基于重测序数据评估南阳牛保种效果

doi:10.11843/j.issn.0366-6964.2024.09.013

摘要/Abstract

摘要：

旨在通过遗传多样性和群体结构分析，评估南阳牛的保种效果。本研究基于30头健康南阳牛的全基因组重测序数据，通过变异检测获得单核苷酸多态性(single nucleotide polymorphism, SNP)信息，综合分析群体遗传多样性、群体结构、亲缘关系以及连续纯和片段(ROH)分布特征，对南阳牛保种群的保种效果进行全面评估。结果显示：1)共检测到高质量SNPs位点数目是25 929 389个；2)保种群遗传多样性丰富，核苷酸多样性为0.002 9，多态性标记比例为0.888 7，最小等位基因频率为0.186 1，期望杂合度为0.274 9，观测杂合度为0.255 7；3)世代有效群体含量在1 000代前为2 834头，在20代前为149头，呈逐年下降趋势；4)主成分分析结果显示南阳牛保种群没有明显分层；5)个体间的遗传距离介于0.80~0.89，平均遗传距离为0.83±0.02；6)30头南阳牛个体共分为7个家系，公牛可分为5个家系；7)共检测到ROH片段数目是4 992个，平均每头南阳牛的ROH片段长度为约74.41 Mb，总长度为2.18 Gb，基于ROH的平均近交系数为0.031，0.5 Mb以下的ROH片段占比最多为75.72%，2~4 Mb的ROH片段占比最少为0.16%。综上所述，南阳牛保种群体遗传多样性丰富，没有出现明显分层，近交水平较低，但仍有个别个体近交较高。因此，未来的保种工作应加强选种和选配管理，以促进群体的可持续发展。

关键词: 南阳牛, 全基因组重测序, 遗传多样性, 群体结构, 保种

Abstract:

The study aimed to evaluate the conservation effect of Nanyang cattle by analyzing genetic diversity and population structure. In this study, based on the whole genome resequencing data of 30 healthy Nanyang cattle, single nucleotide polymorphism (SNP) information was obtained through mutation detection. The genetic diversity, population structure, phylogenetic relationship and runs of homozygosity (ROH) distribution characteristics were analyzed comprehensively to evaluate the conservation effect of Nanyang cattle. The results showed as follows: 1) The total number of high quality SNPs sites was 25 929 389; 2) The conservation population was rich in genetic diversity, nucleotide diversity was 0.002 9, polymorphism marker ratio was 0.888 7, minimum allele frequency was 0.186 1, expected heterozygosity was 0.274 9, observed heterozygosity was 0.255 7; 3) The effective population size was 2 834 before 1 000 generations and 149 before 20 generations, which showed a decreasing trend year by year; 4) The results of principal component analysis showed that there was no obvious stratification in Nanyang cattle conservation population; 5) The genetic distance between individuals ranged from 0.80 to 0.89, and the average genetic distance was 0.83±0.02; 6) The 30 Nanyang cattle were divided into 7 families, and the bulls were divided into 5 families; 7) A total of 4 992 ROH fragments were detected, the average length of ROH fragments per Nanyang cattle was about 74.41 Mb, the total length was 2.18 Gb, the average inbreeding coefficient based on ROH was 0.031, and the maximum proportion of ROH fragments below 0.5 Mb was 75.72%, the proportion of ROH fragments of 2-4 Mb was at least 0.16%. In summary, the genetic diversity of the Nanyang cattle conservation population is rich, there is no obvious stratification, the inbreeding level is low, but there are still some individuals with high inbreeding. Therefore, the future conservation work should strengthen the management of seed selection and mating, in order to promote the sustainable development of the population.

Key words: Nanyang cattle, whole genome resequencing, genetic diversity, population structure, breed conservation

中图分类号:

S823.2

刘思宇, 张曼, 张岩, 魏稚彤, 祁兴磊, 高腾云, 刘贤, 梁栋, 付彤. 基于重测序数据评估南阳牛保种效果[J]. 畜牧兽医学报, 2024, 55(9): 3876-3886.

Siyu LIU, Man ZHANG, Yan ZHANG, Zhitong WEI, Xinglei QI, Tengyun GAO, Xian LIU, Dong LIANG, Tong FU. Evaluation of the Conservation Effect in Nanyang Cattle Based on Resequencing Data[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(9): 3876-3886.

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参数 Parameter	SNPs数量 Number of SNPs	最小等位基因频率 (MAF) Minor allele frequency	多态性标记比例(P_N) Proportion of polymorphic marker	期望杂合度(He) Expected heterozygosity	观测杂合度(Ho) Observed heterozygosity	核苷酸多样性 (π) Nucleotide diversity
南阳牛 Nanyang cattle	25 929 389	0.186 1	0.888 7	0.274 9	0.255 7	0.002 9

家系 Family	性别 Sex	数量 Number	个体号 Individual number
家系A Family A	公	3	NY010M、NY022M、NY027M
家系B Family B	公	2	NY023M、NY026M
	母	5	NY004F、NY008F、NY012F、NY015F、NY030F
家系C Family C	母	6	NY005F、NY007F、NY009F、NY011F、NY014F、NY029F
家系D Family D	公	1	NY025M
	母	3	NY006F、NY013F、NY028F
家系E Family E	母	2	NY001F、NY003F
家系F Family F	公	2	NY018M、NY020M
家系G Family G	公	4	NY017M、NY019M、NY021M、NY024M
	母	2	NY002F、NY016F

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