Application of Whole Genome Re-Sequencing for Accelerated Genetic Improvement of Crops: Examples from Rice

The recent advances in next-generation sequencing (NGS) technologies have provided rapid and cost effective methods that accelerated the completion of reference genome sequences for many crops as well as enabled high throughput genome re-sequencing.  As a result, genomics-based methods are now becoming routine at least in model species for various applications including, among others, genome-wide diversity analyses, genome-wide association studies (GWAS), and mapping and identification of genes and QTLs of agronomic importance in crops.  Taking advantage of the advances in NGS, we have recently developed different whole genome sequencing (WGS)-based methods namely MutMap (Abe et al. 2012, Nature Biotechnol. 30: 174), MutMap-Gap (Takagi et al. 2013, New Phytol. 200: 276), MutMap+ (Fekih, Takagi, Tamiru et al. 2013, PLOS One 8(7): e68529) and QTL-seq (Takagi et al. 2013, Plant J. 74: 174), which we have successfully applied for simultaneous mapping and identification of mutated genes and mapping of QTLs in rice.  Here, we present the applications of these methods in rice and other crops, including those for which reference genome sequences have not been published, as well as show their potential impact on plant breeding and crop improvement.