College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan, 655011, China.
Key Laboratory of Yunnan Province Universities of the Diversity and Ecological Adaptive Evolution for Animals and Plants on YunGui Plateau, Qujing Normal University, Qujing, Yunnan, 655011, China.
Sci Rep. 2017 Oct 27;7(1):14183. doi: 10.1038/s41598-017-14738-6.
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.
云南石蒜是一种具有较高产量潜力的重要蔬菜作物。本研究利用 RAD-seq 技术，对中国西南部的 16 个野生和 20 个栽培云南石蒜个体进行了总计 166GB 的基因组测序。我们比较了野生和栽培群体之间的全基因组变异。基于特有等位基因数、期望杂合度、观测杂合度和核苷酸多样性，野生群体的遗传多样性高于栽培群体。STRUCTURE 分析、主成分分析（PCA）和最大似然（ML）树表明，云南石蒜群体可分为三个组（一个栽培组和两个野生组），存在显著的遗传分化。栽培群体中发现的低遗传多样性和浅遗传分化可能是由于连续选择和驯化过程中的克隆繁殖方法所致。野生群体之间的显著分化可能表明由于种群小和人为干扰导致的强烈遗传漂变。本研究中鉴定的全基因组单核苷酸多态性（SNP）将为进一步的育种改良和种质资源的有效利用提供宝贵资源。
