Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

We initiated the OryzaSNP project (www.OryzaSNP.org) to discover genetic variation within 20 rice varieties and landraces. Most varieties belong to the 2 main groups, indica and japonica, including tropical and temperate japonica, whereas others represent the aus, deep water, and aromatic rice groups. Here, we describe the discovery of high-quality, nonredundant SNPs distributed across the entire genomes of the OryzaSNPset.

我们启动了水稻SNP（OryzaSNP）项目（官网：www.OryzaSNP.org），旨在发掘20个水稻品种及地方品种的遗传变异。本研究涉及的多数品种隶属于籼稻（indica）与粳稻（japonica）两大核心类群，涵盖热带粳稻与温带粳稻亚型；剩余品种则分别归属Aus稻、深水稻以及香稻类群。本文详述了OryzaSNP数据集（OryzaSNPset）全基因组范围内分布的高质量、非冗余单核苷酸多态性（Single Nucleotide Polymorphisms，SNPs）的发掘过程。