Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations

Fan Jiang,Changyi Xiao,Xiaoyong Du,Jianhai Chen,Yaoxin Jiang,Pan Ni,Jianlin Han,Wing-Kin Sung,Ruiyi Lin,Tanghui Xie,Shijun Li

doi:10.1186/s12711-021-00627-0

Abstract

BackgroundThe most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations.ResultsBased on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100–11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8, THAP5, and DNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R).ConclusionsOur findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.

Highlights

The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations
We obtained a set of 3,902,414 high-quality Single nucleotide polymorphisms (SNPs), which were used to construct genetic relationships using a neighbor-joining maximum likelihood method and principal component analysis (PCA)
Both methods revealed that these populations from different geographic regions clustered into three major genetic groups, i.e. local Chinese populations, wild populations, and Southeast/South Asian populations (Fig. 1b, c)

Summary

Introduction

The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations. Thanks to their high reproductive capacity, the duck (Anas platyrhynchos) industry achieves great economic benefits from meat, eggs, and feathers [1]. Based on whole-genome data and using diffusion approximation to the allele frequency spectrum [6], divergence between the Chinese domesticated ducks and the wild ducks has been estimated to have occurred ~ 2200 generations ago. Using demographic modeling [15], Zhang et al [6] found relatively high gene flow estimates between Chinese wild and domestic ducks, i.e. 1.12 and 3.92 migrants per generation from the meat and egg/dualpurpose breeds, respectively, into the wild duck

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