山羊基因组与遗传变异图谱研究进展

doi:10.13560/j.cnki.biotech.bull.1985.2019-0691

生物技术通报 ›› 2020, Vol. 36 ›› Issue (4): 175-184.doi: 10.13560/j.cnki.biotech.bull.1985.2019-0691

山羊基因组与遗传变异图谱研究进展

李晓凯¹, 范一星¹, 乔贤¹, 张磊¹, 王凤红¹, 王志英¹, 王瑞军^1,2,3, 张燕军^1,2,3, 刘志红^1,2,3, 王志新¹, 何利兵⁴, 李金泉^1,2,3, 苏蕊^1,2,3, 张家新¹

1. 内蒙古农业大学动物科学学院,呼和浩特 010018;
2. 农业部肉羊遗传育种重点实验室,呼和浩特 010018;
3. 内蒙古自治区山羊遗传育种工程技术研究中心,呼和浩特 010018;
4. 内蒙古金莱牧业科技有限责任公司,呼和浩特 010018

收稿日期:2019-08-02 出版日期:2020-04-26 发布日期:2020-04-30
作者简介:李晓凯,男,博士研究生,研究方向：绒山羊分子遗传育种;E-mail：lixiaokai1990@126.com
基金资助:
国家自然科学基金项目（31660639,31860637）,国家绒毛用羊现代农业产业技术体系(CARS-39-06),内蒙古自治区研究生教育创新计划资助项目（B20171012901Z）,内蒙古农业大学“双一流”学科创新团队建设人才培育项目（NDSC2018-01）

Research Progress of Goat Genome and Genetic Variation Map

LI Xiao-kai¹, FAN Yi-xing¹, QIAO Xian¹, ZHANG Lei¹, WANG Feng-hong¹, WANG Zhi-ying¹, WANG Rui-jun^1,2,3, ZHANG Yan-jun^1,2,3, LIU Zhi-hong^1,2,3, WANG Zhi-xin¹, HE Li-bing⁴, LI Jin-quan^1,2,3, SU Rui^1,2,3, ZHANG Jia-xin¹

1. College of Animal Science,Inner Mongolia Agricultural University,Hohhot 010018;
2. Key Laboratory of Mutton Sheep Genetics and Breeding,Ministry of Agriculture,Hohhot 010018;
3. Engineering Research Center for Goat Genetics and Breeding,Inner Mongolia Autonomous Region,Hohhot 010018;
4. Inner Mongolia Jinlai Livestock Technology Co.,Ltd,Hohhot 010018

Received:2019-08-02 Published:2020-04-26 Online:2020-04-30

摘要/Abstract

摘要： 高通量测序技术和生物信息学的发展极大的促进了山羊分子生物学研究。山羊参考基因组的不断完善以及基因组重测序技术的应用,在全基因组水平上发现了大量的遗传变异信息（SNP、Indel和CNV）,丰富了山羊分子群体遗传学研究利用的分子标记。综述了山羊参考基因组组装和全基因组变异图谱的构建及其在山羊上的研究进展,以期为进一步利用分子遗传标记进行山羊的各种性状的遗传基础研究和遗传资源保护利用提供科学依据和参考。

关键词: 山羊, 参考基因组, 遗传变异, 单核苷酸多态性, 插入缺失, 拷贝数变异

Abstract: The development of high-throughput sequencing technology and bioinformatics has greatly promoted the research of goat molecular biology. With the continuous improvement of goat reference genome and the application of whole genome re-sequencing technology,a large number of genetic variation information has been found at the whole genome level（SNP,Indel and CNV）,which enriches the available molecular markers used in goat molecular population genetics research. This paper reviews the research and application progress of goat reference genome and whole genome variation map on goat,aiming at providing scientific basis and reference for further genetic basic research and genetic resource conservation and utilization of goat traits by using molecular genetic markers.

Key words: goat, reference genome, genetic variation, single nucleotide polymorphism, insertion and deletion, copy number variation

李晓凯, 范一星, 乔贤, 张磊, 王凤红, 王志英, 王瑞军, 张燕军, 刘志红, 王志新, 何利兵, 李金泉, 苏蕊, 张家新. 山羊基因组与遗传变异图谱研究进展[J]. 生物技术通报, 2020, 36(4): 175-184.

LI Xiao-kai, FAN Yi-xing, QIAO Xian, ZHANG Lei, WANG Feng-hong, WANG Zhi-ying, WANG Rui-jun, ZHANG Yan-jun, LIU Zhi-hong, WANG Zhi-xin, HE Li-bing, LI Jin-quan, SU Rui, ZHANG Jia-xin. Research Progress of Goat Genome and Genetic Variation Map[J]. Biotechnology Bulletin, 2020, 36(4): 175-184.

参考文献

[1] Zeder MA, Hesse B.The initial domestication of goats(Capra hircus)in the Zagros mountains 10, 000 years ago[J]. Science, 2000, 287(5461):2254-2257.
[2] Daly KG, Maisano Delser P, Mullin VE, et al.Ancient goat genomes reveal mosaic domestication in the Fertile Crescent[J]. Science, 2018, 361(6397):85-88.
[3] Devendra C.Dynamics of goat meat production in extensive systems in Asia:improvement of productivity and transformation of livelihoods[J]. Agrotechnology, 2015, 106(2):275-277.
[4] Bertolini F, Servin B, Talenti A, et al.Signatures of selection and environmental adaptation across the goat genome post-domestication[J]. Genetics, Selection, Evolution, 2018, 50(1):421-444.
[5] Boettcher PJ, Hoffmann I, Baumung R, et al.Genetic resources and genomics for adaptation of livestock to climate change[J]. Frontiers in Genetics, 2015, 5(461):107-109.
[6] Bett RC, S Kosgey I, Bebe B, et al. Breeding goals for the Kenya dual purpose goat. I. model development and application to smallholder production systems[J]. Tropical Animal Health and Production, 2007, 39:477-492.
[7] Zook JM, Chapman B, Wang J, et al.Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls[J]. Nature Biotechnology, 2014, 32(3):246-251.
[8] Liao PY, H. Lee K. From SNPs to functional polymorphism:The insight into biotechnology applications[J]. Biochemical Engineering Journal, 2010, 49:149-158.
[9] Kwok PY, Chen X.Detection of single nucleotide polymorphisms[J]. Current Issues in Molecular Biology, 2003, 5(2):43-60.
[10] Davey JW, Hohenlohe PA, Etter PD, et al.Genome-wide genetic marker discovery and genotyping using next-generation sequencing[J]. Nature Reviews. Genetics, 2011, 12(7):499-510.
[11] Helyar SJ, Hemmer-Hansen J, Bekkevold D, et al.Application of SNPs for population genetics of nonmodel organisms:new opportunities and challenges[J]. Molecular Ecology Resources, 2011, 1:123-136.
[12] Elsik CG, Tellam RL, Worley KC, et al.The genome sequence of taurine cattle:a window to ruminant biology and evolution[J]. Science, 2009, 324(5926):522-528.
[13] Wade CM, Giulotto E, Sigurdsson S, et al.Genome sequence, comparative analysis, and population genetics of the domestic horse[J]. Science, 2009, 326(5954):865-867.
[14] Groenen MA, Archibald AL, Uenishi H, et al.Analyses of pig genomes provide insight into porcine demography and evolution[J]. Nature, 2012, 491(7424):393-398.
[15] Dong Y, Xie M, Jiang Y, et al.Sequencing and automated whole-genome optical mapping of the genome of a domestic goat(Capra hircus)[J]. Nature Biotechnology, 2013, 31(2):135-141.
[16] Jiang Y, Xie M, Chen W, et al.The sheep genome illuminates biology of the rumen and lipid metabolism[J]. Science, 2014, 344(6188):1168-1173.
[17] Matukumalli LK, Lawley CT, Schnabel RD, et al.Development and characterization of a high density SNP genotyping assay for cattle[J]. PLoS One, 2009, 4(4):24-36.
[18] Levy SE, Boone BE.Next-generation sequencing strategies[J]. Cold Spring Harbor Perspectives in Medicine, 2019, 9(7):a025791.
[19] Zhang J, Chiodini R, Badr A, et al.The Impact of next-generation sequencing on genomics[J]. Journal of Genetics and Genomics, 2011, 38:95-109.
[20] Tosser-Klopp G, Bardou P, Bouchez O, et al.Design and characterization of a 52K SNP chip for goats[J]. PLoS One, 2014, 9(1):e86227.
[21] Qiao X, Su R, Wang Y, et al.Genome-wide target enrichment-aided chip design:a 66 K SNP chip for cashmere goat[J]. Scientific Reports, 2017, 7(1):8621-8633.
[22] Bickhart DM, Rosen BD, Koren S, et al.Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome[J]. Nature Genetics, 2017, 49(4):643-650.
[23] Vaiman D, Schibler L, Bourgeois F, et al.A linkage map of the male goats genome[J]. Genetics, 1996, 144:279-305.
[24] Schibler L, Vaiman D, Oustry A, et al.Construction and extensive characterization of a goat bacterial artificial chromosome library with threefold genome coverage[J]. Mammalian Genome, 1998, 9(2):119-124.
[25] Schibler L, Vaiman D, Oustry A, et al.Comparative gene mapping:a fine-scale survey of chromosome rearrangements between ruminants and humans[J]. Genome Research, 1998, 8(9):901-915.
[26] Maddox JF.A presentation of the differences between the sheep and goat genetic maps[J]. Genetics, Selection, Evolution, 2005, 37(1):S1-S10.
[27] Goss SJ, Harris H.New method for mapping genes in human chromosomes[J]. Nature, 1975, 255(5511):680-684.
[28] Du XY, Womack EJ, Owens EK, et al.A whole-genome radiation hybrid panel for goat[J]. Small Ruminant Research, 2012, 105:114-116.
[29] Du XY, Servin B, Womack JE, et al.An update of the goat genome assembly using dense radiation hybrid maps allows detailed analysis of evolutionary rearrangements in Bovidae[J]. BMC Genomics, 2014, 15(625):625-640.
[30] Schibler L, Di Meo GP, Cribiu EP, et al.Molecular cytogenetics and comparative mapping in goats(Capra hircus, 2n = 60)[J]. Cytogenetic and Genome Research, 2009, 126(1-2):77-85.
[31] Le Provost F, Lepingle A, Martin P.A survey of the goat genome transcribed in the lactating mammary gland[J]. Mammalian Genome, 1996, 7(9):657-666.
[32] Le Provost F, Schibler L, Oustry-Vaiman A, et al.Cytogenetic mapping of 25 goat mammary gland expressed sequence tags(ESTs)[J]. Genetics, Selection, Evolution, 2000, 32(3):311-320.
[33] Mobuchon L, Marthey S, Boussaha M, et al.Annotation of the goat genome using next generation sequencing of microRNA expressed by the lactating mammary gland:comparison of three approaches[J]. BMC Genomics, 2015, 16(285):1471-1486.
[34] Liu Y, Wang LL, Li XY, et al.High-throughput sequencing of hair follicle development-related micrornas in cashmere goat at various fetal periods[J]. Saudi Journal of Biological Sciences, 2018, 25(7):1494-1508.
[35] Liu ZH, Xiao HM, Li HP, et al.Identification of conserved and novel microRNAs in cashmere goat skin by deep sequencing[J]. PLoS One, 2012, 7(12):e50001.
[36] Ling YH, Ren CH, Guo XF, et al.Identification and characterization of microRNAs in the ovaries of multiple and uniparous goats
(Capra hircus)during follicular phase[J]. BMC Genomics, 2014, 15(339):1471-2164.
[37] Ye J, Yao ZQ, Si WY, et al.Identification and characterization of microRNAs in the pituitary of pubescent goats[J]. Reproductive Biology and Endocrinology, 2018, 16(1):370-379.
[38] Ma S, Wang Y, Zhou GX, et al.Synchronous profiling and analysis of mRNAs and ncRNAs in the dermal papilla cells from cashmere goats[J]. BMC Genomics, 2019, 20(1):5861-5875.
[39] Guo JZ, Zhao W, Zhan SY, et al.Identification and expression profiling of miRNAome in goat longissimus dorsi muscle from prenatal stages to a neonatal stage[J]. PLoS One, 2016, 11(10):e0165764.
[40] Zhan SY, Dong Y, Zhao W, et al.Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat[J]. BMC Genomics, 2016, 17(666):3009-3018.
[41] Liu Y, Qi B, Xie J, et al.Filtered reproductive long non-coding RNAs by genome-wide analyses of goat ovary at different estrus periods[J]. BMC Genomics, 2018, 19(1):5268-5280.
[42] Zhou GX, Kang DJ, Ma S, et al.Integrative analysis reveals ncRNA-mediated molecular regulatory network driving secondary hair follicle regression in cashmere goats[J]. BMC Genomics, 2018, 19(1):222-237.
[43] Tosser-Klopp G, Bardou P, Cabau C, et al.Goat genome assembly, availability of an international 50K SNP chip and RH panel:an update of the international goat genome consortium projects[C]. San Diego, CA:Plant and Animal Genome, 2012.
[44] Dong Y, Zhang XL, Xie M, et al.Reference genome of wild goat(Capra aegagrus)and sequencing of goat breeds provide insight into genic basis of goat domestication[J]. BMC Genomics, 2015, 16(431):431-441.
[45] Low WY, Tearle R, Bickhart DM, et al.Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity[J]. Nature Communications, 2019, 10(1):260-270.
[46] Simpson JT, Wong K, Jackman SD, et al.ABySS:a parallel assembler for short read sequence data[J]. Genome Research, 2009, 19(6):1117-1123.
[47] Paszkiewicz K, Studholme DJ.De novo assembly of short sequence reads[J]. Briefings in Bioinformatics, 2010, 11(5):457-472.
[48] Assefa S, Keane TM, Otto TD, et al.ABACAS:algorithm-based automatic contiguation of assembled sequences[J]. Bioinformatics, 2009, 25(15):1968-1969.
[49] Seppey M, Manni M, Zdobnov EM.BUSCO:assessing genome assembly and annotation completeness[J]. Methods in Molecular Biology, 2019:9170-9173.
[50] Siddiki AZ, Baten A, Billah M, et al.The genome of the Black Bengal goat(Capra hircus)[J]. BMC Research Notes, 2019, 12(1):362-364.
[51] Faruque S, Chowdhury SA, Siddiquee NU, et al.Performance and genetic parameters of economically important traits of Black Bengal goat[J]. Journal of the Bangladesh Agricultural University, 2010, 8:67-78.
[52] Pollex RL, Hegele RA.Copy number variation in the human genome and its implications for cardiovascular disease[J]. Circulation, 2007, 115(24):3130-3138.
[53] Fontanesi L, Martelli PL, Beretti F, et al.An initial comparative map of copy number variations in the goat(Capra hircus)genome[J]. BMC Genomics, 2010, 11(639):1471-2164.
[54] Liu M, Zhou Y, Rosen BD, et al.Diversity of copy number variation in the worldwide goat population[J]. Heredity, 2018, 6(10):150-161.
[55] Benjelloun B, Alberto FJ, Streeter I, et al.Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats(Capra hircus)using WGS data[J]. Frontiers in Genetics, 2015, 6(107):107-121.
[56] Zhang B, Chang L, Lan YX, et al.Genome-wide definition of selective sweeps reveals molecular evidence of trait-driven domestication among elite goat(Capra species)breeds for the production of dairy, cashmere, and meat[J]. Gigascience, 2018,7(12). doi:10.1093/gigascience/giy105.
[57] Alberto FJ, Boyer F, Orozco-Terwengel P, et al.Convergent genomic signatures of domestication in sheep and goats[J]. Nature Communications, 2018, 9(1):813-822.
[58] Li XK, Su R, Wan WT, et al.Identification of selection signals by large-scale whole-genome resequencing of cashmere goats[J]. Scientific Reports, 2017, 7(1):142-151.
[59] Lee W, Ahn S, Taye M, et al.Detecting positive selection of Korean native goat populations using next-generation sequencing[J]. Molecules and Cells, 2016, 39(12):862-868.
[60] Kim JY, Jeong S, Kim KH, et al.Discovery of genomic characteristics and selection signatures in Korean indigenous goats through comparison of 10 goat breeds[J]. Frontiers in Genetics, 2019, 10(699):699-716.
[61] Cao YH, Xu H, Li R, et al.Genetic basis of phenotypic differences between Chinese Yunling black goats and Nubian goats revealed by allele-specific expression in their F1 hybrids[J]. Frontiers in Genetics, 2019, 10(145):145-156.
[62] Lai FN, Zhai HL, Cheng M, et al.Whole-genome scanning for the litter size trait associated genes and SNPs under selection in dairy goat(Capra hircus)[J]. Scientific Reports, 2016, 6. doi: 10.1038/srep38096.
[63] Zhang SL, Cao XY, Li Y, et al.Detection of polled intersex syndrome(PIS)and its effect on phenotypic traits in goats[J]. Animal Biotechnology, 2019, 14:1-5.
[64] Zhang RQ, Wang JJ, Zhang T, et al.Copy-number variation in goat genome sequence:A comparative analysis of the different litter size trait groups[J]. Gene, 2019, 696:40-46.
[65] E GX, Zhao YJ, Huang YF. Selection signatures of litter size in Dazu black goats based on a whole genome sequencing mixed pools strategy[J]. Molecular Biology Reports, 2019, 7(10):4904-4911.
[66] E GX, Jin ML, Zhao YJ, et al. Genome-wide analysis of Chongqing native intersexual goats using next-generation sequencing[J]. 3 Biotech, 2019, 9(3):99-112.
[67] Wang XL, Liu J, Zhou GX, et al.Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits[J]. Scientific Reports, 2016, 6(38932):932-941.
[68] Song S, Yao N, Yang M, et al.Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cash-mere goat(Capra hircus)[J]. BMC Genomics, 2016, 17(122):2449-2461.
[69] Wang LL, Zhang YJ, Zhao M, et al.SNP discovery from transcrip-tome of cashmere goat skin[J]. Asian-Australasian Journal of Animal Sciences, 2015, 28(9):1235-1243.
[70] Guan DL, Marmol-Sanchez E, Cardoso TF, et al.Genomic analysis of the origins of extant casein variation in goats[J]. Journal of Dairy Science, 2019, 102(6):5230-5241.
[71] Hawe JS, Theis FJ, Heinig M.Inferring interaction networks from multi-omics data[J]. Frontiers in Genetics, 2019, 10(535):535-548.
[72] Teng C, Du DZ, Xiao L, et al.Mapping and identifying a candidate gene(Bnmfs)for female-male sterility through whole-genome resequencing and RNA-Seq in rapeseed(Brassica napus L.)[J]. Frontiers in Plant Science, 2017, 8(2086):2086-2088.
[73] Sun YV, Hu YJ.Integrative analysis of multi-omics data for discovery and functional studies of complex human diseases[J]. Advances in Genetics, 2016, 93:147-190.

山羊基因组与遗传变异图谱研究进展

Research Progress of Goat Genome and Genetic Variation Map

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

本文评价

[1]	张道磊, 甘雨军, 乐亮, 普莉. 玉米产量性状的表观遗传调控机制和育种应用[J]. 生物技术通报, 2023, 39(8): 31-42.
[2]	余世洲, 曹领改, 王世泽, 刘勇, 边文杰, 任学良. 烟草种质基因分型核心SNP标记的开发[J]. 生物技术通报, 2023, 39(3): 89-100.
[3]	盛雪晴, 赵楠, 林亚秋, 陈定双, 王瑞龙, 李傲, 王永, 李艳艳. 山羊ZNF32的克隆及表达分析[J]. 生物技术通报, 2022, 38(12): 300-311.
[4]	张浩, 何长晟, 李艳艳, 王永, 朱江江, 俄木曲者, 林亚秋. miR-301b对山羊肌内脂肪细胞分化的调控作用[J]. 生物技术通报, 2022, 38(10): 254-261.
[5]	朱雯, 汤莹莹, 孙昕旸, 周明, 张子军, 陈兴勇. 低蛋白饲粮对山羊肝脏转录组的影响[J]. 生物技术通报, 2021, 37(9): 203-211.
[6]	张浩, 张亚楠, 李鑫, 王佳美, 王永, 朱江江, 熊燕, 林亚秋. PDK4对山羊肌内脂肪细胞脂代谢的影响[J]. 生物技术通报, 2021, 37(12): 151-159.
[7]	郭丽丽, 李昱莹, 郭大龙, 侯小改. 重要花卉植物高密度遗传连锁图谱构建研究进展[J]. 生物技术通报, 2021, 37(1): 246-254.
[8]	张乐超, 刘月琴, 段春辉, 张英杰, 王泳, 郭云霞. 7个地方山羊品种遗传多样性及遗传结构分析[J]. 生物技术通报, 2020, 36(6): 183-190.
[9]	余钧剑, 迟美丽, 贾永义, 刘士力, 竺俊全, 顾志敏. 四引物扩增受阻突变体系PCR技术及其在动植物遗传育种研究中的应用[J]. 生物技术通报, 2020, 36(5): 32-38.
[10]	宋绍征, 陆睿, 张婷, 何正义, 吴赵曼秋, 成勇, 周鸣鸣. CRISPR /Cas9基因编辑技术在山羊和绵羊中的应用研究进展[J]. 生物技术通报, 2020, 36(3): 62-68.
[11]	周敏雅, 陆睿, 张婷, 袁婷婷, 卢瑶瑶, 严坤宁, 袁玉国, 成勇. 重组人SOD1/3转基因山羊的制备及表达产物的检测[J]. 生物技术通报, 2019, 35(5): 85-92.
[12]	黄龙, 吴本丽, 何吉祥, 陈静, 宋光同, 汪翔, 张烨, 武松. 中华鳖MyoD1基因SNP鉴定及其与生长性状的关联分析[J]. 生物技术通报, 2019, 35(4): 76-81.
[13]	李晓凯 ,王贵 ,乔贤 ,范一星 ,张磊 ,马宇浩 ,聂瑞雪 ,王瑞军 ,何利兵 ,苏蕊. 全基因组测序在重要家畜上的研究进展[J]. 生物技术通报, 2018, 34(6): 11-21.
[14]	乃门塔娜,张燕军,刘东军,李金泉. HFSC标记在阿尔巴斯绒山羊毛囊及毛囊干细胞中的表达[J]. 生物技术通报, 2018, 34(5): 201-205.
[15]	贾启鹏,申培磊,张欢,张勇. CRISPR/Cas9系统介导敲除CSN2基因奶山羊胎儿成纤维突变细胞的制备[J]. 生物技术通报, 2017, 33(9): 131-138.