基于全基因组重测序分析大尾寒羊基因组变异特征和群体结构

doi:10.11843/j.issn.0366-6964.2024.11.016

摘要/Abstract

摘要：

旨在了解大尾寒羊基因组遗传变异特征和群体结构，可以为更好地保护和利用大尾寒羊提供指导。本研究对170只(66只公羊，104只母羊)大尾寒羊进行了全基因组重测序，利用GATK、Manta、Plink等软件对大尾寒羊基因组遗传变异、群体结构和连锁不平衡等进行了分析，以期了解大尾寒羊基因组变异特征和群体结构。测序共获得1 599.56 G高质量数据(平均9.409 G·只^-1)。大尾寒羊群体中共发现50 276 079个SNPs和7 240 540个InDel，它们多分布于基因间和内含子区域。群体的基因组结构性变异(SV)最多的类型为染色体间的易位(CTX)，平均每只羊有415.82个CTX，主要分布在基因间区域；发生拷贝数变异(CNV)最多的区域在外显子，平均每只羊有175个。主成分分析显示, 大尾寒羊个体较分散，聚集不集中。结合亲缘关系、系统发育树和群体结构，将大尾寒羊分为6个家系，各家系含量差别较大，体型有差异。群体聚类分析中发现有些个体祖先成分较为单一。群体连锁不平衡(LD)分析显示LD衰减速度快，群体遗传多样性较高。驯化中受选择的基因主要与脂质代谢和产热有关。综上，大尾寒羊群体包含6个家系，遗传多样性较丰富，保种效果良好，建议对小家系进行扩繁，大家系注意减少近交，确保家系结构平衡，同时注重大尾寒羊的开发和利用。

关键词: 大尾寒羊, 全基因组重测序, 基因组变异, 群体结构

Abstract:

This study aimed to analyze the genomic variations and population structure of Large-tailed Han (LTH) sheep to provide guidance for scientific conservation and sustainable utilization. Whole-genomic sequencing data from 170 LTH sheep (66 rams, 104 ewes) was used to investigate the genomic variations, population structure and linkage disequilibrium by GATK, Manta, Plink and other softwares. The 1 599.56 G clean data was obtained and on average, 9.409 G clean data per sheep. In the LTH sheep population, 50 276 079 SNPs and 7 240 540 InDel were found, which were mostly distributed in intergenic and intronic region. The interchromosomal translocation (CTX) was the most common type of structural variation (SV) in the genome of LTH sheep, on average, 415.82 CTX per sheep, and also mainly distributed in the intergenic region. The copy number variation (CNV) was mostly distributed in exons, 175 CNV per sheep on average. The result of principal component analysis showed that individuals were relatively scattered and poorly clustered. According to the genetic relationship, phylogenetic tree and population structure, the 170 LTH sheep were clustered into 6 families, and there was a significant difference in family size and body size. The results of cluster analysis showed that ancestry component of some individuals was single. The linkage disequilibrium analysis showed that LTH sheep population had a relatively fast attenuation rate. The selected genes during domestication were mainly related with lipids metabolism and thermogenesis. In conclusion, LTH sheep population contains 6 families and has rich genetic diversity and remarkable conservation effect. It is suggested to expand the number of small families and to prevent inbreeding in the big families to keep a balanced population size and structure and focus on the utilization of LTH sheep.

Key words: Large-tailed Han sheep, whole genome resequencing, genomic variation, population structure

中图分类号:

S826.2

梁慧丽, 解玉静, 司博文, 王桂英, 姜运良, 曹贵玲. 基于全基因组重测序分析大尾寒羊基因组变异特征和群体结构[J]. 畜牧兽医学报, 2024, 55(11): 4968-4979.

Huili LIANG, Yujing XIE, Bowen SI, Guiying WANG, Yunliang JIANG, Guiling CAO. Analysis on Genomic Variation and Population Structure of Large-tailed Han Sheep Based on Whole Genome Resequencing[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(11): 4968-4979.

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变异类型Variation type	基因型位点总数Total sites number	位点缺失数量Miss sites number	非缺失位点总数No miss sites number	纯合型数量Homozygote number	杂合型数量Heterozygote number	纯合型比例/% Homozygote rate	杂合型比例/% Heterozygote rate
SNP	49 530 191	6 950 441	42 679 749	36 554 780	6 124 969	85.649	14.351
InDel	6 010 541	998 272	5 012 268	4 143 729	868 539	82.672	17.328

位置Location	基因型数量Genotype number	比例/% Percentage	InDel数量InDel number	比例/% Percentage
内含子Intronic	16 978 650	33.771	2 524 292	34.863
基因间Intergenic	31 878 775	63.407	4 433 588	61.233
基因上游Upstream	340 540	0.677	96 459	1.332
基因下游Downstream	295 506	0.588	53 434	0.738
一个基因下游同时另一个基因上游Upstream/downstream	10 598	0.021	3 173	0.044
形成终止密码子Stop gain	2 487	0.005	365	0.005
引起终止密码子消失Stop loss	337	0.001	36	< 0.001
可变剪切位点Splicing	4 669	0.009	3 124	0.043
基因5′-UTR区域UTR5	198 349	0.395	38 908	0.537
基因3′-UTR区域UTR3	248 668	0.495	51 835	0.716
同义突变Synonymous	157 590	0.313	－	－
非同义突变Non-synonymous	159 910	0.318	－	－
导致移码突变的缺失位点Frameshift deletion	－	－	13 014	0.180
导致移码突变的插入位点Frameshift insertion	－	－	17 228	0.238
非移码突变的缺失位点Non-frameshift deletion	－	－	2 511	0.035
非移码突变的插入位点Non-frameshift insertion	－	－	2 573	0.036
总计Total	50 276 079	100.000	7 240 540	100.000

家系(数量) Family	体高/cm Body height	体斜长/cm Body length	胸围/cm Chest circumference	管围/cm Shank circumference	臀高/cm Hip height	腰高/cm Waist height	尾长/cm Tail length	尾宽/cm Tail width
家系1(17) Family 1	70.59±6.53	66.79±5.27	94.53±10.15	8.47±0.80	69.03±5.20	60.09±5.18	48.97±0.56	35.09±4.99
家系2(31) Family 2	69.90±5.98	66.58± 5.18	93.02±10.10	8.32±0.64	70.00±5.23	59.79±4.84	49.33±9.22	35.08±5.51
家系3(36) Family 3	69.36±5.25	66.99±6.03	95.68±9.17	8.21±0.63	68.76±4.24	59.56±3.73	51.99±9.41	38.43±8.11
家系4(15) Family 4	70.70±4.86	67.07±4.50	94.10±8.23	7.90±0.71	70.67±4.40	60.07±5.82	45.48±10.80	33.70±6.88
家系5(28) Family 5	66.43±3.34	62.71±4.05	92.80 ±9.32	7.93±0.50	65.75±2.82	55.88±4.15	48.82±6.68	35.18±5.34
家系6(35) Family 6	66.80±4.39	63.39±4.38	92.53±8.74	8.13±0.62	66.13±3.48	56.86±4.10	48.17±7.64	35.74±5.72
A组(4) A group	72.63±1.44	69.00±4.24	108.13±5.01	8.38±0.63	73.75±1.89	60.38±2.14	52.63±7.32	33.38±3.64
B组(4) B group	72.75±0.65	70.75±2.63	103.50±4.88	8.13±0.25	70.25±0.96	56.13±2.72	49.63±5.02	36.00±4.24

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