Molecular markers are efficient and essential genotyping tools for molecular breeding and genetic analysis of rice. We developed two 96-plex indica–japonica single nucleotide polymorphism (SNP) genotyping sets for genetic analysis and molecular breeding in rice using the Fluidigm platform. Informative SNPs between indica and japonica were selected from SNP data of the Rice Diversity database, HapRice world SNP data of the Q-TARO database, and our 40 rice cultivar resequencing dataset. SNPs in set 1 were evenly distributed across all 12 rice chromosomes at a spacing of 4–5 Mb between adjacent SNPs. SNPs in set 2 mapped to the long genetic intervals in set 1 and included 14 functional or linked SNPs in genes previously cloned and associated with agronomic traits. Additionally, we used the SNP sets developed in this study to perform genetic diversity analysis of various cultivated and wild rice accessions, construction and validation of a subspecies diagnostic subset, linkage map construction and quantitative trait locus (QTL) analysis of a japonica × indica F₂ population, and background profiling during marker-assisted backcrossing. Furthermore, we identified subspecies-specific SNPs and discuss their distribution and association with agronomic traits and subspecies differentiation. Our results indicate that these subspecies-specific SNPs were present in wild rice prior to domestication. This genotyping system will serve as an efficient and quick tool for genetic analysis and molecular breeding in rice.

分子标记是水稻分子育种和遗传分析的有效和必不可少的基因分型工具。我们开发了两个96重籼稻-粳稻单核苷酸多态性（SNP）基因分型集使用Fluidigm的平台，在水稻遗传分析和分子育种。d和粳稻之间的信息性SNP选自水稻多样性数据库的SNP数据，Q-TARO数据库的HapRice world SNP数据以及我们的40个水稻品种重测序数据集。第1组中的SNP在所有12个水稻染色体上均匀分布，相邻SNP之间的间隔为4-5 Mb。第2组中的SNP映射到第1组中较长的遗传间隔，并且在先前克隆并与农艺性状相关的基因中包含14个功能性或连锁SNP。此外，我们使用在本研究中开发的SNP集合以执行一个亚种诊断子集，图谱构建和数量性状基因座（QTL）的分析的各种栽培和野生稻种质，建筑和验证的遗传多样性分析粳稻×籼稻˚F ₂标记和辅助标记回交过程中的背景特征分析。此外，我们确定了亚种特异性SNP，并讨论了它们的分布以及与农艺性状和亚种分化的关系。我们的结果表明，这些亚种特异性SNP在驯化之前存在于野生稻中。该基因分型系统将成为水稻遗传分析和分子育种的高效，快捷工具。