Browse > Article
http://dx.doi.org/10.5713/ab.21.0569

Whole-genome resequencing reveals domestication and signatures of selection in Ujimqin, Sunit, and Wu Ranke Mongolian sheep breeds  

Wang, Hanning (State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University)
Zhong, Liang (Hebei Provincial Key Laboratory of Basic Medicine for Diabetes, The Shijiazhuang Second Hospital)
Dong, Yanbing (State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University)
Meng, Lingbo (State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University)
Ji, Cheng (State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University)
Luo, Hui (State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University)
Fu, Mengrong (State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University)
Qi, Zhi (State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University)
Mi, Lan (State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University)
Publication Information
Animal Bioscience / v.35, no.9, 2022 , pp. 1303-1313 More about this Journal
Abstract
Objective: The current study aimed to perform whole-genome resequencing of Chinese indigenous Mongolian sheep breeds including Ujimqin, Sunit, and Wu Ranke sheep breeds (UJMQ, SNT, WRK) and deeply analyze genetic variation, population structure, domestication, and selection for domestication traits among these Mongolian sheep breeds. Methods: Blood samples were collected from a total of 60 individuals comprising 20 WRK, 20 UJMQ, and 20 SNT. For genome sequencing, about 1.5 ㎍ of genomic DNA was used for library construction with an insert size of about 350 bp. Pair-end sequencing were performed on Illumina NovaSeq platform, with the read length of 150 bp at each end. We then investigated the domestication and signatures of selection in these sheep breeds. Results: According to the population and demographic analyses, WRK and SNT populations were very similar, which were different from UJMQ populations. Genome wide association study identified 468 and 779 significant loci from SNT vs UJMQ, and UJMQ vs WRK, respectively. However, only 3 loci were identified from SNT vs WRK. Genomic comparison and selective sweep analysis among these sheep breeds suggested that genes associated with regulation of secretion, metabolic pathways including estrogen metabolism and amino acid metabolism, and neuron development have undergone strong selection during domestication. Conclusion: Our findings will facilitate the understanding of Chinese indigenous Mongolian sheep breeds domestication and selection for complex traits and provide a valuable genomic resource for future studies of sheep and other domestic animal breeding.
Keywords
Domestication; Metabolism; Sheep; Selection; Whole-genome Resequencing;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Abied A, Xu L, Sahlu BW, et al. Genome-wide analysis revealed homozygosity and demographic history of five Chinese sheep breeds adapted to different environments. Genes (Basel) 2020;11:1480. https://doi.org/10.3390/genes11121480   DOI
2 Abied A, Bagadi A, Bordbar F, et al. Genomic diversity, population structure, and signature of selection in five chinese native sheep breeds adapted to extreme environments. Genes (Basel) 2020;11:494. https://doi.org/10.3390/genes 11050494   DOI
3 Zhang Y, Xue X, Liu Y, et al. Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep. Sci Rep 2021;11:2466. https://doi.org/10.1038/s41598-021-81932-y   DOI
4 Zhi D, Da L, Liu M, et al. Whole genome sequencing of hulunbuir short-tailed sheep for identifying candidate genes related to the short-tail phenotype. G3 (Bethesda) 2018;8: 377-83. https://doi.org/10.1534/g3.117.300307   DOI
5 Pan Z, Li S, Liu Q, et al. Rapid evolution of a retro-transposable hotspot of ovine genome underlies the alteration of BMP2 expression and development of fat tails. BMC Genomics 2019;20:261. https://doi.org/10.1186/s12864-019-5620-6   DOI
6 McLaren W, Gil L, Hunt SE, et al. The ensembl variant effect predictor. Genome Biol 2016;17:122. https://doi.org/10.1186/s13059-016-0974-4   DOI
7 Zhang T, Gao H, Sahana G, et al. Genome-wide association studies revealed candidate genes for tail fat deposition and body size in the Hulun Buir sheep. J Anim Breed Genet 2019; 136:362-70. https://doi.org/10.1111/jbg.12402   DOI
8 Li X, Yang J, Shen M, et al. Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits. Nat Commun 2020; 11:2815. https://doi.org/10.1038/s41467-020-16485-1   DOI
9 Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114-20. https://doi.org/10.1093/bioinformatics/btu170   DOI
10 Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010;26:589-95. https://doi.org/10.1093/bioinformatics/btp698   DOI
11 Yin L, Zhang H, Tang Z, et al. rMVP: A memory-efficient, visualization-enhanced, and Parallel-accelerated tool for genome-wide association study. Genomics Proteomics Bioinformatics 2021;19:619-28. https://doi.org/10.1016/j.gpb.2020.10.007   DOI
12 Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res 2009;19:1655-64. https://doi.org/10.1101/gr.094052.109   DOI
13 Li H, Durbin R. Inference of human population history from individual whole-genome sequences. Nature 2011;475:493-6. https://doi.org/10.1038/nature10231   DOI
14 Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution 1984;38:1358-70. https://doi.org/10.1111/j.1558-5646.1984.tb05657.x   DOI
15 McKenna A, Hanna M, Banks E, et al. The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20:1297-303. https://doi.org/10.1101/gr.107524.110   DOI
16 Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989;123:585-95. https://doi.org/10.1093/genetics/123.3.585   DOI
17 Ganbold O, Lee S-H, Seo D, et al. Genetic diversity and the origin of Mongolian native sheep. Livest Sci 2019;220:17-25. https://doi.org/10.1016/j.livsci.2018.12.007   DOI
18 Li M, Tian S, Jin L, et al. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nat Genet 2013;45:1431-8. https://doi.org/10.1038/ng.2811   DOI
19 Lehmkuhl F, Owen LA. Late quaternary glaciation of Tibet and the bordering mountains: a review. Boreas 2005;34:87-100. https://doi.org/10.1111/j.1502-3885.2005.tb01008.x   DOI
20 Kim J, Hu Z, Cai L, et al. CPS1 maintains pyrimidine pools and DNA synthesis in KRAS/LKB1-mutant lung cancer cells. Nature 2017;546:168-72. https://doi.org/10.1038/nature22359   DOI
21 Zhong T, Han JL, Guo J, et al. Tracing genetic differentiation of Chinese Mongolian sheep using microsatellites. Anim Genet 2011;42:563-5. https://doi.org/10.1111/j.1365-2052.2011.02181.x   DOI
22 Matsumoto M, Miki T, Shibasaki T, et al. Noc2 is essential in normal regulation of exocytosis in endocrine and exocrine cells. Proc Natl Acad Sci USA 2004;101:8313-8. https://doi.org/10.1073/pnas.0306709101   DOI
23 Ganbold O, Manjula P, Lee SH, et al. Sequence characterization and polymorphism of melanocortin 1 receptor gene in some goat breeds with different coat color of Mongolia. Asian-Australas J Anim Sci 2019;32:939-48. https://doi.org/10.5713/ajas.18.0819   DOI
24 Dutta P, Talenti A, Young R, et al. Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication. Nat Commun 2020;11:4739. https://doi.org/10.1038/s41467-020-18550-1   DOI
25 Pan ZY, Li SD, Liu QY, et al. Whole-genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi-feralization. Gigascience 2018;7: giy019. https://doi.org/10.1093/gigascience/giy019   DOI
26 Wei C, Wang H, Liu G, et al. Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds. BMC Genomics 2015;16:194. https://doi.org/10.1186/s12864-015-1384-9   DOI
27 Ehlers J, Gibbard PL. The extent and chronology of cenozoic global glaciation. Quat Int 2007;164-65:6-20. https://doi.org/10.1016/j.quaint.2006.10.008   DOI
28 Jiang Y, Xie M, Chen WB, et al. The sheep genome illuminates biology of the rumen and lipid metabolism. Science 2014; 344:1168-73. https://doi.org/10.1126/science.1252806   DOI
29 Zhao YX, Yang J, Lv FH, et al. 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 2017;34:2380-95. https://doi.org/10.1093/molbev/msx181   DOI
30 Yang J, Li WR, Lv FH, et al. Whole-genome sequencing of native sheep provides insights into rapid adaptations to extreme environments. Mol Biol Evol 2016;33:2576-92. https://doi.org/10.1093/molbev/msw129   DOI
31 Liu ZH, Ji ZB, Wang GZ, Chao T, Hou L, Wang J. Genomewide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions. BMC Genomics 2016;17:863. https://doi.org/10.1186/s12864-016-3212-2   DOI
32 Alberto FJ, Boyer F, Orozco-terWengel P, et al. Convergent genomic signatures of domestication in sheep and goats. Nat Commun 2018;9:813. https://doi.org/10.1038/s41467-018-03206-y   DOI
33 Talebi M, Mehrjardi MYV, Kalhor K, Dehghani M. Is there any relationship between mutation in CPS1 Gene and pregnancy loss? Int J Reprod Biomed 2019;17:371-4. https://doi.org/10.18502/ijrm.v17i5.4604   DOI
34 Tong SQ, Bao YH, Te RL, Ma Q, Ha S, Lusi A. Analysis of drought characteristics in Xilingol Grassland of Northern China based on SPEI and its impact on vegetation. Math Probl Eng 2017;2017:5209173. https://doi.org/10.1155/2017/5209173   DOI
35 Beissbarth T, Speed TP. GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 2004;20:1464-5. https://doi.org/10.1093/bioinformatics/bth088   DOI
36 Kang L, Han X, Zhang Z, Sun OJ. Grassland ecosystems in China: review of current knowledge and research advancement. Philos Trans R Soc Lond B Biol Sci 2007;362:997-1008. https://doi.org/10.1098/rstb.2007.2029   DOI