https://doi.org/10.1016/j.tplants.2018.11.008

Abstract

The swift development of next-generation sequencing (NGS) has accelerated quantitative trait locus (QTL) mapping and gene discovery in crops. High-throughput NGS-based genotyping platforms provide an extensive capacity to develop comprehensive polymorphism datasets including SNPs, InDels, structural variations, and genomic rearrangement. Whole-genome resequencing combined with bulk-segregant analysis offers a high density of informative SNPs, helping to detect QTLs without genotyping the entire mapping population. However, phenotyping of the entire population is still required. RNA-seq is useful to simultaneously genotype and phenotype segregating populations, releasing genomic information on mRNA and expression levels. Polymorphism databases generated by whole-genome sequencing using large-accession collections constitute new shared resources that facilitate QTL detection and gene discovery.