Genome-Wide Identification of Insertion and Deletion Markers in Chinese Commercial Rice Cultivars, Based on Next-Generation Sequencing Data

Abstract

Rice, being a staple food crop for over one-third of the world’s population, has become a potential target for many dishonest traders and stakeholders for mixing with low-grade, low-cost grains/products and poorly nutritious adulterants to make a profit with the least effort. Single-nucleotide and insertion–deletion (InDel) polymorphisms have been widely used as DNA markers, not only in plant breeding but also to identify various traits in rice. Recently, next-generation sequencing (NGS) has produced sequences that allow for genome-wide detection of these molecular markers. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. PCR-based techniques are rapid and successful methods to deal with the problem of adulteration at a commercial level. Here, we report the genome-wide analysis of InDel markers of 17 commercially available Chinese cultivars. In order to achieve accurate results, all samples were sequenced at approximately 30× genome coverage using Illumina HiSeq 2500™ system. An average of 10.6 GB clean reads per sample was produced and ~96.3% of the reads could be mapped to the rice genome reference IRGSP 1.0. After a series of filtering, we selected five InDel markers for PCR validation. The results revealed that these InDel markers can be used for authentication of Korean elite cultivars from the adulterants.