肃南牦牛群体遗传结构、选择信号分析和ROH检测

doi:10.16431/j.cnki.1671-7236.2022.08.015

中国畜牧兽医 ›› 2022, Vol. 49 ›› Issue (8): 2992-3005.doi: 10.16431/j.cnki.1671-7236.2022.08.015

肃南牦牛群体遗传结构、选择信号分析和ROH检测

鲍麒^1,2,3, 包鹏甲^1,2,3, 马晓明^1,2,3, 吴晓云^1,2,3, 孟光耀^1,2,3, 褚敏^1,2,3, 曹红梅⁴, 郎建英⁴, 安玉峰⁴, 梁春年^1,2,3, 阎萍^1,2,3

1. 中国农业科学院兰州畜牧与兽药研究所, 兰州 730050;
2. 农业农村部青藏高原畜禽遗传育种重点实验室, 兰州 730050;
3. 甘肃省牦牛繁育工程重点实验室, 兰州 730050;
4. 肃南裕固族自治县畜牧兽医服务中心, 肃南 734400

收稿日期:2022-01-17 出版日期:2022-08-05 发布日期:2022-07-21
通讯作者: 梁春年, 阎萍 E-mail:chunnian2006@163.com;pingyanlz@163.com
作者简介:鲍麒,E-mail:baoqinetwon@163.com;包鹏甲,E-mail:baopengjia@caas.cn。
基金资助:
国家重点研发计划(2021YFD1600200);现代农业(肉牛牦牛)产业技术体系建设专项资金(CARS-37);中国农业科学院创新工程项目(25-LZIHPS-01);科技援青合作专项(2020-QY-212);甘肃省科技计划资助(20JR5RA580)

Genetic Structure,Selection Signal Analysis and ROH Detection of Sunan Yak Population

BAO Qi^1,2,3, BAO Pengjia^1,2,3, MA Xiaoming^1,2,3, WU Xiaoyun^1,2,3, MENG Guangyao^1,2,3, CHU Min^1,2,3, CAO Hongmei⁴, LANG Jianying⁴, AN Yufeng⁴, LIANG Chunnian^1,2,3, YAN Ping^1,2,3

1. Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
2. Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China;
3. Key Laboratory of Gansu for Yak Breeding Engineering, Lanzhou 730050, China;
4. Animal Husbandry and Veterinary Service Center of Sunan County, Sunan 734400, China

Received:2022-01-17 Online:2022-08-05 Published:2022-07-21

摘要/Abstract

摘要： 【目的】试验旨在对肃南牦牛进行群体遗传结构、选择信号分析和连续纯合片段(ROH)检测,挖掘肃南牦牛的种质特性相关基因。【方法】选择肃南牦牛、巴州牦牛、斯布牦牛、九龙牦牛和天祝白牦牛5个牦牛品种共计48头牦牛进行全基因组重测序,采用基因组变异检测流程(GATK)获得高质量的单核苷酸多态性(SNP)标记进行下游分析;对5个牦牛品种的基因型数据进行主成分分析、祖先成分分析和系统进化树分析以确定其群体结构;对5个牦牛群体进行ROH检测以及近交系数计算;采用综合单倍型评分(iHS)方法筛选共有高频ROH区域内受选择位点。【结果】5个牦牛品种共鉴定出15 092 883个SNPs,主要分布于内含子区域。亲缘关系计算结果显示,所有个体均不存在三代以内亲缘关系,满足后续分析要求。主成分分析表明,5个牦牛品种可以显著地分为5个类群,其中肃南牦牛群体内遗传变异较小。群体结构分析显示,肃南牦牛包含其他4种牦牛祖先成分,其中天祝白牦牛祖先成分所占的比例最大。ROH分析显示,5个牦牛品种共检测到8 426个ROHs片段,其中高频ROH区域421个。相比于其他4个牦牛品种,肃南牦牛的ROH片段总长度和数目最多,具有较高的连锁程度,其近交系数远大于其他牦牛群体。在肃南牦牛高频ROH区域上注释得到465个候选基因,主要富集到与机体发育、大脑形态形成、脂肪氧化相关的通路,包括胚胎骨骼系统形态发生、前后模式规范、甲状腺发育通路和Hippo通路,其中与胚胎发育及组织分化过程相关的基因有同源框A3(HOXA3)、HOXA5、HOXD3,与肉品质相关的基因有花生四烯酸12B (ALOX12B)、ALOX15B、ALOXE3,与中脑发育相关的基因为成纤维细胞生长因子8(FGF8)。在7号染色体1个高频ROH区域中(Chr7:12 661 870-13 045 935)鉴定到3个共享基因(核内不均一性核糖核蛋白K (HNRNPK)、驱动蛋白27(KIF27)、G激酶锚定蛋白1(GKAP1))与牦牛共有的高原适应性有关。对共有高频ROH区域内的位点进行iHS分析,鉴定到的受选择基因主要与抗病性、内质网分泌蛋白加工及细胞周期调节相关,包括N-α乙酰转移酶25(NAA25)、内质网分子伴侣29(ERP29)、跨膜蛋白16(TMEM116)、TRAF型锌指结构域蛋白1(TRAFD1)、HECT结构域E3泛素连接酶4(HECTD4)基因。【结论】本研究从全基因组水平系统评估肃南牦牛的遗传多样性和遗传背景,鉴定了肃南牦牛ROH区域内与表型相关的基因,并重点挖掘了与其他牦牛品种共享高频ROH区域内的受选择基因,为肃南牦牛种质资源开发、利用提供了重要理论依据。

关键词: 肃南牦牛; 群体遗传结构; 连续纯合片段; 选择信号

Abstract: 【Objective】 The analysis of population genetic structure,selection signal analysis and ROH detection were performed to Sunan yak to explore the genes related to the germplasm characteristics of Sunan yak.【Method】 A total of 48 yaks were collected from Sunan yak,Bazhou yak,Sibu yak,Jiulong yak and Tianzhu White yak for genome resequencing.Genome Analysis Toolkit (GATK) mutation detection process was used to obtain high-quality single nucleotide polymorphism (SNP) for downstream analysis.Principal component analysis,ancestral component analysis and phylogenetic tree analysis were used to determine the population structure of 5 yak breeds.ROH detection and inbreeding coefficient calculation of 5 yak populations were carried out.A comprehensive haplotype score (iHS) was used to screen selected sites in shared high-frequency ROH regions.【Result】 By analyzing the SNPs identified from 5 yak breeds,a total of 15 092 883 SNPs were identified.The identified SNPs were mainly distributed in the intron regions.The results of kinship calculation showed that all individuals did not have kinship within 3 generations,which met the requirements of subsequent analysis.Principal component analysis showed that the 5 yak breeds could be significantly divided into 5 groups,and the genetic variation within the Sunan yak group was small.The population structure showed that Sunan yak contained other 4 yak ancestors,among which Tianzhu White yak accounted for the largest proportion.ROH analysis showed that a total of 8 426 ROH fragments were detected in 5 yak breeds,of which 421 were in high-frequency ROH regions.Compared with the other 4 yak breeds,Sunan yak had the largest total length and number of ROH regions and had a higher degree of linkage,and its inbreeding coefficient was much larger than that of other yak populations.465 candidate genes were annotated on the high-frequency ROH region of Sunan yak,mainly enriched in pathways related to body development,brain morphogenesis,and fat oxidation,including embryonic skeletal system morphogenesis,anterior and posterior pattern specification,thyroid development pathways and Hippo path.Among them,genes related to embryonic development and tissue differentiation (homeobox A3 (HOXA3),HOXA5,HOXD3),meat quality (arachidonic acid 12B (ALOX12B),ALOX15B,ALOXE3),and midbrain development (fibroblast growth factor 8 (FGF8)) were identified.In addition,3 shared genes (heterogeneous nuclear ribonucleoprotein K (HNRNPK),kinesin family member 27(KIF27),G kinase anchor protein 1 (GKAP1)) were identified in a high-frequency ROH region on chromosome 7 (Chr7:12 661 870-13 045 935),which were related to the plateau adaptation shared by yak.The iHS analysis of loci within the shared high-frequency ROH region identified selected genes that were mainly associated with disease resistance,endoplasmic reticulum-secreted protein processing,and cell cycle regulation,including N-alpha-acetyltransferase 25 (NAA25),endoplasmic reticulum protein 29 (ERP29),transmembrane protein16 (TMEM116),TRAF-type zinc finger domain containing 1 (TRAFD1) and HECT domain E3 ubiquitin protein ligase 4 (HECTD4) genes.【Conclusion】 This study systematically investigated the genetic diversity and identified candidate genes related to traits of Sunan yak at the genome-wide level,providing an important theoretical basis for the development and utilization of Sunan yak germplasm resources.

Key words: Sunan yak; population genetic structure; ROH; selection signal

中图分类号:

S827.2

鲍麒, 包鹏甲, 马晓明, 吴晓云, 孟光耀, 褚敏, 曹红梅, 郎建英, 安玉峰, 梁春年, 阎萍. 肃南牦牛群体遗传结构、选择信号分析和ROH检测[J]. 中国畜牧兽医, 2022, 49(8): 2992-3005.

BAO Qi, BAO Pengjia, MA Xiaoming, WU Xiaoyun, MENG Guangyao, CHU Min, CAO Hongmei, LANG Jianying, AN Yufeng, LIANG Chunnian, YAN Ping. Genetic Structure,Selection Signal Analysis and ROH Detection of Sunan Yak Population[J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 2992-3005.

参考文献

[1] 王理中.牦牛驯化的基因组学证据[D].兰州:兰州大学,2016. WANG L Z.Genomic evidence for yak domestication[D].Lanzhou:Lanzhou University,2016.(in Chinese)
[2] 孟庆辉,陈永杏,董红敏,等.牦牛分布特点及其种群数量[J].家畜生态学报,2017,38(3):80-85. MENG Q H,CHEN Y X,DONG H M,et al.The distribution characteristics and populations of yak[J].Journal of Domestic Animal Ecology,2017,38(3):80-85.(in Chinese)
[3] 蔡欣,赵芳芳,孙磊.牦牛与其他家牛属动物SRY基因多态性及其父系进化关系分析[J].中国畜牧兽医,2014,41(5):190-195. CAI X,ZHAO F F,SUN L.Analysis of SRY gene polymorphisms and patrilineal phylogenetic relationships for Bos grunniens and other Bos species[J].China Animal Husbandry&Veterinary Medicine,2014,41(5):190-195.(in Chinese)
[4] 王光凯.绵羊全基因组连锁不平衡分析和选择信号检测[D].北京:中国农业科学院,2014. WANG G K.Genomic linkage analysis and detection of selection signatures on sheep[D].Beijing:Chinese Academy of Agricultural Sciences,2014.(in Chinese)
[5] 潘章源,贺小云,王翔宇,等.家养动物选择信号研究进展[J].遗传,2016,38(12):1069-1080. PAN Z Y,HE X Y,WANG X Y,et al.Selection signatures in domesticated animals[J].Hereditas,2016,38(12):1069-1080.(in Chinese)
[6] 刘真.肥尾和瘦尾羊全基因组选择信号检测[D].北京:中国农业科学院,2015. LIU Z.Genome-wide detection of selection signature sbetween fat-tailed and thin-tailed sheep population[D]. Beijing:Chinese Academy of Agricultural Sciences,2015.(in Chinese)
[7] SHEN J,HANIF Q,CAO Y,et al.Whole genome scan and selection signatures for climate adaption in Yanbian cattle[J].Frontiers in Genetics,2020,11:94.
[8] 吴林慧,孙琦,王荔茹,等.恩施黑猪基因组群体遗传学参数的估计与选择信号研究[J].畜牧兽医学报,2019,50(3):485-494. WU L H,SUN Q,WANG L R,et al.A study of the population genetics parameters and selection signatures in Enshi Black pig[J]. Acta Veterinaria et Zootechnica Sinica,2019,50(3):485-494.(in Chinese)
[9] CEBALLOS F C,JOSHI P K,CLARK D W,et al.Runs of homozygosity:Windows into population history and trait architecture[J].Nature Reviews Genetics,2018,19(4):220-234.
[10] 赵国耀.基于肉牛基因组纯合片段的性状关联与预测[D].北京:中国农业科学院,2021. ZHAO G Y.Association and prediction of traits based on genomic homozygous segments in beef cattle[D].Beijing:Chinese Academy of Agricultural Sciences,2021.(in Chinese)
[11] FEREN AČG AKOVI AC'G M,HAMZI AC'G E,GREDLER B,et al.Estimates of autozygosity derived from runs of homozygosity:Empirical evidence from selected cattle populations[J].Journal of Animal Breeding and Genetics,2013,130(4):286-293.
[12] WU X,ZHOU R,ZHANG W,et al.Genome-wide scan for runs of homozygosity identifies candidate genes in Wannan Black pigs[J].Asian-Australasian Journal of Animal Sciences,2021,34(12):1895.
[13] 莫家远,李月月,路玉洁,等.广西地方猪群体遗传结构、选择信号分析和ROH检测[J].中国畜牧杂志,2021,57(S1):206-213. MO J Y,LI Y Y,LU Y J,et al.Genetic structure,selection signal analysis and ROH detection of local pig population in Guangxi[J].Chinese Journal of Animal Science,2021,57(S1):206-213.(in Chinese)
[14] XU Z,SUN H,ZHANG Z,et al.Assessment of autozygosity derived from runs of homozygosity in Jinhua pigs disclosed by sequencing data[J].Frontiers in Genetics,2013,10:274.
[15] NANDOLO W,UTSUNOMIYA Y T,MÉSZÁROS G,et al.Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances[J].Genetics Selection Evolution,2018,50(1):1-13.
[16] BOLGER A M,LOHSE M,USADEL B.Trimmomatic:A flexible trimmer for Illumina sequence data[J].Bioinformatics,2014,30(15):2114-2120.
[17] LI H,HANDSAKER B,WYSOKER A,et al.The sequence alignment/map format and SAMtools[J].Bioinformatics,2009,25(16):2078-2079.
[18] MCKENNA A,HANNA M,BANKS E,et al.The Genome Analysis Toolkit:A MapReduce framework for analyzing next-generation DNA sequencing data[J].Genome Research,2010,20(9):1297-1303.
[19] PURCELL S,NEALE B,TODD-BROWN K,et al.PLINK:A tool set for whole-genome association and population-based linkage analyses[J].The American Journal of Human Genetics,2007,81(3):559-575.
[20] KALYAANAMOORTHY S,MINH B Q,WONG T K,et al.ModelFinder:Fast model selection for accurate phylogenetic estimates[J].Nature Methods,2017,14(6):587-589.
[21] EVANNO G,REGNAUT S,GOUDET J.Detecting the number of clusters of individuals using the software STRUCTURE:A simulation study[J].Molecular Ecology,2005,14(8):2611-2620.
[22] MANICHAIKUL A,MYCHALECKYJ J C,RICH S S,et al.Robust relationship inference in genome-wide association studies[J].Bioinformatics,2010,26(22):2867-2873.
[23] ZHANG C,DONG S S,XU J Y,et al.PopLDdecay:A fast and effective tool for linkage disequilibrium decay analysis based on variant call format files[J].Bioinformatics,2019,35(10):1786-1788.
[24] MCQUILLAN R,LEUTENEGGER A L,ABDEL-RAHMAN R,et al.Runs of homozygosity in European populations[J].The American Journal of Human Genetics,2008,83(3):359-372.
[25] GAUTIER M,VITALIS R.rehh:An R package to detect footprints of selection in genome-wide SNP data from haplotype structure[J].Bioinformatics,2012,28(8):1176-1177.
[26] 张发慧.肃南牦牛导入野牦牛杂交改良试验观察[J].中国畜牧兽医,2005,32(7):25-26. ZHANG F H.Experimental observation on cross improvement of Sunan yak introduced into wild yak[J]. China Animal Husbandry&Veterinary Medicine,2005,32(7):25-26.(in Chinese)
[27] 罗文学.天祝白牦牛产业发展的思考[J].畜牧兽医杂志,2020,39(6):44-45. LUO W X.Thoughts on the development of Tianzhu White yak industry[J].Journal of Animal Science and Veterinary,2020,39(6):44-45.(in Chinese)
[28] LEOCARD,S.Selective sweep and the size of the hitchhiking set[J]. Advances in Applied Probability,2009,41(3):731-764.
[29] PATTERSON L T,PEMBAUR M,POTTER S S.Hoxa11 and Hoxd11 regulate branching morphogenesis of the ureteric bud in the developing kidney[J].Development,2001,128(11):2153.
[30] 吴江鸿,闫祖威,胡斯乐,等.Hoxc13在毛囊发育中的作用[J].遗传,2010,32(7):656-662. WU J H,YAN Z W,HU S L,et al.Hoxc13 and the development of hair follicle[J].Hereditas,2010,32(7):656-662.(in Chinese)
[31] CROSSLEY P H,MARTINEZ S,MARTIN G R.Midbrain development induced by FGF8 in the chick embryo[J].Nature,1996,380(6569):66-68.
[32] CROSSLEY P H,MINOWADA G,MACARTHUR C A,et al.Roles for FGF8 in the induction,initiation,and maintenance of chick limb development[J].Cell,1996,84(1):127-136.
[33] WANG Z,CHEN Y,CHEN M,et al.Overexpression of FGF8 in the epidermis inhibits hair follicle development[J].Experimental Dermatology,2021,30(4):494-502.
[34] ZHENG Y,BRASH A R.Dioxygenase activity of epidermal lipoxygenase-3 unveiled:Typical and atypical features of its catalytic activity with natural and synthetic polyunsaturated fatty acids[J]. Journal of Biological Chemistry,2010,285(51):39866-39875.
[35] KIYOHARA R,YAMAGUCHI S,RIKIMARU K,et al.Supplemental arachidonic acid-enriched oil improves the taste of thigh meat of Hinai-jidori chickens[J].Poultry Science,2011,90(8):1817-1822.
[36] PATEL S H,CAMARGO F D,YIMLAMAI D.Hippo signaling in the liver regulates organ size,cell fate,and carcinogenesis[J].Gastroenterology,2017,152(3):533.
[37] BAO Q,ZHANG X,BAO P,et al.Using weighted gene co-express ion network analysis (WGCNA) to identify the hub genes related to hypoxic adaptation in yak (Bos grunniens)[J].Genes&Genomics,2021,43(10):1231-1246.
[38] 郝向伟.家蚕Hedgehog信号通路相关基因的克隆、鉴定及其功能分析[D].重庆:西南大学,2013. HAO X W.Positional cloning of silkworm plain extra-legs (E) and the expression and evolution analysis of its canddate gene[D].Chongqing:Southwest University,2013.(in Chinese)
[39] 张志远.Hedgehog信号通路在低氧肺血管重建中的作用及机制研究[D].重庆:第三军医大学,2009. ZHANG Z Y.Study of role and mechanism of Hedgehog signaling pathway in pulmonary vascular remodeling induced by hypoxia[D].Chongqing:Third Military Medical University,2009.(in Chinese)
[40] YANG G,BISWASA C,LIN Q S,et al.Heme oxygenase-1 regulates postnatal lung repair after hyperoxia:Role of β-catenin/hnRNPK signaling[J].Redox Biology,2013,1(1):234-243.
[41] YANG B,YU S,CUI Y,et al.Morphological analysis of the lung of neonatal yak[J].Anatomia Histologia Embryologia,2010,39(2):138-151.
[42] VOIGHT B F,KUDARAVALLI S,WEN X,et al.A map of recent positive selection in the human genome[J].PLoS Biology,2006,4(3):e72.
[43] STARHEIM K K,ARNESEN T,GROMYKO D,et al.Identification of the human N (alpha)-acetyltransferase complex B (hNatB):A complex important for cell-cycle progression[J].Biochemical Journal,2008,415(2):325-331.
[44] BO Z,WANG M,YANG Y,et al.ERp29 is a radiation-responsive gene in IEC-6 cell[J].Journal of Radiation Research,2008,6:587-596.
[45] 魏晶,陈纪飞,王冰,等.TMEM家族成员免疫功能的研究进展[J].中国免疫学杂志,2016,32(1):127-130. WEI J,CHEN J F,WANG B,et al.Research progress on immune function of TMEM family members[J]. Chinese Journal of Immunology,2016,32(1):127-130.(in Chinese)
[46] YAN J,ZHANG Y,TAN Y,et al.Black carp TRAFD1 restrains MAVS-mediated antiviral signaling during the innate immune activation[J].Fish&Shellfish Immunology,2020,5:103.
[47] 余益本,王建平.TLR信号通路研究进展[J].细胞与分子免疫学杂志,2012,28(12):4. YU Y B,WANG J P.Research progress of TLR signaling pathway[J].Chinese Journal of Cellular and Molecular Immunology,2012,28(12):4.(in Chinese)
[48] 李园园,史伟峰.RLR信号通路在病毒感染中作用机制研究进展[J].临床检验杂志,2014,32(11):852-855. LI Y Y,SHI W F.Research progress on the mechanism of RLR signaling pathway in viral infection[J].Chinese Journal of Clinical Laboratory Science,2014,32(11):852-855.(in Chinese)
[49] NAKAGAWA-SENDA H,HACHIYA T,SHIMIZU A,et al.A genome-wide association study in the Japanese population identifies the 12q24 locus for habitual coffee consumption:The J-MICC study[J].Scientific Reports,2018,8(1):1493.

肃南牦牛群体遗传结构、选择信号分析和ROH检测

Genetic Structure,Selection Signal Analysis and ROH Detection of Sunan Yak Population

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[6]	金美林, 陆健, 费晓娟, 卢曾奎, 权凯, 储明星, 狄冉, 王慧华, 魏彩虹. 西藏山羊高海拔适应性的选择信号筛选[J]. 中国畜牧兽医, 2020, 47(10): 3214-3223.
[7]	阿地力江·卡德尔, 刘雪雪, 杨敏, 玛哈巴·肉孜, 蒋琳, 马月辉. 全基因组选择信号检测方法在家畜研究中的应用进展[J]. , 2016, 43(6): 1641-1646.
[8]	贺三刚;黄锡霞;史洪才;田可川;徐新明;劳荃蘅. 超细型细毛羊基因组DNA的AFLP检测研究[J]. , 2008, 1(7): 32-36.