BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, Guangdong 518120, China.
ShenZhen Engineering Laboratory for Genomics-Assisted Animal Breeding, BGI-Shenzhen, Shenzhen, Guangdong 518083, China.
G3 (Bethesda). 2021 Apr 15;11(4). doi: 10.1093/g3journal/jkab054.
Distinctive indigenous duck (Anas platyrhynchos) populations of Guangxi, China, evolved due to the geographical, cultural, and environmental variability of this region. To investigate the genetic diversity and population structure of the indigenous ducks of Guangxi, 78 individuals from eight populations were collected and sequenced by whole-genome resequencing with an average depth of ∼9.40×. The eight indigenous duck populations included four breeds and four resource populations. Moreover, the genome data of 47 individuals from two typical meat-type breeds and two native egg-type breeds were obtained from a public database. Calculation of heterozygosity, nucleotide diversity (π), Tajima's D, and FST indicated that the Guangxi populations were characterized by higher genetic diversity and lower differentiation than meat-type breeds. The highest diversity was observed in the Xilin-Ma ducks. Principal component, structure, and phylogenetic tree analyses revealed the relationship between the indigenous duck populations of Guangxi. A mild degree of differentiation was observed among the Guangxi populations, although three populations were closer to the meat or egg breeds. Indigenous populations are famous for their special flavor, small body size, and slow growth rates. Selective sweep analysis revealed the candidate genes and pathways associated with these growth traits. Our findings provide a valuable source of information regarding genetic diversity, population conservation, and genome-associated breeding of ducks.
中国广西具有独特特征的本地鸭（Anas platyrhynchos）种群是由于该地区的地理、文化和环境变化而进化而来的。为了研究广西本地鸭的遗传多样性和种群结构，我们从 8 个种群中采集了 78 个个体，并进行了全基因组重测序，平均深度约为 9.40×。这 8 个本地鸭种群包括 4 个品种和 4 个资源种群。此外，我们还从公共数据库中获得了来自 2 个典型肉用型品种和 2 个本地蛋用型品种的 47 个个体的基因组数据。杂合度、核苷酸多样性 (π)、Tajima's D 和 FST 的计算表明，广西种群的遗传多样性较高，分化程度较低，与肉用型品种相比。西林-麻鸭的多样性最高。主成分、结构和系统发育树分析揭示了广西本地鸭种群之间的关系。尽管有三个种群与肉用或蛋用品种更为接近，但广西种群之间存在轻度分化。本地种群以其特殊的风味、较小的体型和缓慢的生长速度而闻名。选择扫描分析揭示了与这些生长性状相关的候选基因和途径。我们的研究结果为鸭的遗传多样性、种群保护和基因组相关的选育提供了有价值的信息来源。
