基于全基因组重测序对赣州番鸭的群体进化分析

doi:10.11843/j.issn.0366-6964.2024.11.018

Abstract

Abstract:

The study aimed to understand the population structure and genetic differences of Ganzhou Muscovy duck. The blood samples of 20 Fujian Muscovy ducks (FJ), 20 Guizhou Tianzhu Muscovy ducks (TZ), 20 Northwest Jiangxi Muscovy ducks (GXB) and 40 Ganzhou Muscovy ducks (GZ) were collected for whole genome resequencing with a depth of 10×. Subsequently, sequence data of 15 Peking ducks (PK), 15 Mallard ducks (MD), 10 Cherry Valley ducks (CV) and 2 French Muscovy ducks (FF) were downloaded from the NCBI database. Principal component analysis, phylogenetic tree construction, heterozygosity analysis, population differentiation analysis, gene flow analysis and population linkage disequilibrium analysis were carried out using the sequence data of the above 8 populations. The results showed that the French Muscovy duck, Tianzhu Muscovy duck and Northwest Jiangxi Muscovy duck could not be completely distinguished according to the second and third principal components in the principal component analysis, and there might be hybridization among them. In phylogenetic tree analysis, the populations of Ganzhou Muscovy duck and other breeds of ducks were obviously clustered into different branches, which showed obvious genetic uniqueness and were different from other populations. In the analysis of heterozygosity, the observed heterozygosity of all populations except French Muscovy duck was lower than expected heterozygosity, indicating that the genetic diversity of 7 populations including Ganzhou Muscovy duck was decreased. According to the analysis of population differentiation, the degree of differentiation between Ganzhou Muscovy duck and other populations, from high to low, was as follows: Beijing duck, Cherry Valley duck, Mallard duck, French Muscovy duck, Fujian Muscovy duck, Tianzhu Muscovy duck, and Northwest Jiangxi Muscovy duck. In gene flow analysis, there was no single gene transfer between Ganzhou Muscovy duck and French Muscovy duck, Tianzhu Muscovy duck, and Fujian Muscovy duck, and there was also not much gene exchange with other populations. In the analysis of population genetic structure, when K=3, Ganzhou Muscovy duck was identified as an independent population, showing its unique genetic background. In the analysis of linkage disequilibrium, Ganzhou Muscovy duck showed the lowest degree of linkage disequilibrium, indicating that it had low inbreeding degree, higher genetic diversity and stronger environmental adaptability. In conclusion, the Ganzhou Muscovy duck is distinct from the other 7 duck populations and can be regarded as an independent genetic resource.

Key words: whole genome resequencing, Ganzhou Muscovy duck, population structure

CLC Number:

S834.2

Zhenni LIU, Jianjun LI, Hai LIAN, Xiaowen LEI, Donghai TAN, Qingyuan ZENG, Di CHENG, Yuling TIAN, Zhiwei KONG, Hualiang XIE, Yunping ZHONG. Population Evolution Analysis of Ganzhou Muscovy Duck Based on Whole Genome Resequencing[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(11): 4992-5002.

Figures/Tables 8

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群体Group	观测杂合度Observed heterozygosity	期望杂合度Eexpected heterozygosity
赣州番鸭GZ	0.057 1	0.062 6
天柱番鸭TZ	0.048 3	0.062 1
赣西北番鸭GXB	0.051 0	0.062 5
福建番鸭FJ	0.051 9	0.061 0
樱桃谷鸭CV	0.057 2	0.070 3
绿头鸭MD	0.078 6	0.085 9
北京鸭PK	0.063 1	0.072 6
法国番鸭FF	0.062 6	0.052 7

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Population Evolution Analysis of Ganzhou Muscovy Duck Based on Whole Genome Resequencing

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