본문 바로가기
KERD
논문KCI 등재

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

2

조회

0

다운로드

0

인용

0

참고문헌

키워드

초록

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 μg 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.

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 μg 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.

참고문헌 (36)

  1. Li M, "Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars", Nat Genet, 45, pp.1431~1438 (2013)[DOI]
  2. Dutta P, "Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication", Nat Commun, 11, pp.4739~ (2020)[DOI]
  3. Pan ZY, "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, pp.giy019~ (2018)[DOI]
  4. Jiang Y, "The sheep genome illuminates biology of the rumen and lipid metabolism", Science, 344, pp.1168~1173 (2014)[DOI]
  5. Zhao YX, "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, pp.2380~2395 (2017)[DOI]
  6. Yang J, "Whole-genome sequencing of native sheep provides insights into rapid adaptations to extreme environments", Mol Biol Evol, 33, pp.2576~2592 (2016)[DOI]
  7. Zhong T, "Tracing genetic differentiation of Chinese Mongolian sheep using microsatellites", Anim Genet, 42, pp.563~565 (2011)[DOI]
  8. Liu ZH, "Genomewide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions", BMC Genomics, 17, pp.863~ (2016)[DOI]
  9. Kang L, "Grassland ecosystems in China : review of current knowledge and research advancement", Philos Trans R Soc Lond B Biol Sci, 362, pp.997~1008 (2007)[DOI]
  10. Alberto FJ, "Convergent genomic signatures of domestication in sheep and goats", Nat Commun, 9, pp.813~ (2018)[DOI]
  11. Abied A, "Genome-wide analysis revealed homozygosity and demographic history of five Chinese sheep breeds adapted to different environments", Genes(Basel), 11, pp.1480~ (2020)[DOI]
  12. Abied A, "Genomic diversity, population structure, and signature of selection in five chinese native sheep breeds adapted to extreme environments", Genes(Basel), 11, pp.494~ (2020)[DOI]
  13. Zhang Y, "Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep", Sci Rep, 11, pp.2466~ (2021)[DOI]
  14. Zhang T, "Genome-wide association studies revealed candidate genes for tail fat deposition and body size in the Hulun Buir sheep", J Anim Breed Genet, 136, pp.362~370 (2019)[DOI]
  15. Dafu Zhi, "Whole Genome Sequencing of Hulunbuir Short-Tailed Sheep for Identifying Candidate Genes Related to the Short-Tail Phenotype", G3 Genes|Genomes|Genetics, 8(2), pp.377~383 (2018), Oxford University Press (OUP)[DOI]
  16. Pan Z, "Rapid evolution of a retro-transposable hotspot of ovine genome underlies the alteration of BMP2expression and development of fat tails", BMC Genomics, 20, pp.261~ (2019)[DOI]
  17. Li X, "Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits", Nat Commun, 11, pp.2815~ (2020)[DOI]
  18. Bolger AM, "Trimmomatic : a flexible trimmer for Illumina sequence data", Bioinformatics, 30, pp.2114~2120 (2014)[DOI]
  19. Li H, "Fast and accurate long-read alignment with Burrows-Wheeler transform", Bioinformatics, 26, pp.589~595 (2010)[DOI]
  20. McKenna A, "The genome analysis toolkit : a mapreduce framework for analyzing next-generation DNA sequencing data", Genome Res, 20, pp.1297~1303 (2010)[DOI]
  21. McLaren W, "The ensembl variant effect predictor", Genome Biol, 17, pp.122~ (2016)[DOI]
  22. Yin L, "rMVP : A memory-efficient, visualization-enhanced, and Parallel-accelerated tool for genome-wide association study", Genomics Proteomics Bioinformatics, 19, pp.619~628 (2021)[DOI]
  23. Alexander DH, "Fast model-based estimation of ancestry in unrelated individuals", Genome Res, 19, pp.1655~1664 (2009)[DOI]
  24. Li H, "Inference of human population history from individual whole-genome sequences", Nature, 475, pp.493~496 (2011)[DOI]
  25. Weir BS, "Estimating F-statistics for the analysis of population structure", Evolution, 38, pp.1358~1370 (1984)[DOI]
  26. Tajima F, "Statistical method for testing the neutral mutation hypothesis by DNA polymorphism", Genetics, 123, pp.585~595 (1989)[DOI]
  27. Beissbarth T, "GOstat : find statistically overrepresented Gene Ontologies within a group of genes", Bioinformatics, 20, pp.1464~1465 (2004)[DOI]
  28. Wei C, "Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds", BMC Genomics, 16, pp.194~ (2015)[DOI]
  29. Ganbold O, "Genetic diversity and the origin of Mongolian native sheep", Livest Sci, 220, pp.17~25 (2019)[DOI]
  30. Ehlers J, "The extent and chronology of cenozoic global glaciation", Quat Int, 164-65, pp.6~20 (2007)[DOI]
  31. Lehmkuhl F, "Late quaternary glaciation of Tibet and the bordering mountains : a review", Boreas, 34, pp.87~100 (2005)[DOI]
  32. Kim J, "CPS1 maintains pyrimidine pools and DNA synthesis in KRAS", LKB1-mutant lung cancer cells, 2017, pp.546, 168~172
  33. Talebi M, "Is there any relationship between mutation in CPS1 Gene and pregnancy loss?", Int J Reprod Biomed, 17, pp.371~374 (2019)[DOI]
  34. Matsumoto M, "Noc2 is essential in normal regulation of exocytosis in endocrine and exocrine cells", Proc Natl Acad Sci USA, 101, pp.8313~8318 (2004)[DOI]
  35. Onolragchaa Ganbold, "Sequence characterization and polymorphism of melanocortin 1 receptor gene in some goat breeds with different coat color of Mongolia", Animal Bioscience, 32(7), pp.939~948 (2019), 아세아·태평양축산학회[DOI]
  36. Tong SQ, "Analysis of drought characteristics in Xilingol Grassland of Northern China based on SPEI and its impact on vegetation", Math Probl Eng, 2017, pp.5209173~ (2017)[DOI]

관련 논문AI추천

Genetic diversity and selection of Tibetan sheep breeds revealed by whole-genome resequencingHan Buying, Liu Dehui, Li Xue, Pei Quanbang, Tian Dehong, Wang Lei, Zhang Nan, Zhao Chunchuan, Zhao Kai, Zhou Baicheng아세아·태평양축산학회 · Animal Bioscience2023 · 제36권 제7호Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breedingMin Yang, Wei Zhang, Xiaodong Zhang, Xudong Wu, Yuanlang Wang, Yueyun Ding, Zongjun Yin아세아·태평양축산학회 · Animal Bioscience2020 · 제33권 제5호Whole genome sequencing of Luxi Black Head sheep for screening selection signatures associated with important traitsCai Zhongfeng, Cui Xukui, Jin Qing, Liu Zhaohua, Meng Xianfeng, Tan Xiuwen, Wang Jianying, Wang Ke아세아·태평양축산학회 · Animal Bioscience2022 · 제35권 제9호Whole-genome selection signatures identified candidate genes associated with cashmere traits in Inner Mongolia cashmere goatsAo Xiaofang, Han Mingxuan, Lv Qi, Rong Youjun, Shang Fangzheng, Su Rui, Wang Ruijun, Wang Zhiying, Xia Qincheng, Zhang Yanjun, Zhao Yanhong아세아·태평양축산학회 · Animal Bioscience2025 · 제38권 제12호Genetic diversity and population structure in five Inner Mongolia cashmere goat populations using whole-genome genotypingLi Chun, Li Jinquan, Liu Yifan, Li Yaming, Lv Qi, Su Rui, Wang Ruijun, Wang Zhiying, Zhang Tao, Zhang Yanjun, Zhou Bohan아세아·태평양축산학회 · Animal Bioscience2024 · 제37권 제7호Luzhong mutton sheep: inbreeding and selection signaturesFengyan Wang, Lin Tao, Linxiang Pan, Ming-xing Chu, Ran Di, Shangquan Gan, Xiangyu Wang, Xiaoyun He, Yingjie Zhong한국축산학회 · 한국축산학회지2020 · 제62권 제6호

이 간행물의 다른 논문 (16건)