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Research Progress of Selection Signatures Analysis in Functional Gene Identification of Goat (Capra hircus) and Sheep (Ovis aries) |
LIU Wen-Xuan1, LIU Qian-Wei2, CHEN Chong1, WANG Wan-Ting1, LUO Jun1, LI Cong1,* |
1 Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; 2 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China |
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Abstract Goat (Capra hircus) and sheep (Ovis aries) are main domestic animals raised by human beings. Goat and sheep can be divided into four categories including milk, meat, fleece and both according to its economic use. A clear understanding of the genetic evolution and selection progress of population can be provided through exploring the characteristics of selection signatures among different population. Moreover, the genetic progress can be accelerated and the breeding process can be shortened by applying positive selection. The functional genes detected by the selection signature analyses can be further verified as the causal genes, so as to realize molecular design breeding and the improvement of important economic traits. In this review, the differences and application scopes of five commonly used selection signature detection methods are summarized, and the research progress of functional genes determined using selection signature analyses for important economic traits in goat and sheep are also summarized. This study lays a theoretical foundation for further analysis of the molecular mechanism of functional genes regulating the formation of important economic traits in goat and sheep, and provides genetic sources and molecular materials for population genetic improvement or new varieties (lines) cultivation through molecular design breeding.
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Received: 26 February 2021
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Corresponding Authors:
*congl@nwafu.edu.cn
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[1] 蔡惠芬, 陈志, 罗卫星, 等. 2012. RERG基因多态性与黔北麻羊生长性状的相关性研究[J].广东农业科学, 39(13):152-154. (Cai H F, Chen Z, Luo W X, et al.2012. Study on the relationship between polymorphism of RERG gene and growth traits of Qianbei Ma goat[J]. Guangdong Agriculture Sciences, 39(13): 152-154.) [2] 韩威, 沈华伟, 殷建玫, 等. 2020. 基于RAD-seq简化基因组测序的金湖乌凤鸡遗传进化研究[J].福建农林大学学报(自然科学版), 49(02):206-211. (Han W, Shen H W, Yin J M, et al.2020. Mechanism of the genetic evolution of Jinhu Wufeng chicken based on RAD-seq[J]. Journal of Fujian Agriculture and Forestry University (Natural Science Edition), 49(02): 206-211.) [3] 何传启. 2019. 人类文明进程的周期表[C]. 中国科学院中国现代化研究中心——2019年科学与现代化论文集(上). 中国科学院中国现代化研究中心, 2019: 6. (He C Q.2019. The periodic table of the progress of human civilization[C] Center for Chinese Modernization Research, Chinese Academy of Sciences—2019 Proceedings on Science and Modernization (I). Center for Chinese Modernization Research, Chinese Academy of Sciences, 2019: 6.) [4] 姜雨, 王文. 2015. 羊的驯化之路[J]. 科学世界, 000(003): 48-51. (Jiang Y, Wang W.2015. The road to sheep domestication[J]. Science World, 000(003): 48-51.) [5] 李国辉, 魏清宇, 张会永, 等. 2019. 基于RAD-seq技术分析边鸡保种群体的遗传进化[J]. 农业生物技术学报, 27(12): 2198-2206. (Li G H, Wei Q Y, Zhang H Y, et al.2019. The analysis on genetic evolution of Bian chicken (gallus gallus) population based on RAD-seq technology[J]. Journal of Agricultural Biotechnology, 27(12): 2198-2206.) [6] 刘彬, 宋桃伟, 罗卫星, 等. 2013. GHSR基因多态性与黔北麻羊生长性状关联性分析[J].广东农业科学, 40(22): 161-165. (Liu B, Song T W, Luo W X, et al.2013. Study on relationship between polymorphism of GHSR gene and growth traits in Qianbei Ma goat[J]. Guangdong Agriculture Sciences, 40(22): 161-165.) [7] 刘恩民. 2018. 中国地方山羊品种群体遗传结构和选择信号分析[D]. 硕士学位论文, 兰州大学, 导师: 乐祥鹏, pp.1-45. (Liu E M.2018. Analysis of population genetic structure and select signal in Chinese indigenous goat breeds[D]. Thesis for M.S. Lanzhou University, Supervisor: Le X P, pp.1-45.) [8] 刘家鑫, 魏霞, 邓天宇, 等. 2019. 绵羊全基因组ROH检测及候选基因鉴定[J].畜牧兽医学报, 50(08): 1554-1566. (Liu J X, Wei X, Deng T Y, et al.2019. Genome-wide scan for run of homozygosity and identification of corresponding candidate genes in sheep populations[J]. Acta Veterinaria et Zootechnica Sinica, 50(08): 1554-1566.) [9] 刘真, 王慧华, 刘瑞凿, 等. 2015. 不同尾型绵羊全基因组选择信号检测[J].畜牧兽医学报, 46(10): 1721-1732. (Liu Z, Wang H H, Liu R Z, et al.2015. Genome-wide detection of selection signatures of distinct tail types in sheep populations[J]. Acta Veterinaria et Zootechnica Sinica, 46(10): 1721-1732.) [10] 宋桃伟, 蔡惠芬, 罗卫星, 等. 2013. 山羊FGFR-1基因的多态性分析[J].中国畜牧杂志, 49(15): 19-22. (Song T W, Cai H F, Luo W X, et al.2013. Polymorphism analysis of FGFR-1 gene of goat[J]. Chinese Journal of Animal Science, 49(15): 19-22.) [11] 宋文静, 王凭青, 张宝云, 等. 2011. 表皮生长因子受体基因(EGFR)多态性及其与山羊产羔数的相关分析[J].农业生物技术学报, 19(06): 1034-1041. (Song W J, Wang P Q, Zhang B Y, et al.2011. Polymorphism of epidermal growth factor receptor gene (EGFR) and its relationship with litter size in goats[J]. Journal of Agricultural Biotechnology, 19(06): 1034-1041.) [12] 王光凯, 曾滔, 王慧华, 等. 2014. 苏尼特羊全基因组选择信号检测[J].中国农业科学, 47(06): 1190-1199. (Wang G K, Zeng T, Wang H H, et al.2014. Genome-wide detection of selection signature on sunite sheep[J]. Scientia Agricultura Sinica, 47(06): 1190-1199.) [13] 韦宏伟, 徐刚毅, 汪代华, 等. 2011. Myf5基因多态性与山羊生长性状相关分析[J].中国畜牧杂志, 47(07): 15-17. (Wei H W, Xu G Y, Wang D H, et al.2011. Correlation analysis of Myf5 gene polymorphism and goat growth traits[J]. Chinese Journal of Animal Science, 47(07): 15-17.) [14] 杨宇昕, 邹枨. 2019. 基于温带和热带玉米群体全基因组FST和XP-EHH的选择信号检测[J].中国农业科学, 52(04): 579-590. (Yang Y X, Zou C.2019. Genome-Wide detection of selection signal in temperate and tropical maize populations with use of FST and XP-EHH[J]. Scientia Agricultura Sinica, 52(04): 579-590.) [15] 曾滔, 赵福平, 王光凯, 等. 2013. 基于群体分化指数FST的绵羊全基因组选择信号检测[J].畜牧兽医学报, 44(12): 1891-1899. (Zeng T, Zhao F P, Wang G K, et al.2013. Genome-wide detection of selection signatures in sheep populations with use of population differentiation index FST[J]. Acta Veterinaria et Zootechnica Sinica, 44(12): 1891-1899.) [16] 朱云芬, 殷建玫, 张吉发, 等. 2020. 基于RAD-seq测序的狼山鸡基因组选择信号分析[J].中国畜牧兽医, 47(09): 2706-2714. (Zhu Y F, Yin J M, Zhang J F, et al.2020. Selective signal analysis of Langshan chickens based on RAD-seq[J]. China Animal Husbandry & Veterinary Medicine, 47(09): 2706-2714.) [17] Amills M.2014. The Application of genomic technologies to investigate the inheritance of economically important traits in goats[J]. Advances in Biology, 2014: 1-13. [18] An X P, Ma T, Hou J X, et al.2015. Association analysis between variants in KISS1 gene and litter size in goats[J]. BMC Genetics, 558(1): 126-130. [19] Bemji M N, Isa A M, Ibeagha-awemu E M, et al.2018. Polymorphisms of caprine GnRHR gene and their association with litter size in West African Dwarf goats[J]. Molecular Biology Reports, 45(1): 63-69. [20] Benjelloun B, Alberto F J, Streeter I, et al.2015. Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data[J]. Frontiers in Genetics, 6: 107. [21] Berihulay H, Li Y, Gebrekidan B, et al.2019. Whole genome resequencing reveals selection signatures associated with important traits in ethiopian indigenous goat populations[J]. Frontiers in Genetics, 10: 1190. [22] Bonhomme M, Chevalet C, Servin B, et al.2010. Detecting selection in population trees: The lewontin and krakauer test extended[J]. Genetics, 186(1): 241-262. [23] Brito L F, Kijas J W, Ventura R V, et al.2017. Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers[J]. BMC Genomics, 18(1): 229. [24] Burren A, Neuditschko M, Signer-hasler H, et al.2016. Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds[J]. Animal Genetics, 47(6): 727-739. [25] Cesar A S M, Regitano L C A, Mourão G B, et al.2014. Genome-wide association study for intramuscular fat deposition and composition in Nellore cattle[J]. BMC Genetics, 15(1): 39. [26] Charlier C, Li W, Harland C, et al.2016. NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock[J]. Genome Research, 26(10): 1333-1341. [27] Cole J B, Vanraden P M, O'connell J R, et al.2009. Distribution and location of genetic effects for dairy traits[J]. Journal of Dairy Science, 92(6): 2931-2946. [28] Corona E, Wang L, Ko D, et al.2018. Systematic detection of positive selection in the human-pathogen interactome and lasting effects on infectious disease susceptibility[J]. PLOS ONE, 13(5): e0196676. [29] Crispim A C, Kelly M J, Guimaraes S E F, et al.2015. Multi-trait GWAS and new candidate genes annotation for growth curve parameters in brahman cattle[J]. PLOS ONE, 10(10): 1-19. [30] Cui Y, Yan H L, Wang K, et al.2018. Insertion/deletion within the KDM6A gene is significantly associated with litter size in goat[J]. Frontiers in Genetics, 9: 91. [31] E G, Yang B G, Basang W D, et al.2019a. Screening for signatures of selection of Tianzhu white yak using genome-wide re-sequencing[J]. Animal Genetics, 50(5): 534-538. [32] E G X, Zhao Y J, Huang Y F.2019b. Selection signatures of litter size in Dazu black goats based on a whole genome sequencing mixed pools strategy[J]. Molecular Biology Reports, 46(5): 5517-5523. [33] Fariello M I, Boitard S, Naya H, et al.2013. Detecting signatures of selection through haplotype differentiation among hierarchically structured populations[J]. Genetics, 193(3): 929-941. [34] Ferrao R, Wallweber H J, Ho H, et al.2016. The structural basis for class II cytokine receptor recognition by JAK1[J]. Structure, 24(6): 897-905. [35] Frischknecht M, Jagannathan V, Plattet P, et al.2015. A Non-synonymous HMGA2 variant decreases height in shetland ponies and other small horses[J]. PLOS ONE, 10(10): e0140749. [36] Gao J, Lyu Y, Zhang D, et al.2020. Genomic characteristics and selection signatures in indigenous chongming white goat (Capra hircus)[J]. Frontiers in Genetics, 11: 901. [37] Ghasemi M, Zamani P, Vatankhah M, et al.2019. Genome-wide association study of birth weight in sheep[J]. Animal, 13(9): 1797-1803. [38] Gouveia J J D, Da Silva M V G B, Paiva S R, et al.2014. Identification of selection signatures in livestock species[J]. Genetics and Molecular Biology, 37(2): 330-342. [39] Guan D, Luo N, Tan X, et al.2016. Scanning of selection signature provides a glimpse into important economic traits in goats (Capra hircus)[J]. Scientific Reports, 6(1): 36372. [40] Guo J, Tao H, Li P, et al.2018. Whole-genome sequencing reveals selection signatures associated with important traits in six goat breeds[J]. Scientific Reports, 8(1): 10405. [41] Hou J X, An X P, Han P, et al.2015. Two missense mutations in exon 9 of caprine PRLR gene were associated with litter size[J]. Animal Genetics, 46(1): 87-90. [42] Islam R, Li Y, Liu X, et al.2019. Genome-wide runs of homozygosity, effective population size, and detection of positive selection signatures in six chinese goat breeds[J]. Genes (Basel), 10(11): 938 [43] Jin M, Lu J, Fei X, et al.2020. Selection signatures analysis reveals genes associated with high-altitude adaptation in tibetan goats from Nagqu, Tibet[J]. Animals (Basel), 10(9): 1599. [44] Kalkan Z, Durasi I M, Sezerman U, et al.2016. Potential of GRID2 receptor gene for preventing TNF-induced neurodegeneration in autism[J]. Neuroscience Letters, 620: 62-69. [45] Kemper K E, Visscher P M, Goddard M E.2012. Genetic architecture of body size in mammals[J]. Genome Biology, 13(4): 244. [46] Kijas J W, Townley D, Dalrymple B P, et al.2009. A genome wide survey of SNP variation reveals the genetic structure of sheep breeds[J]. PLOS ONE, 4(3): e4668. [47] Kijas J W, Lenstra J A, Hayes B, et al.2012. Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection[J]. PLoS Biology, 10(2): e1001258. [48] Kim E S, Elbeltagy A R, Aboul-naga A M, et al.2016. Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment[J]. Heredity (Edinb), 116(3): 255-264. [49] Kim J Y, Jeong S, Kim K H, et al.2019. Discovery of genomic characteristics and selection signatures in korean indigenous goats through comparison of 10 goat breeds[J]. Frontiers in Genetics, 10: 699. [50] Kristiansson K, Perola M, Tikkanen E, et al.2012. Genome-wide screen for metabolic syndrome susceptibility Loci reveals strong lipid gene contribution but no evidence for common genetic basis for clustering of metabolic syndrome traits[J]. Circulation: Cardiovascular Genetics, 5(2): 242-249. [51] Kumar C, Song S, Dewani P, et al.2018. Population structure, genetic diversity and selection signatures within seven indigenous Pakistani goat populations[J]. Animal Genetics, 49(6): 592-604. [52] Lai F N, Zhai H L, Cheng M, et al.2016. Whole-genome scanning for the litter size trait associated genes and SNPs under selection in dairy goat (Capra hircus)[J]. Scientific reports, 6(1): 38096-38096. [53] Li Y J, Zhang L, Shang L Q, et al.2010. Genetic polymorphisms at three loci of PRLR and FSHR gene correlate with litter size in Chinese Haimen goat[J]. Journal of Animal and Veterinary Advances, 9(22): 2835-2838. [54] Liu Z, Ji Z, Wang G, et al.2016. Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions[J]. BMC Genomics, 17(1): 863. [55] Martin P, Palhiere I, Maroteau C, et al.2017. A genome scan for milk production traits in dairy goats reveals two new mutations in Dgat1 reducing milk fat content[J]. Scientific Reports, 7(1): 1872. [56] McRae K M, Mcewan J C, Dodds K G, et al.2014. Signatures of selection in sheep bred for resistance or susceptibility to gastrointestinal nematodes[J]. BMC Genomics, 15: 637. [57] Miguel M A, Mingala C N.2019. Screening of pig (Sus scrofa) bactericidal permeability-increasing protein (BPI) gene as marker for disease resistance[J]. Animal Biotechnology, 30(2): 146-150. [58] Omoumi A, Fok A, Hsiung G.2012. Analysis of two immune function genes (CR1 and CD2AP) in Alzheimer's disease in two large Canadian cohorts[J]. Alzheimer's & dementia, 8(4): 722. [59] Onzima R B, Upadhyay M R, Doekes H P, et al.2018. Genome-wide characterization of selection signatures and runs of homozygosity in ugandan goat breeds[J]. Frontiers in Genetics, 9: 318. [60] Pellegrina D, Severino P, Barbeiro H V, et al.2017. Insights into the function of long noncoding RNAs in sepsis revealed by gene co-expression network analysis[J]. Noncoding RNA, 3(1): 5. [61] Ryans K, Omosun Y, Mckeithen D N, et al.2017. The immunoregulatory role of alpha enolase in dendritic cell function during Chlamydia infection[J]. BMC Immunology, 18(1): 27. [62] Sabeti P C, Reich D E, Higgins J M, et al.2002. Detecting recent positive selection in the human genome from haplotype structure[J]. Nature, 419(6909): 832-837. [63] Sabeti P C, Varilly P, Fry B, et al.2007. Genome-wide detection and characterization of positive selection in human populations[J]. Nature, 449(7164): 913-918. [64] Saif R, Henkel J, Jagannathan V, et al.2020. The LCORL locus is under selection in large-sized Pakistani goat breeds[J]. Genes (Basel), 11(2): 168. [65] Santana M H, Ventura R V, Utsunomiya Y T, et al.2015. A genomewide association mapping study using ultrasound-scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle[J]. Journal of Animal Breeding and Genetics, 132(6): 420-427. [66] Seo M, Kim K, Yoon J, et al.2016. RNA-seq analysis for detecting quantitative trait-associated genes[J]. Scientific Reports, 6(1): 24375. [67] Shokrollahi B, Morammazi S.2018. Polymorphism of GDF9 and BMPR1B genes and their association with litter size in Markhoz goats[J]. Reproduction in Domestic Animals, 53(4): 971-978. [68] Shriver M D, Kennedy G C, Parra E J, et al.2004. The genomic distribution of population substructure in four populations using 8, 525 autosomal SNPs[J]. Human Genomics, 1(4): 274-286. [69] Silpa M V, Naicy T, Aravindakshan T V, et al.2018. Sirtuin3 (SIRT3) gene molecular characterization and SNP detection in prolific and low prolific goat breeds[J]. Theriogenology, 122: 47-52. [70] Tosser-Klopp G, Bardou P, Bouchez O, et al.2014. Design and characterization of a 52K SNP chip for goats[J]. PLOS ONE, 9(1): e86227. [71] Voight B F, Kudaravalli S, Wen X, et al.2006. A map of recent positive selection in the human genome[J]. PLoS Biology, 4(3): e72. [72] Wang J J, Zhang T, Chen Q M, et al.2020a. Genomic signatures of selection associated with litter size trait in jining gray goat[J]. Frontiers in Genetics, 11: 286. [73] Wang K, Hui Y, Zhang S, et al.2020b. A deletion mutation within the atbf1 gene is strongly associated with goat litter size[J]. Animal Biotechnology, 31(2): 174-180. [74] Wang K, Liu D, Hernandez-sanchez J, et al.2015. Genome wide association analysis reveals new production trait genes in a male duroc population[J]. PLOS ONE, 10(9): e0139207. [75] Wang X, Liu J, Zhou G, et al.2016. Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits[J]. Scientific Reports, 6:38932. [76] Wang X, Yang Q, Wang K, et al.2019. Two strongly linked single nucleotide polymorphisms (Q320P and V397I) in GDF9 gene are associated with litter size in cashmere goats[J]. Theriogenology, 125: 115-121. [77] Wei C, Wang H, Liu G, et al.2015. Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds[J]. BMC Genomics, 16: 194. [78] Xu S S, Gao L, Xie X L, et al.2018. Genome-wide association analyses highlight the potential for different genetic mechanisms for litter size among sheep breeds[J]. Frontiers in Genetics, 9: 118. [79] Yan W, Zheng C, He J, et al.2018. Eleutheroside B1 mediates its anti-influenza activity through POLR2A and N-glycosylation[J]. International Journal of Molecular Medicine, 42(5): 2776-2792. [80] Yang J, Li W R, Lv F H, et al.2016. Whole-genome sequencing of native sheep provides insights into rapid adaptations to extreme environments[J]. Molecular Biology and Evolution, 33(10): 2576-2592. [81] Yang W, Yan H, Wang K, et al.2019. Goat PDGFRB: Unique mRNA expression profile in gonad and significant association between genetic variation and litter size[J]. Royal Society Open Science, 6(1): 180805. [82] Zhang R Q, Lai F N, Wang J J, et al.2018. Analysis of the SNP loci around transcription start sites related to goat fecundity trait base on whole genome resequencing[J]. Gene, 643: 1-6. [83] Zhang R Q, Wang J J, Zhang T, et al.2019a. Copy-number variation in goat genome sequence: A comparative analysis of the different litter size trait groups[J]. Gene, 696: 40-46. [84] Zhang Y, Cui W, Yang H, et al.2019b. A novel missense mutation (L280V) within POU1F1 gene strongly affects litter size and growth traits in goat[J]. Theriogenology, 135: 198-203. [85] Zheng Z, Wang X, Li M, et al.2020. The origin of domestication genes in goats[J]. Science Advances, 6(21): eaaz5216. [86] Zhu B, Niu H, Zhang W, et al.2017. Genome wide association study and genomic prediction for fatty acid composition in Chinese Simmental beef cattle using high density SNP array[J]. BMC Genomics, 18(1): 464. [87] Zhu H, Zhang Y, Bai Y, et al.2019. Relationship between SNPs of POU1F1 Gene and litter size and growth traits in Shaanbei white cashmere goats[J]. Animals (Basel), 9(3): 114. |
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