Genetic diversity and structure of wild and cultivated Amorphophallus paeoniifolius populations in southwestern China as revealed by RAD-seq

Yong Gao,Haibo Wang,Dongqin Dai,Lifang Wu,Chao Liu,Lizhou Tang,Si Yin

doi:10.1038/s41598-017-14738-6

Abstract

Amorphophallus paeoniifolius, is a commercially important vegetable crop because of its high production potential. In this study, we generated a total of 166 Gb of genomic data from 16 wild and 20 cultivated A. paeoniifolius individuals in southwestern China using restriction site associated DNA sequencing (RAD-seq). We compared the genome-wide variations between the wild and cultivated populations. Wild populations exhibited higher genetic diversity than did cultivated populations based on private allele number, expected heterozygosity, observed heterozygosity and nucleotide diversity. STRUCTURE analysis, principal component analysis (PCA) and a maximum likelihood (ML) tree indicated that A. paeoniifolius populations could be divided into three groups (a cultivated group and two wild groups) with significant genetic differentiation. The low genetic diversity and shallow genetic differentiation found within cultivated populations are likely caused by continuous selection and the clonal propagation methods used during domestication. The significant differentiation between the wild populations may suggest strong genetic drift due to small populations and human disturbance. The genome-wide single nucleotide polymorphisms (SNPs) identified in our study will provide a valuable resource for further breeding improvement and effective use of the germplasm.

Highlights

Crop domestication modifies the economic and agronomic traits and leaves a genetic signature that affects both the genetic diversity and population structure of domesticated plants[1,2]
Conservation measures must be taken to prevent the further decline of A. paeoniifolius resources, and information about genetic diversity and population structure is essential for formulating management and conservation approaches
To access the genetic diversity of A. paeoniifolius at the germplasm level, the 36 samples were divided into two groups

Summary

Introduction

Crop domestication modifies the economic and agronomic traits and leaves a genetic signature that affects both the genetic diversity and population structure of domesticated plants[1,2]. Genetic information before domestication and artificial selection might have been reserved in wild populations, which are particular resources for studying the influence of human selection on genetic variation in the A. paeoniifolius genome. Developing genomic resources, increasing understanding of the A. paeoniifolius gene pool (including wild germplasms), and gaining information about genetic diversity and population structure should speed the progress of biological research and genetic improvement. To contribute to the understanding of A. paeoniifolius domestication and accelerate its agricultural application, we generated and analysed genome-wild SNPs for the wild and cultivated populations of A. paeoniifolius (2n = 2x = 28) in southwestern China by RAD-seq to provide a better understanding of the genetic diversity, genetic structure and divergence of this species. Our study will enhance the future genetic improvement of this important crop

Methods

Results

Conclusion