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

doi:10.6048/j.issn.1001-4330.2023.05.029

Abstract

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

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

CLC Number:

S813.1

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.

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.

Figures/Tables 9

References 41

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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

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

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

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

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