全基因组重测序解析秦川牛保种群遗传多样性和遗传结构

doi:10.16288/j.yczz.23-115

遗传 ›› 2023, Vol. 45 ›› Issue (7): 602-616.doi: 10.16288/j.yczz.23-115

全基因组重测序解析秦川牛保种群遗传多样性和遗传结构

马钧¹(), 樊安平², 王武生², 张金川², 江晓军², 马瑞军², 贾社强², 刘飞², 雷初朝¹, 黄永震¹()

1.西北农林科技大学动物科技学院，杨凌 712100
2.陕西省农牧良种场，宝鸡 722203

收稿日期:2023-04-25 修回日期:2023-06-11 出版日期:2023-07-20 发布日期:2023-06-30
通讯作者: 黄永震 E-mail:Junma96@163.com;hyzsci@nwafu.edu.cn
作者简介:马钧，在读博士研究生，专业方向：动物遗传育种与繁殖。E-mail: Junma96@163.com
基金资助:
陕西省重点研发计划项目(2023-YBNY-141);财政部与农业农村部-国家现代农业产业技术体系(CARS-37)

Analysis of genetic diversity and genetic structure of Qinchuan cattle conservation population using whole-genome resequencing

Jun Ma¹(), Anping Fan², Wusheng Wang², Jinchuan Zhang², Xiaojun Jiang², Ruijun Ma², Sheqiang Jia², Fei Liu², Chuchao Lei¹, Yongzhen Huang¹()

1. College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
2. Shaanxi Provincial Livestock Breeding Farm, Baoji 722203, China

Received:2023-04-25 Revised:2023-06-11 Online:2023-07-20 Published:2023-06-30
Contact: Yongzhen Huang E-mail:Junma96@163.com;hyzsci@nwafu.edu.cn
Supported by:
Supported by the Key R&D project of Shaanxi Province(2023-YBNY-141);Ministry of Finance and Ministry of Agriculture and Rural Affairs-National Modern Agricultural Industry Technology System(CARS-37)

摘要/Abstract

摘要：

在畜禽资源保护中，群体遗传多样性和遗传结构是决定保种效果的重要因素。本研究采用全基因组重测序技术检测100头秦川牛(30头公牛、70头母牛)的基因组变异，通过分析群体遗传多样性、连续纯合片段(runs of homozygosity，ROH)分布特征、亲缘关系和家系结构，对秦川牛的保种效果进行了综合评估。结果显示，100头秦川牛共检测到20,968,017个高质量SNPs位点，平均最小等位基因频率为0.191±0.124，平均多态信息含量为0.279±0.131，平均观察杂合度为0.275±0.131，平均期望杂合度为0.279±0.131，表明秦川保种群遗传多样性较为丰富。秦川牛保种群体平均状态同源(identity by state，IBS)遗传距离为0.243±0.020，其中公牛为0.242±0.021，亲缘关系G矩阵结果与IBS距离矩阵结果一致，均显示秦川牛保种群部分个体间亲缘关系较近。100头秦川牛个体共检测到8258个基因组ROH，ROH总长度为9.64 GB，平均ROH长度为1.167±1.203 Mb，69.35%的ROH是长度为0.5~1 Mb的短ROH。个体平均ROH总长度为96.40 Mb。基于ROH的平均近交系数为0.039±0.039，其中30头秦川公牛的平均近交系数为0.044±0.035，表明部分公牛个体存在一定程度的近交积累。进化树结果显示，秦川牛保种群所测个体可分为8个家系，包括7个含公牛家系和1个不含公牛家系。本研究表明，秦川牛保种群的遗传多样性较为丰富，未出现较大程度近交积累，但部分个体间存在近交风险，应强化选配以确保秦川牛资源的可持续发展。

关键词: 秦川牛, 全基因组重测序, 遗传多样性, 遗传结构

Abstract:

In the conservation of livestock and poultry resources, population genetic diversity and genetic structure of the conservation population are important factors affecting the effectiveness of conservation. In this study, whole-genome resequencing technology was used to detect genomic variation in 100 Qinchuan cattle (30 bulls and 70 cows). By analyzing population genetic diversity, runs of homozygosity (ROH) distribution features, kinship relationships, and family structure, the conservation effectiveness of Qinchuan cattle was comprehensively evaluated. The results showed that a total of 20,968,017 high-quality SNPs were detected in 100 Qinchuan cattle, the average minimum allele frequency was 0.191±0.124, the average polymorphic information content was 0.279±0.131, and the average observed heterozygosity was 0.275±0.131, the average expected heterozygosity is 0.279±0.131, indicating that the genetic diversity of the Qinchuan cattle conservation population is relatively rich. The average identity by state (IBS) distance of the Qinchuan conservation population was 0.243±0.020, with a value of 0.242±0.021 for the bulls. The results of the kinship G-matrix were consistent with the results of the IBS distance matrix, both showing that some individuals in the conservation population had close kinship. A total of 8258 genomic ROH were detected in 100 Qinchuan cattle, with a total length of 9.64 GB. The average length of ROH fragments was 1.167±1.203 Mb, 69.35% of the ROH were short ROH with a length of 0.5~1 Mb, and the average total length of ROH per individual was 96.40 Mb. The average inbreeding coefficient based on ROH was 0.039±0.039, with a value of 0.044±0.035 for the bulls, indicating that some bulls had a certain degree of inbreeding accumulation. The results of the phylogenetic tree combined with kinship analysis showed that the individuals in the Qinchuan cattle conservation population could be divided into eight families, including seven families with bulls and one family without bulls. This study demonstrated that the genetic diversity of the Qinchuan conservation population is relatively rich, with no significant inbreeding accumulation, but there is a risk of inbreeding among some individuals. Therefore, it is necessary to strengthen selection and mating to ensure the sustainable development of Qinchuan cattle resources.

Key words: Qinchuan cattle, whole-genome resequencing, genetic diversity, genetic structure

马钧, 樊安平, 王武生, 张金川, 江晓军, 马瑞军, 贾社强, 刘飞, 雷初朝, 黄永震. 全基因组重测序解析秦川牛保种群遗传多样性和遗传结构[J]. 遗传, 2023, 45(7): 602-616.

Jun Ma, Anping Fan, Wusheng Wang, Jinchuan Zhang, Xiaojun Jiang, Ruijun Ma, Sheqiang Jia, Fei Liu, Chuchao Lei, Yongzhen Huang. Analysis of genetic diversity and genetic structure of Qinchuan cattle conservation population using whole-genome resequencing[J]. Hereditas(Beijing), 2023, 45(7): 602-616.

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性别	样本量	个体号
公	30	1192M、1257M、1262M、1263M、1271M、1273M、1278M、1282M、1291M、1292M、1293M、1294M、1295M、1297M、1299M、1300M、1301M、1303M、1304M、1308M、1309M、1315M、 1318M、1320M、1321M、1324M、1325M、1327M、1328M、1329M
母	70	1052F、1087F、1097F、1109F、1111F、1117F、1124F、1144F、1150F、1154F、1158F、1177F、1185F、1197F、1210F、1214F、1216F、1222F、1223F、1231F、1233F、1236F、1237F、1238F、 1239F、1240F、1244F、1245F、1250F、1253F、1260F、1265F、1271F、1273F、1277F、1284F、1286F、1287F、1290F、1292F、1294F、1300F、1301F、1302F、1303F、1305F、1310F、1313F、1316F、1321F、1324F、1331F、1337F、1341F、1350F、1351F、1353F、1360F、1364F、1366F、1369F、1372F、1374F、1379F、1384F、1385F、1397F、1409F、1416F、1424F

遗传多样性指标	平均值
最小等位基因频率(MAF)	0.191±0.124
多态信息含量(PIC)	0.279±0.131
观察杂合度(Ho)	0.275±0.131
期望杂合度(He)	0.279±0.131

家系名称	性别	数量	个体号
家系A	公	10	1282M、1291M、1292M、1293M、1295M、1297M、1299M、1300M、1304M、1309M
家系A	母	10	1144F、1185F、1337F、1341F、1350F、1353F、1360F、1372F、1384F、1385F
家系B	公	7	1262M、1263M、1273M、1308M、1315M、1320M、1321M
家系B	母	17	1087F、1109F、1144F、1177F、1216F、1231F、1233F、1273F、1284F、1287F、1292F、1294F、1300F、1301F、1305F、1369F、1379F
家系C	公	2	1257M、1324M
家系C	母	8	1144F、1197F、1210F、1238F、1303F、1310F、1331F、1364F
家系D	公	3	1329M、1271M、1278M
家系D	母	14	1109F、1111F、1117F、1158F、1222F、1239F、1240F、1250F、1313F、1316F、1351F、1366F、1397F、1409F
家系E	公	3	1318M、1325M、1329M
家系E	母	5	1154F、1158F、1245F、1409F、1424F
家系F	公	2	1327M、1328M
家系F	母	3	1124F、1144F、1150F
家系G	公	4	1192M、1294M、1301M、1303M
家系G	母	8	1052F、1097F、1185F、1214F、1260F、1277F、1290F、1416F
家系H	公	0
家系H	母	12	1223F、1236F、1237F、1244F、1253F、1265F、1271F、1286F、1302F、1321F、1324F、1374F

全基因组重测序解析秦川牛保种群遗传多样性和遗传结构

Analysis of genetic diversity and genetic structure of Qinchuan cattle conservation population using whole-genome resequencing

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