基于全基因组重测序对赣州番鸭的群体进化分析

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

为了深入了解赣州番鸭的群体结构和遗传差异,本研究采集20只福建番鸭(FJ)、20只贵州天柱番鸭(TZ)、20只赣西北番鸭(GXB)和40只赣州番鸭(GZ)的血样用于全基因组重测序,测序深度为10×。随后,从NCBI数据库下载15只北京鸭(PK)、15只绿头鸭(MD)、10只樱桃谷鸭(CV)和2只法国番鸭(FF)4个品种的序列数据。使用上述8个群体的序列数据,进行了主成分分析、系统进化树构建、杂合度分析、群体分化分析、基因流分析、群体连锁不平衡分析。结果表明,主成分分析中,法国番鸭、天柱番鸭、赣西北番鸭按照第二和第三主成分无法完全区分开来,它们之间可能存在杂交现象。系统进化树分析中,赣州番鸭与其他品种鸭群体非常明显的聚集成不同的分支,其在遗传上表现出明显的独特性,与其他群体存在差异。杂合度分析中,除法国番鸭外,所有群体的观测杂合度均低于期望值,说明包括赣州番鸭在内的7个群体存在遗传多样性下降的现象。群体分化分析中,赣州番鸭与其他群体分化程度由高到低分别为北京鸭、樱桃谷鸭、绿头鸭、法国番鸭、福建番鸭、天柱番鸭、赣西北番鸭。基因流分析中,赣州番鸭与法国番鸭、天柱番鸭和福建番鸭之间不存在单独的基因迁移,与其他群体之间也没有过多的基因交流。群体遗传结构分析中,当K=3时,赣州番鸭作为一个独立的群体被识别出来,显示了其独特的遗传背景。连锁不平衡分析中,赣州番鸭表现出最低程度的连锁不平衡,表明其具有低近亲交配程度、更高的遗传多样性和更强的环境适应性。综上说明,赣州番鸭可区别于其他7个鸭群体,可作为一个独立的遗传资源群体。

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.