Whole-genome resequencing: changing the paradigms of SNP detection, molecular mapping and gene discovery

Next-generation sequencing (NGS) technologies open up a wealth of opportunities for plant breeding and genomic research and change the paradigms of DNA marker detection, genotyping, and gene discovery. Abundant genomic resources have been generated using a whole-genome resequencing (WGR) strategy and utilized in genome-wide association, genome diversity, and evolution studies in many crops with a reference genome such as rice and maize. The WGR-based quantitative trait loci mapping approach developed in soybean combines single nucleotide polymorphism (SNP) discovery, validation and genotyping and has the potential to identify candidate genes and causal SNPs without a time-consuming fine-mapping process. Given that this approach solves issues caused by genome duplications and repetitive sequences, it can be widely utilized in crops with a reference genome. The combination of WGR with bulked segregant analysis provides a rapid way to identify genes or causal mutations. Currently, DNA sequencing technologies are being improved rapidly. Third-generation sequencing platforms can overcome some inherent disadvantages of NGS and are expected to promote the application of WGR-based approaches and revolutionize plant breeding, genomic and genetic research.