Abstract
Next-generation sequencing technologies have enabled the discovery of numerous sequence variations among closely related crop varieties. We analyzed genome resequencing data from 24 Korean temperate japonica rice varieties and discovered 954,233 sequence variations, including 791,121 single nucleotide polymorphisms (SNPs) and 163,112 insertions/deletions (InDels). On average, there was one variant per 391 base-pairs (bp), a variant density of 2.6 per 1 kbp. Of the InDels, 10,860 were longer than 20 bp, which enabled conversion to markers resolvable on an agarose gel. The effect of each variant on gene function was predicted using the SnpEff program. The variants were categorized into four groups according to their impact: high, moderate, low, and modifier. These groups contained 3524 (0.4%), 27,656 (2.9%), 24,875 (2.6%), and 898,178 (94.1%) variants, respectively. To test the accuracy of these data, eight InDels from a pre-harvest sprouting resistance QTL (qPHS11) target region, four highly polymorphic InDels, and four functional sequence variations in known agronomically important genes were selected and successfully developed into markers. These results will be useful to develop markers for marker-assisted selection, to select candidate genes in map-based cloning, and to produce efficient high-throughput genome-wide genotyping systems for Korean temperate japonica rice varieties.
Highlights
Rice is the world’s second most important cereal crop, following only maize (Zea mays)
We identified 954,233 sequence variants, including 791,121 single nucleotide polymorphisms (SNPs) and 163,112 InDels, between the 24 Korean japonica rice varieties
We identified 10,860 InDels longer than 20 bp; their full details are provided in Supplementary Table S4
Summary
Rice is the world’s second most important cereal crop, following only maize (Zea mays). Rice (Oryza sativa) can be classified into two main subgroups: indica and japonica. The genetic diversity of japonica varieties is lower than that of indica varieties [1]. Korean japonica rice varieties belong to the temperate japonica group and have a low level of genetic diversity. They exhibit low levels of polymorphism with traditional molecular markers, including restriction fragment length polymorphisms (RFLPs) and simple sequence repeats (SSRs), and this has hindered gene mapping and marker-assisted selection. Show wide phenotypic variation in many important traits, including flowering time, plant architecture, disease and pest resistance, seed size, grain quality, pre-harvest sprouting resistance, and resistance to abiotic stress. Mapping and identification of the genes responsible for this variation and the development of selective markers are required to facilitate molecular breeding
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