, M., Gao, L., et al., 2020. Paternal origins and migratory episodes of domestic sheep. Curr. Biol. 30, 4085-4086.

Du, L.X., Li, J.Q., Ma, N., Ma, Y.H., Wang, J.M., Yin, C.A., Luo, J., Liu, N., JIa, Z.H.,Fu, C.X., 2011. Animal genetic resources in China - sheep and goats. China Agriculture Press, Beijing.

Ebert, P., Audano, P.A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M.J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al., 2021. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science 372.

Eggertsson, H.P., Jonsson, H., Kristmundsdottir, S., Hjartarson, E., Kehr, B., Masson, G., Zink, F., Hjorleifsson, K.E., Jonasdottir, A., Jonasdottir, A., et al., 2017. Graphtyper enables population-scale genotyping using pangenome graphs. Nat. Genet. 49, 1654-1660.

Eissmann, M., Schwamb, B., Melzer, I.M., Moser, J., Siele, D., Kohl, U., Rieker, R.J., Wachter, D.L., Agaimy, A., Herpel, E., et al., 2013. A functional yeast survival screen of tumor-derived cDNA libraries designed to identify anti-apoptotic mammalian oncogenes. PLoS One 8, e64873.

Fan, W., Shao, K.,Luo, M., 2024. Structural view of cryo-electron microscopy-determined ATP-binding cassette transporters in human multidrug resistance. Biomolecules 14, 231.

Felsenstein, J., 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.

Gan, B., Chen, S.Z., Liu, H., Min, J.R.,Liu, K., 2019. Structure and function of eTudor domain containing TDRD proteins. Crit. Rev. Biochem. Mol. Biol. 54, 119-132.

Gebreselase, H.B., Nigussie, H., Wang, C.,Luo, C., 2024. Genetic diversity, population structure and selection signature in Begait goats revealed by whole-genome sequencing. Animals (Basel) 14.

Han, B., Tian, D., Li, X., Liu, S., Tian, F., Liu, D., Wang, S.,Zhao, K., 2024. Multiomics analyses provide new insight into genetic variation of reproductive adaptability in Tibetan sheep. Mol. Biol. Evol. 41.

Handakas, E., Xu, Y., Segal, A.B., Huerta, M.C., Bowman, K., Howe, L.D., Sassi, F.,Robinson, O., 2022. Molecular mediators of the association between child obesity and mental health. Front. Genet. 13, 947591.

He, X., Zhou, Z., Pu, Y., Chen, X., Ma, Y.,Jiang, L., 2016. Mapping the four-horned locus and testing the polled locus in three Chinese sheep breeds. Anim. Genet. 47, 623-627.

Hu, X.J., Yang, J., Xie, X.L., Lv, F.H., Cao, Y.H., Li, W.R., Liu, M.J., Wang, Y.T., Li, J.Q., Liu, Y.G., et al., 2019. The genome landscape of Tibetan sheep reveals adaptive introgression from argali and the history of early human settlements on the Qinghai-Tibetan plateau. Mol. Biol. Evol. 36, 283-303.

Hu, Z.-L., Park, C.A.,Reecy, J.M., 2021. Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services. Nucleic Acids Res. 50, D956-D961.

Huang, X.L., Qu, R.M., Ouyang, J., Zhong, S.Z.,Dai, J.X., 2020. An overview of the cytoskeleton-associated role of PDLIM5. Front. Physiol. 11, 975.

Huse, M., Chen, Y.G., Massague, J.,Kuriyan, J., 1999. Crystal structure of the cytoplasmic domain of the type I TGF beta receptor in complex with FKBP12. Cell 96, 425-436.

Jiang, Y., Xie, M., Chen, W.B., Talbot, R., Maddox, J.F., Faraut, T., Wu, C.H., Muzny, D.M., Li, Y.X., Zhang, W.G., et al., 2014. The sheep genome illuminates biology of the rumen and lipid metabolism. Science 344, 1168-1173.

Jin, M., Wang, H., Liu, G., Lu, J., Yuan, Z., Li, T., Liu, E., Lu, Z., Du, L.,Wei, C., 2024. Whole-genome resequencing of Chinese indigenous sheep provides insight into the genetic basis underlying climate adaptation. Genet., Sel., Evol. 56, 26.

Johnston, S.E., Gratten, J., Berenos, C., Pilkington, J.G., Clutton-Brock, T.H., Pemberton, J.M.,Slate, J., 2013. Life history trade-offs at a single locus maintain sexually selected genetic variation. Nature 502, 93-95.

Johnston, S.E., McEwan, J.C., Pickering, N.K., Kijas, J.W., Beraldi, D., Pilkington, J.G., Pemberton, J.M.,Slate, J., 2011. Genome-wide association mapping identifies the genetic basis of discrete and quantitative variation in sexual weaponry in a wild sheep population. Mol. Ecol. 20, 2555-2566.

Kamaliyan, Z., Pouriamanesh, S., Soosanabadi, M., Gholami, M.,Mirfakhraie, R., 2018. Investigation of piwi-interacting RNA pathway genes role in idiopathic non-obstructive azoospermia. Sci. Rep. 8, 142.

Karlsson, M., Zhang, C., Mear, L.R., Zhong, W., Digre, A., Katona, B., Sjostedt, E., Butler, L., Odeberg, J., Dusart, P., et al., 2021. A single-cell type transcriptomics map of human tissues. Sci. Adv. 7, eabh2169.

Kijas, J.W., Lenstra, J.A., Hayes, B., Boitard, S., Porto Neto, L.R., San Cristobal, M., Servin, B., McCulloch, R., Whan, V., Gietzen, K., et al., 2012. Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol. 10, e1001258.

Kim, J., Lee, T., Kim, T.-H., Lee, K.-T.,Kim, H., 2012. An integrated approach of comparative genomics and heritability analysis of pig and human on obesity trait: evidence for candidate genes on human chromosome 2. BMC Genomics 13, 711.

Kronenberg, Z.N., Osborne, E.J., Cone, K.R., Kennedy, B.J., Domyan, E.T., Shapiro, M.D., Elde, N.C.,Yandell, M., 2015. Wham: identifying structural variants of biological consequence. PLoS Comput. Biol. 11, e1004572.

Letunic, I.,Bork, P., 2021. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293-W296.

Li, H., 2021. New strategies to improve minimap2 alignment accuracy. Bioinformatics 37, 4572-4574.

Li, H.,Durbin, R., 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760.

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R.,Proc, G.P.D., 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079.

Li, M., Xia, H., Chen, D., Ji, D., Kenji, T., Li, R., Liao, X., Mao, Y., Sun, W., Geng, R.,Yang, Z., 2018. Genetic differentiation and phylogeny of 27 sheep populations based on structural gene loci. Mol. Cell Probes 37, 55-59.

Li, R., Gong, M., Zhang, X., Wang, F., Liu, Z., Zhang, L., Yang, Q., Xu, Y., Xu, M., Zhang, H., et al., 2023. A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes. Genome Res. 33, 463-477.

Li, X., Yang, J., Shen, M., Xie, X.L., Liu, G.J., Xu, Y.X., Lv, F.H., Yang, H., Yang, Y.L., Liu, C.B., et al., 2020. Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits. Nat. Commun. 11, 2815.

Li, Y.L.,Liu, J.X., 2018. STRUCTURESELECTOR: a web-based software to select and visualize the optimal number of clusters using multiple methods. Mol. Ecol. Resour. 18, 176-177.

Liu, T., Guo, W.R., Zhang, T.W., Zhang, Y.N., Yang, L., Xie, J.K., Kang, L.T., Wang, W.H., Sun, L.N., Duan, Y.,Su, R.N., 2022. Analysis of differences between different sheep breeds based on whole-genome resequencing technology. PREPRINT (Version 1).

Liu, Z., Ji, Z., Wang, G., Chao, T., Hou, L.,Wang, J., 2016. Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions. BMC Genomics 17, 863.

Luhken, G., Krebs, S., Rothammer, S., Kupper, J., Mioc, B., Russ, I.,Medugorac, I., 2016. The 1.78-kb insertion in the 3′-untranslated region of RXFP2 does not segregate with horn status in sheep breeds with variable horn status. Genet., Sel., Evol. 48, 78.

Lv, F.H., Peng, W.F., Yang, J., Zhao, Y.X., Li, W.R., Liu, M.J., Ma, Y.H., Zhao, Q.J., Yang, G.L., Wang, F., et al., 2015. Mitogenomic meta-analysis identifies two phases of migration in the history of eastern Eurasian sheep. Mol. Biol. Evol. 32, 2515-2533.

Lv, X., Chen, W., Wang, S., Cao, X., Yuan, Z., Getachew, T., Mwacharo, J.M., Haile, A.,Sun, W., 2023. Whole-genome resequencing of Dorper and Hu sheep to reveal selection signatures associated with important traits. Anim. Biotechnol. 34, 3016-3026.

Maclean, C.A., Hong, N.P.C.,Prendergast, J.G.D., 2015. Hapbin: an efficient program for performing haplotype-based scans for positive selection in large genomic datasets. Mol. Biol. Evol. 32, 3027-3029.

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M.,DePristo, M.A., 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303.

Members, C.-N.,Partners, 2021. Database resources of the National Genomics Data Center, china national center for bioinformation in 2022. Nucleic Acids Res. 50, D27-D38.

Mulsant, P., Lecerf, F., Fabre, S., Schibler, L., Monget, P., Lanneluc, I., Pisselet, C., Riquet, J., Monniaux, D., Callebaut, I., et al., 2001. Mutation in bone morphogenetic protein receptor-IB is associated with increased ovulation rate in Booroola Merino ewes. Proc. Natl. Acad. Sci. U. S. A. 98, 5104-5109.

Niu, L.L., Li, H.B., Ma, Y.H.,Du, L.X., 2012. Genetic variability and individual assignment of Chinese indigenous sheep populations (Ovis aries) using microsatellites. Anim. Genet. 43, 108-111.

Pan, Z.Y., Li, S.D., Liu, Q.Y., Wang, Z., Zhou, Z.K., Di, R., Miao, B.P., Hu, W.P., Wang, X.Y., Hu, X.X., et al., 2018. Whole-genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi-feralization. Gigascience 7, giy019.

Pedersen, B.S., Layer, R.,Quinlan, A.R. 2020. Smoove: structural-variant calling and genotyping with existing tools.

Pickrell, J.K.,Pritchard, J.K., 2012. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967.

Piper, L.R.,Bindon, B.M., 1983. The Booroola Merino and the performance of medium non-Peppin crosses at Armidale. Wool Technol. Sheep Breed. 31, 14-&.

Piper, L.R., Bindon, B.M.,Davis, G.H. 1985. The single gene inheritance of the high litter size of the Booroola Merino, Genetics of Reproduction in Sheep, pp. 115-125.

Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A.R., Bender, D., Maller, J., Sklar, P., de Bakker, P.I.W., Daly, M.J.,Sham, P.C., 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575.

Quinlan, A.R.,Hall, I.M., 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842.

Rausch, T., Zichner, T., Schlattl, A., Stutz, A.M., Benes, V.,Korbel, J.O., 2012. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333-i339.

Robinson, D.R., Kalyana-Sundaram, S., Wu, Y.M., Shankar, S., Cao, X., Ateeq, B., Asangani, I.A., Iyer, M., Maher, C.A., Grasso, C.S., et al., 2011. Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer. Nat. Med. 17, 1646-1651.

Robinson, J.T., Thorvaldsdottir, H., Turner, D.,Mesirov, J.P., 2023. Igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). Bioinformatics 39.

Rumpf, M., Pautz, S., Drebes, B., Herberg, F.W.,Muller, H.-A.J., 2023. Microtubule-associated serine/threonine (MAST) kinases in development and disease. Int. J. Mol. Sci. 24, 11913.

Schiffels, S.,Wang, K., 2020. MSMC and MSMC2: the multiple sequentially markovian coalescent. Methods Mol. Biol. 2090, 147-166.

Selionova, M., Aibazov, M., Mamontova, T., Malorodov, V., Sermyagin, A., Zinovyeva, N.,Easa, A.A., 2022. Genome-wide association study of live body weight and body conformation traits in young Karachai goats. Small Ruminant Res. 216, 106836.

Singh, R.V., Sivakumar, A., Sivashankar, S., Das, G., Walkden-Brown, S., Werf, J.V.D., Nimbkar, C.,Gupta, V., 2009. Evaluation of the Booroola (FecB) gene in Muzaffarnagari sheep. ACIAR Proc. 133, 223-224.

Smit, A., Hubley, R.,Green, P. 2013. RepeatMasker.

Souza, C.J.H., MacDougall, C., Campbell, B.K., McNeilly, A.S.,Baird, D.T., 2001. The Booroola (FecB) phenotype is associated with a mutation in the bone morphogenetic receptor type 1 B (BMPR1B) gene. J. Endocrinol. 169, R1-R6.

Sun, W., Chang, H., Ji, D., Liao, X., Du, L., Lu, S.,Kenji, T., 2007. Analysis on genetic diversity and isolation mechanism by distance of different ecological type sheep breeds in Mongolia sheep group. J. Genet. Genomics 34, 1001-1009.

Terhorst, J., Kamm, J.A.,Song, Y.S., 2017. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nat. Genet. 49, 303-309.

Wang, K., Li, M.Y.,Hakonarson, H., 2010a. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164.

Wang, W., Zhang, X., Zhou, X., Zhang, Y., La, Y., Zhang, Y., Li, C., Zhao, Y., Li, F., Liu, B.,Jiang, Z., 2019a. Deep genome resequencing reveals artificial and natural selection for visual deterioration, plateau adaptability and high prolificacy in Chinese domestic sheep. Front. Genet. 10, 300.

Wang, X., Fredericksen, Z.S., Vierkant, R.A., Kosel, M.L., Pankratz, V.S., Cerhan, J.R., Justenhoven, C., Brauch, H., Consortium, G., Olson, J.E.,Couch, F.J., 2010b. Association of genetic variation in mitotic kinases with breast cancer risk. Breast Cancer Res. Treat. 119, 453-462.

Wang, Y., Zhang, C., Wang, N., Li, Z., Heller, R., Liu, R., Zhao, Y., Han, J., Pan, X., Zheng, Z., et al., 2019b. Genetic basis of ruminant headgear and rapid antler regeneration. Science 364.

Wei, C., Wang, H., Liu, G., Zhao, F., Kijas, J.W., Ma, Y., Lu, J., Zhang, L., Cao, J., Wu, M., et al., 2016. Genome-wide analysis reveals adaptation to high altitudes in Tibetan sheep. Sci. Rep. 6, 26770.

Wei, C.H., Wang, H.H., Liu, G., Wu, M.M., Cao, J.X.V., Liu, Z., Liu, R.Z., Zhao, F.P., Zhang, L., Lu, J., et al., 2015. Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds. BMC Genomics 16, 194.

Wiedemar, N.,Drogemuller, C., 2015. A 1.8-kb insertion in the 3'-UTR of RXFP2 is associated with polledness in sheep. Anim. Genet. 46, 457-461.

Wilson, T., Wu, X.Y., Juengel, J.L., Ross, I.K., Lumsden, J.M., Lord, E.A., Dodds, K.G., Walling, G.A., McEwan, J.C., O'Connell, A.R., et al., 2001. Highly prolific Booroola sheep have a mutation in the intracellular kinase domain of bone morphogenetic protein IB receptor (ALK-6) that is expressed in both oocytes and granulosa cells. Biol. Reprod. 64, 1225-1235.

Yang, J., Li, W.R., Lv, F.H., He, S.G., Tian, S.L., Peng, W.F., Sun, Y.W., Zhao, Y.X., Tu, X.L., Zhang, M., et al., 2016. Whole-genome sequencing of native sheep provides insights into rapid adaptations to extreme environments. Mol. Biol. Evol. 33, 2576-2592.

Yang, B.G., Yuan, Y., Zhou, D.K., Ma, Y.H., Mahrous, K.F., Wang, S.Z., He, Y.M., Duan, X.H., Zhang, W.Y.,E, G.X., 2021. Genome-wide selection signal analysis of Australian Boer goat reveals artificial selection imprinting on candidate genes related to muscle development. Anim. Genet. 52, 550-555.

Yuan, Z., Liu, E., Liu, Z., Kijas, J.W., Zhu, C., Hu, S., Ma, X., Zhang, L., Du, L., Wang, H.,Wei, C., 2017. Selection signature analysis reveals genes associated with tail type in Chinese indigenous sheep. Anim. Genet. 48, 55-66.

Zhang, C., Dong, S.S., Xu, J.Y., He, W.M.,Yang, T.L., 2019. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics 35, 1786-1788.

Zhao, F., Xie, R., Fang, L., Xiang, R., Yuan, Z., Liu, Y.,Wang, L., 2024a. Analysis of 206 whole-genome resequencing reveals selection signatures associated with breed-specific traits in Hu sheep. Evol. Appl. 17, e13697.

Zhao, L., Yuan, L., Li, F., Zhang, X., Tian, H., Ma, Z., Zhang, D., Zhang, Y., Zhao, Y., Huang, K., et al., 2024b. Whole-genome resequencing of Hu sheep identifies candidate genes associated with agronomic traits. J. Genet. Genomics 51, 866-876.

Zhao, Y., Zhang, X.X., Li, F.D., Zhang, D.Y., Zhang, Y.K., Li, X.L., Song, Q.Z., Zhou, B.B., Zhao, L.M., Wang, J.H., et al., 2022. Whole genome sequencing analysis to identify candidate genes associated with the rib eye muscle area in Hu sheep. Front. Genet. 13, 824742.

Zhao, Y.X., Yang, J., Lv, F.H., Hu, X.J., Xie, X.L., Zhang, M., Li, W.R., Liu, M.J., Wang, Y.T., Li, J.Q., et al., 2017. Genomic reconstruction of the history of native sheep reveals the peopling patterns of nomads and the expansion of early pastoralism in east Asia. Mol. Biol. Evol. 34, 2380-2395.

Zhong, T., Hou, D., Zhao, Q., Zhan, S., Wang, L., Li, L., Zhang, H., Zhao, W., Yang, S.,Niu, L., 2024. Comparative whole-genome resequencing to uncover selection signatures linked to litter size in Hu Sheep and five other breeds. BMC Genomics 25, 480.

Zhou, X.,Stephens, M., 2012. Genome-wide efficient mixed-model analysis for association studies. Nat. Genet. 44, 821-824.

Zhu, K.Z., 1973. A preliminary study on climate change in China in the past five thousand years. Sci. China 2, 15-38.

Zhu, M., Yang, Y., Yang, H., Zhao, Z., Zhang, H., Blair, H.T., Zheng, W., Wang, M., Fang, C., Yu, Q., et al., 2023. Whole-genome resequencing of the native sheep provides insights into the microevolution and identifies genes associated with reproduction traits. BMC Genomics 24, 392.

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