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

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

• Research Article • Previous Articles Next Articles

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)

Abstract

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

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.

Figures/Tables 10

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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

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

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