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

Abstract

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

CLC Number:

S823.2

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.

Figures/Tables 11

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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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Evaluation of the Conservation Effect in Nanyang Cattle Based on Resequencing Data

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