基于全基因组重测序分析新疆细毛羊遗传多样性

doi:10.6048/j.issn.1001-4330.2023.05.029

新疆农业科学 ›› 2023, Vol. 60 ›› Issue (5): 1292-1300.DOI: 10.6048/j.issn.1001-4330.2023.05.029

• 微生物·畜牧兽医 • 上一篇

基于全基因组重测序分析新疆细毛羊遗传多样性

陈开旭(), 郭翠洁, 杨帆, 任斐儿, 李晓斌, 刘武军()

新疆农业大学动物科学学院,乌鲁木齐 830052

收稿日期:2022-09-01 出版日期:2023-05-20 发布日期:2023-05-22
通信作者: 刘武军(1966-),女,河南鹿邑人,教授,博士,硕士生/博士生导师研究方向为动物遗传育种,(E-mail) lwj_ws@163.com
作者简介:陈开旭(1983-),男,四川三台人,讲师,博士,研究方向为动物遗传育种,(E-mail) chenkaixu@126.com
基金资助:
新疆维吾尔自治区高校科研计划项目“基于简化基因组的新疆地方绵羊品种群体遗传学分析”(XJEDU2020Y014);中国博士后科学基金“新疆绵羊线粒体DNA遗传多样性研究”(2017M613307XB)

Genetic diversity analysis of xinjiang sheep with fine wool based on whole-genome Re-sequencing

CHEN Kaixu(), GUO Cuijie, YANG Fan, REN Feier, LI Xiaobin, LIU Wujun()

College of Animal Science, Xinjiang Agricultural University, Urumqi 830052,China

Received:2022-09-01 Online:2023-05-20 Published:2023-05-22
Correspondence author: LIU Wujun (1966-), female, Luyi, Henan. Ph. D, professor, research field: animal genetics and breeding, (E-mail) lwj_ws@163.com
Supported by:
Scientific Research Program of Colleges and Universities of Xinjiang Uygur Autonomous Region "Population Genetic Analysis of Local Sheep Breeds in Xinjiang Based on Reduced-Representation Genome Sequencing"(XJEDU2020Y014);China Postdoctoral Science Foundation " Mitochondrial DNA Genetic Diversity of Sheep in Xinjiang"(2017M613307XB)

摘要/Abstract

摘要：

【目的】基于全基因组重测序研究新疆细毛羊遗传多样性。【方法】利用新疆细毛羊的全基因组重测序数据和NCBI下载获得的策勒黑羊、巴音布鲁克羊、阿勒泰羊全基因组重测序数据,检测不同绵羊品种的核苷酸多态性和单倍型多态性,评估其遗传多样性现状,计算群体分化指数、观望/观测杂合度,分析遗传多样性,评价不同绵羊品种现有的遗传变异水平。【结果】全基因组重测序获得了97647435个高质量的常染色单核苷酸多态性(SNP)位点和15886270个插入或缺失(Indel);新疆细毛羊的遗传多样性水平显著低于阿勒泰羊,低于巴音布鲁克羊,略高于策勒黑羊;4个绵羊群体遗传多样性顺序:阿勒泰羊> 巴音布鲁克羊> 策勒黑羊> 新疆细毛羊。【结论】选取的4个绵羊群体中,新疆细毛羊的遗传多样性水平相对较低。

关键词: 新疆细毛羊; 遗传多样性; 全基因组重测序

Abstract:

【Objective】 To study the genetic diversity of Xinjiang sheep with fine wool by whole-genome resequencing.【Methods】 Whole-genome resequencing data of Xinjiang sheep with fine wool and whole-genome resequencing data of Bayinbruck, Altay, and Qira black sheep downloaded from NCBI were used to assess the existing genetic diversity status of different sheep breeds by detecting nucleotide polymorphism, calculating population differentiation index, watching/observing heterozygosity, and conducting genetic diversity analysis.【Results】 97647435 high-quality autosomal single nucleotide polymorphism (SNP) loci and 15886270 insertions or deletions (Indel) were obtained by whole-genome resequencing.The genetic diversity level of Xinjiang fine-wool sheep was significantly lower than that of Altay sheep and that of Bayinbruck sheep and slightly higher than that of Qira black sheep.The order of genetic diversity of 4 sheep populations was: Altay sheep > Bayinbruck sheep > Qira black sheep > Xinjiang fine-wool sheep.【Conclusion】 The genetic diversity of Xinjiang fine-wool sheep is relatively low in the 4 sheep populations chosen in this study.

Key words: Xinjiang sheep with fine wool; genetic diversity; whole-genome resequencing

中图分类号:

S813.1

陈开旭, 郭翠洁, 杨帆, 任斐儿, 李晓斌, 刘武军. 基于全基因组重测序分析新疆细毛羊遗传多样性[J]. 新疆农业科学, 2023, 60(5): 1292-1300.

CHEN Kaixu, GUO Cuijie, YANG Fan, REN Feier, LI Xiaobin, LIU Wujun. Genetic diversity analysis of xinjiang sheep with fine wool based on whole-genome Re-sequencing[J]. Xinjiang Agricultural Sciences, 2023, 60(5): 1292-1300.

图/表 9

图1 DNA 样品 1% 琼脂糖凝胶电泳检测结果注:M 泳道为λ-HindⅢ DNA Marker,1-10泳道为DNA样品

Fig.1 1% agarose gel electrophoresis of DNA samples Note: M line: λ-HindⅢ DNA Marker, 1-10 line: DNA samples

表1 新疆细毛羊DNA样品浓度及纯度检测

Tab.1 Detection of DNA concentration and purity of Xinjiang fine wool sheep

样品编号 Sample number	纯度 OD₂₆₀/OD₂₈₀	浓度 concentration (ng/μL)
XFW01	1.83	81.426
XFW02	1.91	67.261
XFW03	1.88	79.537
XFW04	1.97	94.253
XFW05	1.89	88.051
XFW06	1.89	62.306
XFW07	2.07	105.364
XFW08	1.89	78.859
XFW09	1.88	96.857
XFW10	1.95	79.925

表2 全基因组测序数据质量统计

Tab.2 Whole genome sequencing data quality statistics

样品编号 Sample number	比对率 Mapping rate (%)	全基因组覆盖度 Coverage (%)	测序深度 Sequencing depth	Q20 (%)	Q30 (%)
XFW01	99.01	97.81	8.943 3X	97.14	92.32
XFW02	99.46	97.89	8.167 2X	97.22	92.48
XFW03	99.44	97.93	7.566 7X	97.12	92.22
XFW04	99.28	97.80	7.223 8X	96.88	91.66
XFW05	99.32	97.90	7.484 3X	97.22	92.41
XFW06	74.88	97.91	6.075 4X	96.81	91.62
XFW07	99.22	97.87	7.613 8X	96.93	91.82
XFW08	94.48	97.93	8.478 5X	96.91	91.81
XFW09	99.31	97.89	7.104 6X	96.73	91.47
XFW10	99.38	97.91	8.189 1X	96.77	91.5

表3 新疆细毛羊全基因组重测序数据遗传变异鉴定、过滤和注释

Tab.3 The genetic variation information of SNPs and indels in sheep breeds

单核苷酸多态性SNP			Indel
Type (alphabetical order)	Count	Percent(%)	Type (alphabetical order)	Count	Percent(%)
DOWNSTREAM	2 232 463	2.29	DOWNSTREAM	469 219	2.95
EXON	775 956	0.79	EXON	234 723	1.48
INTERGENIC	56 743 016	58.11	INTERGENIC	8 705 661	54.80
INTRON	34 744 752	35.58	INTRON	5 588 596	35.18
SPLICE_SITE_ACCEPTOR	995	0.00	SPLICE_SITE_ACCEPTOR	11 111	0.07
SPLICE_SITE_DONOR	2108	0.00	SPLICE_SITE_DONOR	12865	0.08
SPLICE_SITE_REGION	54 513	0.06	SPLICE_SITE_REGION	15 675	0.10
UPSTREAM	2 350 282	2.41	UPSTREAM	684 523	4.31
UTR_3_PRIME	511 316	0.52	UTR_3_PRIME	88 686	0.56
UTR_5_PRIME	232 034	0.24	UTR_5_PRIME	75 211	0.47

图2 4个绵羊群体的杂合度变化注:*表示不同绵羊群体间的杂合度具有显著差异(P<0.05),**表示不同绵羊群体间的杂合度具有极显著差异(P<0.01)

Fig.2 Heterozygosity analysis of 4 sheep populations Note:* indicated the heterozygosity of different sheep groups was significantly different (P<0.05),** indicated the heterozygosity of different sheep groups was extremely significantly different

表4 4个绵羊群体的平均ROH长度和基因组近交系数

Tab.4 Average length and genomic inbreeding coefficient of four sheep groups

品种 Breed	ROH长度 Length of ROH (Mb)		基因组近交系数 Inbreeding coefficient (F_ROH)
品种 Breed	平均值±标准误 Mean±SE	ROH长度区间 Range	平均值±标准误 Mean±SE	F_ROH区间 Range
XFW	110.665±8.744	89.609-178.833	0.042 3±0.003 2	0.034 26-0.068 37
CLE	93.532±6.956	74.687-151.767	0.035 8±0.002 5	0.028 56-0.058 03
BYK	88.417±10.694	47.985-148.081	0.033 8±0.003 9	0.018 34-0.056 62
ALT	74.445±21.225	57.063-131.694	0.028 5±0.0024	0.021 82-0.050 35

图3 4个绵羊群体的ROH片段长度分类注:*表示不同绵羊群体间的ROH片段长度差异显著(P<0.05)

Fig.3 The total length of ROH in different length categories Note:* indicated the length of ROH fragment was significantly different among different sheep groups(P<0.05)

图 4 4个绵羊群体的平均ROH数量和每个个体的 ROH 数量注:**表示不同绵羊群体间的平均ROH片段数量差异极显著(P<0.01)

Fig.4 The average number of ROH and the number of ROH per individual in 4 sheep groups Note:** indicated the average number of ROH fragments among different sheep groups was extremely significantly different(P<0.01)

图5 4个绵羊群体的连锁不平衡变化

Fig.5 Linkage disequilibrium decay (LD decay) in four breeds

参考文献 41

[1]	刘慧. 中国羊毛贸易发展情况分析[J]. 农业展望, 2010, 6(6): 46-49.
	LIU Hui. Analysis of the Chinese wool trade development trend[J]. Agricultural Outlook, 2010, 6(6): 46-49.
[2]	田春英, 王峰, 荣威恒. 内蒙古细毛羊产业可持续发展对策探讨[J]. 畜牧与饲料科学, 2005, 26(4): 48-50.
	TIAN Chunying, WANG Feng, RONG Weiheng. Countermeasures for sustainable development of Inner Mongolia fine-wool sheep industry[J]. Animal Husbandry and Feed Science, 2005, 26(4): 48-50.
[3]	赵有璋. 羊生产学[M]. 中国农业出版社, 2011.
	ZHAO Youzhang. Sheep And Goat Production[M]. China Agriculture Press, 2011.
[4]	曾献存. 新疆绵羊遗传多样性及主要经济性状候选基因研究[D]. 石河子: 石河子大学, 2010.
	ZENG Xiancun. Studies on the genetic diversity of Xinjiang sheep breeds and candidate genes of major economic traits[D]. Shehezi: Shihezi University, 2010.
[5]	沈文, 孙延鸣, 崔茹鹏, 等. 新疆细毛羊KAP6.1基因的克隆及序列分析[J]. 黑龙江畜牧兽医, 2013, 3: 31-34.
	SHEN Wen, SUN Yanming, CUI Rupeng, et al. Cloning and sequence analysis of KAP 6.1 gene in Xinjiang fine-wool sheep[J]. Heilongjiang Animal Science and Veterinary Medicine, 2013(3): 31-34.
[6]	肖非. 新疆绵羊种质资源调查、保护及遗传多样性[D]. 石河子: 石河子大学, 2009.
	XIAO Fei. Investigation, conservation and genetic diversity of germplasm resources in Xinjiang sheep[D]. Shiehzi: Shihezi University, 2009.
[7]	赵永欣, 李孟华. 中国绵羊起源, 进化和遗传多样性研究进展[J]. 遗传, 2017, 39(11):958-973.
	ZHAO Yongxin, LI Menghua. Research advances on the origin, evolution and genetic diversity of Chinese native sheep breeds[J]. Hereditas, 2017, 39(11): 958-973.
[8]	王秀蓉. 基于SSR标记评估青海省家牦牛和藏绵羊遗传多样性及近交程度[D]. 西宁: 青海师范大学, 2019.
	WANG Xiurong. Study on genetic diversity and inbreeding degree of domestic Yak and Tibetan sheep in Qinghai Province based on SSR markers [D]. Xining: Qinghai Normal University, 2019.
[9]	Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM[J]. arXiv e-prints, 2013: arXiv: 1303.3997.
[10]	Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAM tools[J]. Bioinformatics, 2009, 25(16): 2078-2079. DOI URL
[11]	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. DOI PMID
[12]	Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data[J]. Nucleic Acids Research, 2010, 38(16): e164.
[13]	Yang H, Wang K. Genomic variant annotation and prioritization with ANNOVAR and ANNOVAR[J]. Nature Protocols, 2015, 10(10): 1556-1566. DOI PMID
[14]	Haubold B, Pfaffelhuber P, Lynch M. mlRho-a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes[J]. Molecular Ecology, 2010, 19: 277-284. DOI URL
[15]	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. DOI URL
[16]	Bosse M, Megens H J, Madsen O, et al. Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape[J]. PLoS Genetics, 2012, 8(11): e1003100.
[17]	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. DOI PMID
[18]	Garvin M R, Saitoh K, Gharrett A J. Application of single nucleotide polymorphisms to non‐model species: a technical review[J]. Molecular Ecology Resources, 2010, 10(6): 915-934. DOI PMID
[19]	Fan B, Du Z Q, Gorbach D M, et al. Development and application of high-density SNP arrays in genomic studies of domestic animals[J]. Asian-Australasian Journal of Animal Sciences, 2010, 23(7): 833-847.
[20]	张彦斌, 罗海涛, 范鑫, 等. 锡林郭勒绵羊品种遗传多样性研究进展[J]. 中国畜禽种业, 2020, 16(3): 3-6.
	ZHANG Yanbin, LUO Haitao, FAN Xin, et al. Research progresses of the varietal genetic polymorphism of Xilinguole sheep[J]. The Chinese Livestock and Poultry Breeding, 2020, 16(3): 3-6.
[21]	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. DOI PMID
[22]	Broman K W, Weber J L. Long homozygous chromosomal segments in reference families from the centre d'Etude du polymorphisme humain[J]. The American Journal of Human Genetics, 1999, 65(6): 1493-1500. DOI URL
[23]	Caballero A, Villanueva B, Druet T. On the estimation of inbreeding depression using different measures of inbreeding from molecular markers[J]. Evolutionary Applications, 2021, 14(2): 416-428. DOI PMID
[24]	D’ambrosio J, Phocas F, Haffray P, et al. Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding[J]. Genetics Selection Evolution, 2019, 51(1): 1-15. DOI
[25]	Letko A, Minor K M, Jagannathan V, et al. Genomic diversity and population structure of the Leonberger dog breed[J]. Genetics Selection Evolution, 2020, 52(1): 1-12. DOI
[26]	Fang Y, Hao X, Xu Z, et al. Genome-wide detection of runs of homozygosity in Laiwu pigs revealed by sequencing data[J]. Frontiers in Genetics, 2021: 463.
[27]	Liu D, Chen Z, Zhao W, et al. Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits[J]. BMC Genomics, 2021, 22(1): 1-19. DOI
[28]	Gorssen W, Meyermans R, Janssens S, et al. A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species[J]. Genetics Selection Evolution, 2021, 53(1): 1-10. DOI
[29]	Stoffel M A, Johnston S E, Pilkington J G, et al. Mutation load decreases with haplotype age in wild Soay sheep[J]. Evolution Letters, 2021, 5(3): 187-195. DOI PMID
[30]	Zhang X, Kim B, Lohmueller K E, et al. The impact of recessive deleterious variation on signals of adaptive introgression in human populations[J]. Genetics, 2020, 215(3): 799-812. DOI PMID
[31]	Khan A, Patel K, Shukla H, et al. Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers[J]. Proceedings of the National Academy of Sciences, 2021, 118(49): e2023018118.
[32]	Addo S, Klingel S, Thaller G, et al. Genetic diversity and the application of runs of homozygosity-based methods for inbreeding estimation in German White-headed Mutton sheep[J]. PloS One, 2021, 16(5): e0250608.
[33]	Suezawa R, Nikadori H, Sasaki S. Genetic diversity and genomic inbreeding in Japanese Black cows in the islands of Okinawa Prefecture evaluated using single‐nucleotide polymorphism array[J]. Animal Science Journal, 2021, 92(1): e13525.
[34]	Roh H J, Kim S C, Cho C Y, et al. Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers[J]. Asian-Australasian Journal of Animal Sciences, 2020, 33(12): 1896.
[35]	Humble E, Paijmans A J, Forcada J, et al. An 85K SNP array uncovers inbreeding and cryptic relatedness in an Antarctic fur seal breeding colony[J]. G3: Genes, Genomes, Genetics, 2020, 10(8): 2787-2799.
[36]	杨湛澄, 黄河天, 闫青霞, 等. 利用高密度 SNP 标记分析中国荷斯坦牛基因组近交[J]. 遗传, 2017, 39(1): 16-23.
	YANG Zhancheng, HUANG Hetian, YAN Qingxia, et al. Estimation of genomic inbreeding coefficients based on high-density SNP markers in Chinese Holstein cattle[J]. Hereditas, 2017, 39(1): 16-23.
[37]	Stoffel M A, Johnston S E, Pilkington J G, et al. Genetic architecture and lifetime dynamics of inbreeding depression in a wild mammal[J]. Nature Communications, 2021, 12(1): 1-10. DOI
[38]	Ghoreishifar S M, Moradi-Shahrbabak H, Fallahi M H, et al. Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis[J]. BMC Genetics, 2020, 21(1): 1-12. DOI
[39]	Suezawa R, Nikadori H, Sasaki S. Genetic diversity and genomic inbreeding in Japanese Black cows in the islands of Okinawa Prefecture evaluated using single‐nucleotide polymorphism array[J]. Animal Science Journal, 2021, 92(1): e13525.
[40]	Lewontin R C, Kojima K. The evolutionary dynamics of complex polymorphisms[J]. Evolution, 1960: 458-472.
[41]	Slatkin M. Linkage disequilibrium—understanding the evolutionary past and mapping the medical future[J]. Nature Reviews Genetics, 2008, 9(6): 477-485. DOI

基于全基因组重测序分析新疆细毛羊遗传多样性

Genetic diversity analysis of xinjiang sheep with fine wool based on whole-genome Re-sequencing

在线阅读

PDF下载

可视化

摘要/Abstract

引用本文

使用本文

图/表 9

参考文献 41

相关文章 15

编辑推荐

Metrics

[1]	逯涛, 曾庆涛, 张文, 王文博, 王政洋, 杨芮, 孙玉岩. 主成分分析及灰色关联度分析综合评价棉花产量与品质[J]. 新疆农业科学, 2023, 60(5): 1099-1109.
[2]	杨建超, 徐诚, 杨平, 杨鸿基, 张凯浩, 马新超, 高亚宁, 陈有福, 付湘, 轩正英. 氮素指数施肥对设施薄皮甜瓜养分承载及氮吸收利用的影响[J]. 新疆农业科学, 2023, 60(3): 590-600.
[3]	罗影, 努尔孜亚·亚力买买提, 贾文捷, 刘洁莹, 贾培松. 新疆野生大环柄菇的分子鉴定与遗传多样性分析[J]. 新疆农业科学, 2023, 60(10): 2501-2508.
[4]	姚莹莹, 李家辉, 李海英, 吴盈萍, 赵晓钰, 周军, 赵全庄, 李宗福. 也迷里鸡微卫星遗传多样性分析[J]. 新疆农业科学, 2023, 60(10): 2574-2582.
[5]	赵双印, 王为然, 闫雪雪, 比买热木·阿不都艾海提, 董洁, 吐尔逊·吐尔洪, 阿里甫·艾尔西. 120份棉花种质资源品质性状与遗传多样性分析[J]. 新疆农业科学, 2023, 60(1): 17-24.
[6]	李岳雁, 李玉姗, 王帆, 郭雅文, 王飞燕, 高杰, 宋羽. 不同品种番茄果实性状遗传多样性及聚类分析[J]. 新疆农业科学, 2022, 59(9): 2147-2157.
[7]	袁雷, 吉雪花, 张国儒, 石林媛, 郭河瑶, 唐亚萍, 杨涛, 杨生保. 52份辣椒主要果实性状的遗传多样性及聚类分析[J]. 新疆农业科学, 2022, 59(8): 1935-1944.
[8]	吴巧玉, 何天久. 紫色甘薯资源的形态学和ISSR荧光标记分析[J]. 新疆农业科学, 2022, 59(7): 1625-1631.
[9]	杨延龙, 马君, 师维军. 引进陆地棉种质资源表型性状遗传多样性分析[J]. 新疆农业科学, 2022, 59(2): 310-319.
[10]	杨延龙, 马志刚, 吾买尔江·库尔班, 汪鹏龙, 玛依拉·玉素音, 李春平, 阳妮, 马君, 师维军. 189份引进棉花种质资源农艺性状与品质性状的遗传多样性分析[J]. 新疆农业科学, 2022, 59(12): 2870-2878.
[11]	热比耶·玉荪, 吾买尔·库尔班, 张哲, 买买提·莫明, 艾先涛. 288份陆地棉种质资源主要性状遗传多样性分析[J]. 新疆农业科学, 2022, 59(12): 2879-2887.
[12]	马艳明, 赵连佳, 王威, 安学春, 向莉, 苗雨. 大麦种质资源表型性状遗传差异分析[J]. 新疆农业科学, 2022, 59(11): 2628-2636.
[13]	罗影, 贾培松, 努尔孜亚·亚力买买提, 祁颢萱, 赵振豪, 贾文捷. 新疆野生中国美味蘑菇的遗传多样性分析[J]. 新疆农业科学, 2022, 59(11): 2707-2713.
[14]	杨波, 郭春苗, 木巴热克·阿尤普, 龚鹏. 扁桃种质资源坚果数量性状遗传多样性和概率分级[J]. 新疆农业科学, 2021, 58(7): 1297-1305.
[15]	高玉芳, 张彦军, 赵振宁, 赵宝勰, 杜世坤. 引进大豆种质资源的适应性和遗传多样性分析[J]. 新疆农业科学, 2021, 58(6): 1029-1041.