Whole-genome resequencing provides insights into the population structure and domestication signatures of ducks in eastern China

Hua Yang,Lin Yang,Peishi Feng,Jinping Du,Ping Wang,Guohong Chen,Tao Zeng,Zhenrong Tao,Li Chen,Lizhi Lu,Junda Shen

doi:10.1186/s12864-021-07710-2

Abstract

BackgroundDuck is an ancient domesticated animal with high economic value, used for its meat, eggs, and feathers. However, the origin of indigenous Chinese ducks remains elusive. To address this question, we performed whole-genome resequencing to first explore the genetic relationship among variants of these domestic ducks with their potential wild ancestors in eastern China, as well as understand how the their genomes were shaped by different natural and artificial selective pressures.ResultsHere, we report the resequencing of 60 ducks from Chinese spot-billed ducks (Anas zonorhyncha), mallards (Anas platyrhnchos), Fenghua ducks, Shaoxing ducks, Shanma ducks and Cherry Valley Pekin ducks of eastern China (ten from each population) at an average effective sequencing depth of ~ 6× per individual. The results of population and demographic analysis revealed a deep phylogenetic split between wild (Chinese spot-billed ducks and mallards) and domestic ducks. By applying selective sweep analysis, we identified that several candidate genes, important pathways and GO categories associated with artificial selection were functionally related to cellular adhesion, type 2 diabetes, lipid metabolism, the cell cycle, liver cell proliferation, and muscle functioning in domestic ducks.ConclusionGenetic structure analysis showed a close genetic relationship of Chinese spot-billed ducks and mallards, which supported that Chinese spot-billed ducks contributed to the breeding of domestic ducks. During the long history of artificial selection, domestic ducks have developed a complex biological adaptation to captivity.

Highlights

Duck is an ancient domesticated animal with high economic value, used for its meat, eggs, and feathers
In conclusion, we performed whole-genome resequencing to characterize the evolutionary origin of ducks in eastern China and the genome-wide signatures of artificial selection associated with domestication
We have shown that Chinese spot-billed duck was close related to mallard and contributed to domestic duck origination

Summary

Introduction

Duck is an ancient domesticated animal with high economic value, used for its meat, eggs, and feathers. The origin of indigenous Chinese ducks remains elusive To address this question, we performed whole-genome resequencing to first explore the genetic relationship among variants of these domestic ducks with their potential wild ancestors in eastern China, as well as understand how the their genomes were shaped by different natural and artificial selective pressures. Domestication is the process of animal adaptation to captive environment and human interventions such as providing protection, offering food and promoting animal breeding [1] Compared to their wild ancestors, domestic animals have great variation in behavior, morphology and physiology in response to domestication, and this variation is the result of genetic changes across many generations. Through 50 years of systematic breeding, the egg production of Shaoxing ducks reached 300 at the age of 500 days [11] Shanma duck, another famous Chinese indigenous duck, has been domesticated for 400 years in Fujian Province [12]. After more than 100 years of intensive selection, Cherry Valley Pekin ducks are famous for their fast-growth, high lean rate and high feed conversion ratio [13]

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Results

Discussion

Conclusion