Genome-wide Characterization of the Sudanese and Chinese Indigenous Sheep Populations by High Density SNP Arrays
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【Author in Chinese】 Adam Abied；
【Author's Information】 中国农业科学院， 动物遗传育种与繁殖， 2020， 博士
【Abstract in Chinese】 全基因组变异分析可为群体遗传多样性、群体结构及种群内和种群间分化提供重要信息;同时也可鉴定包括绵羊等各种家畜有关生产性能、繁殖性能和适应性等性状相关的潜在基因或基因组区域选择信号。绵羊(Ovis aries)通过长期的自然和人工选择已适应各种生态环境并表现出多种表型特征。遗传多样性特征鉴定和选择信号分析对遗传改良、环境适应的理解以及绵羊遗传资源的利用保护至关重要。高密度SNP芯片和全基因组重测序等高通量基因分型技术的快速发展,使我们能够快速检测绵羊个体基因组中的上百万个SNP,并鉴定绵羊种群中全基因组的遗传变异。然而,由于对苏丹绵羊和中国绵羊群体遗传多样性选择信号研究研究仍然有限,因此本研究使用600K芯片对苏丹地方绵羊和中国地方绵羊品种进行基因多样性、群体结构和选择信号分析。我们采集了5个苏丹沙漠羊群体,其中AL-Ahamda25只、Buzee23只、Hammri 24只、Kabashi 25只和Shanbali 24只;以及4个中国羊品种包括黑藏羊15只、欧拉羊(QOL=15)、滩羊(TS=18)和泽库羊15只,共280个样本个体。此外,我们还对来自干旱环境的和田羊、雅布依羊和卡拉库尔羊以及来自潮湿环境的湖羊和洼地绵羊羊96个个体进行了芯片分析。第二章我们对亚非绵羊起源、驯化和遗传资源,分子鉴定技术及其重要性进行了全面的文献综述,阐明基因组分析在绵羊群体评价、育种和保护的重要意义。第三章为了研究各绵羊群体遗传特征、群体结构及选择信号,应用600 k SNP芯片对5个苏丹瘦尾沙漠绵羊群体和4个中国绵羊地方品种进行了分析。结果表明,苏丹沙漠瘦尾绵羊5个生态类型的遗传多样性较低。主成分分析、系统发育分析和群体结构分析表明,AL-Ahamda群体具有较低的遗传分化。卡巴什生态型的一些个体在K=2时具有遗传特异性。通过比较苏丹瘦尾羊与中国脂尾样本滩羊选择信号分析鉴定到41候选基因组区域,其中包含72个新的和已知的基因与热应激(HSPA5、DNAJB14 YTHDF1),寿命(GAK和CPLX1),生长发育调控(CSMD1 FGFR3,BRCA1)、体重和体高(DIS3L2和TP53),脂肪沉积和尾生长(NPR2、ADD1和SNORA73),代谢途径(ATP1B2 G6BC,U2,STRT3 MYT3,和GLI1)、生产(FGF9和LATS2)、繁殖(TET2、H2AFZ、OVOL1、SPAG4、EEF1A2、NPTX1、MELK、FGF2、PPP2R5D、XRN2和EFNB3)、免疫(COMMD4、ADPP1、FGB、SIGLEC1和ELF4A1)、抗病和炎症反应(POLR2A、TNFSF13、CD68、SAT2、GAA、PPT2、RABEPK、SCAI和LHX2)等相关。我们的发现为苏丹沙漠瘦尾羊的基因组结构提供了新的见解。第四章,为了探究中国绵羊在极端干旱和潮湿环境下对各种生态环境的潜在适应性,我们采用通过600 K芯片对5个中国地方羊品种进行遗传多样性、遗传结构和基因组选择信号分析。本实验共采集了来自极端干燥和潮湿的环境96个绵羊个体。大量的SNP位点被鉴定,其中雅布依羊SNP占比93.3%,洼地羊、湖羊和和田羊占95.5%,群体间遗传分化(FST)的平均为0.048%,变异范围为0.022%~0.054%,为低至中度遗传分化。主成分分析、混合分析和系统发育树分析结果显示,中国绵羊的5个品种聚在一起,与地理分布、尾型、毛色、体型和育种历史等基本一致。基于FST和XP-EHH方法,包括与抗病性状、防御、先天和适应性免疫应答、消化代谢、生长、体型、产乳、产毛和繁殖性状相关的候选基因被鉴定。选择信号分析表明部分与经济性状和环境适应的相关基因受到了选择。本研究为绵羊和其他动物对干旱和寒冷气候的基因组适应提供了新的见解,并为进一步的研究提供了宝贵的资源。此外,也为遗传资源的可持续利用和保护提供了有用的信息。第五章,应用600 k芯片调查每个品种的ROHs的发生和分布,以及识别ROH频率高的基因组区域内个人评估近亲繁殖,评估全基因组连锁不平衡(LD)、有效种群大小(Ne)。对来自包括极端干燥和潮湿极端环境不同区域5个中国绵羊品种96个个体进行分析,共鉴定出3046个ROHs,其中以较长片段(>1-5Mb)为主。大约平均12%的基因组被ROH片段覆盖;OAR20的覆盖率最低,OAR2的覆盖率最高;ROH分布分析表明,检测到的ROH大部分分布在>26~28mb之间,ROH最低的两个品种是和田羊和湖羊。ROH水平分析能够反映近现代和古代近亲繁殖的历史,并表明一些动物经历了近亲杂交(YY,KK,和WD)。基于品种间选择信号分析发现候包括与抗病性状(5S_r RNA)、先天和适应性免疫应答(HERC2和CYFIP1)、消化代谢(CENPJ)、生长(SPP1)体型和发育(GJB2和GJA3)相关的候选基因。该研究内容为今后中国绵羊种群保护策略提供了新的思路。综上,本论文解析了苏丹和中国地方绵羊群体遗传多样性、群体遗传关系、选择信号等全基因组信息,为绵羊资源的可持续利用和保护提供了依据。
【Abstract】 Through long term natural and artificial selection,domestic sheep(Ovis aries)have become adapted to a diverse range of ecological environments and display multiple phenotypic traits.Characterization of diversity and selection signature is essential for genetic improvement,understanding of environmental adaptation,as well as utilization and conservation of sheep genetic resources.The rapid development of high throughput genotyping such as high density SNP Bead Chip arrays and whole genome re-sequencing allow us to discover million SNPs of the individuals’ genome and quantify genome-wide genetic variation in sheep population.However,comprehensive researches are still limited and uncovered in Sudanese sheep as well as Chinses sheep to some extent.Here,we aimed to assess genetic diversity,population structure,and genomic selection among Sudanese native sheep and Chinese native sheep breeds using 600 K HD Bead Chip data.We collected a total of 280 individuals representing five Sudanese desert sheep AL-Ahamda(n =25),Buzee(n = 23),Hammri(n = 24),Kabashi(n =25)and Shanbali(n =24)with four Chinese sheep breeds Black Tibetan(n = 15),Oula(QOL =15),Tan(TS =18)and Zeku(n=15).Moreover,we compared five Chinese sheep breeds from extreme dry environments Hetian(n=19),Yabuyi(n= 20)and Karakul(n=20)and extreme humid environments Hu(n=17)and Wadi(n=17)sheep.In the second chapter,we provided a comprehensive literature review including the origin and domestication of sheep genetic resources in Africa and Asia,overview and distributions of Sudanese indigenous sheep,techniques and importance of molecular characterizations that make them importance targets for research,breeding and conservation.In third chapter,we investigated genome diversity,evolutionary relationship,population structure and genome-wide selection signatures between the five Sudanese thin-tailed desert sheep and four Chinese sheep breeds by using 600 K SNP Bead Chip in order to clearly characteristics the population and properly understand their genomics potential which provides a good opportunity for sustainable utilization,conservation and maintenance for genetic resources improvements in Sudanese sheep population.The analysis has revealed the low genetic diversity in the five Sudanese thin-tailed desert sheep ecotypes.PCA,phylogenetic analysis and ADMIXTURE analysis revealed AL-Ahamda slightly genetically differentiated.Unexpectedly,a few individuals of the Kabashi ecotype had a unique genetic background at K = 2.By comparing Sudanese thin-tailed desert with Chinese fat-tailed Tan sheep,selection signature analysis identified 41 candidate regions spanning 72 potentially novel and known genes that are associated with the response to heat stress(HSPA5,DNAJB14,and YTHDF1),lifespan(GAK and CPLX1),growth regulation(CSMD1,FGFR3,and BRCA1),body weight and height variation(DIS3L2 and TP53),fat deposition and tail growth(NPR2,ADD1,and SNORA73),metabolic pathways(ATP1B2,G6 BC,U2,STRT3,MYT3,and GLI1),production(FGF9 and LATS2),reproduction(TET2,H2 AFZ,OVOL1,SPAG4,EEF1A2,NPTX1,MELK,FGF2,PPP2R5 D,MAPKAP1,and LGR5),proliferation(PDE6B,XRN2,and EFNB3),immunity(COMMD4,ADPP1,FGB,SIGLEC1,and ELF4A1)and disease resistance and inflammatory responses(POLR2A,TNFSF13,CD68,SAT2,GAA,PPT2,RABEPK,SCAI,and LHX2).Our findings have offered insights into the genome architecture of Sudanese thin-tailed desert sheep,which call for the further investigations to determine whether the observed genome structure can characterize other African thin-tailed sheep.In the fourth chapter,we aimed to assess genetic diversity,population genetic structure and genome selection signatures among five Chinese native sheep breeds using 600 K HD Bead Chip in order to breeds characterization and a greater understanding their potential adaptation to diverse range of ecological environments as well as utilization,conservation and its essential for genetic improvement of Chinese sheep from extreme dry and humid environments.A total of 96 animals were selected from different geographical locations with extremes dry and humid environments.We found a high proportion of informative SNPs,ranging from 93.3% in Yabuyi to 95.5% in Wadi,Hu and Hetian breeds.The average estimated pairwise genetic differentiation(FST)among the population was 0.048%,ranging from 0.022% to 0.054% and indicating low to moderate genetic differentiation.PCA,ADMIXTURE,and phylogenetic tree analyses revealed a clustering of five Chinese sheep breeds according to geographical distribution,tail types,coat color,body size and breeding history.The regions of putative signatures of selection frequently overlapped with FST and XP-EHH approaches across the breeds,including candidate genes associated with disease resistance traits,defenses,innate and adaptive immunity response,digestive metabolism,growth,body size,milk production,wool production,and reproduction traits.The selective signature analyses suggested that,at least partially,a selection for economic traits and environmental adaptation into extreme arid and humid lands.The present study offer novel insights into genomic adaptation to arid and cold climates in sheep and other animals,and provides a valuable resource for further investigations.Moreover,it provides useful information for sustainable utilization and maintenance of genetic resource.In the fifth chapter,our aim was to investigate the occurrence and distribution of ROHs to characterize autozygosity of each breed,as well as to identifying the genomic regions with high ROH frequencies within individuals using 600 k HD Bead Chip to assessment the inbreeding and allows inferences the past demographic history and determine the genome-wide linkage disequilibrium(LD),the extent of effective population size(Ne).In total,96 animals were selected from five Chinese sheep breeds,from different geographical locations extremes dry and humid environments.In total,3046 ROHs were identified in all individuals,among which longer segments(>1-5Mb)were predominated.On the average,approximately 12% of the genome was covered by ROH segments;with the lowest coverage on OAR20 and the highest coverage on OAR2;Analysis of distribution ROH showed that,the majority of detected ROH were ranged >26 to 28 Mb,the lowest two breeds are Hetian and Hu sheep.The levels of ROH that were estimated reflect to the recent and ancient inbreeding history,which had an impact on the genome of the sheep breeds and suggesting that several animals experienced recent autozygosity events(YY,KK,and WD).The regions of putative signature of selection frequently overlapped with high ROH across the breeds,included candidate genes associated with disease resistance traits(5S_rRNA),innate and adaptive immunity response(HERC2 and CYFIP1),digestivemetabolism(CENPJ),Growth(SPP1),body size and developments(GJB2 and GJA3).Chapter five provides new insights into ROHs distribution patterns for future conservation strategies of Chinese sheep populations.Overall,the thesis provides valuable genome-wide information of genetic diversity,population relationship and structure,and selection signatures,which could be good opportunity for sustainable utilization and maintenance for the Sudanese and Chinese indigenous sheep populations.