Submitted to: Molecular Breeding
Publication Type: Review Article
Publication Acceptance Date: 9/12/2014
Publication Date: 1/21/2015
Citation: Xu, X., Bai, G. 2015. Whole-genome resequencing: changing the paradigms of SNP detection, molecular mapping and gene discovery. Molecular Breeding. 35(1):33.
Interpretive Summary: The traditional gene mapping is a time-consuming, expensive, laborious, and reiterative process, in which we identify the general location of a gene first, and subsequently narrow down the genomic region harboring the gene by genotyping a larger population with more molecular markers. Due to advances in next generation sequencing technologies, QTL mapping approaches based on whole genome resequencing (WGR) were developed in rice and soybean. The WGR-based gene mapping method developed in soybean not only combines marker discovery, marker validation and genotyping, but also solves issues caused by a complex genome. Thus this approach can be widely utilized in crops with a sequenced genome. The WGR has also been widely utilized to identify sequence variations in many crops. Genome-wide association studies based on sequence data have the potential to rapidly identify genes of interest. In addition, WGR has revolutionized traditional approaches such as bulked segregant analysis (BSA) and targeting induced local lesions in genomes (TILLING). The combination of WGR with BSA and TILLING make it feasible to identify genes or causal mutations rapidly. In light of advances in sequencing technologies, WGR approach may play a more pivotal role in QTL mapping and gene discovery, and subsequently accelerate crop breeding.
Technical Abstract: The next generation sequencing (NGS) technologies have opened a wealth of opportunities for plant breeding and genomics research, and changed the paradigms of 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 (GWA), genome diversity and evolution studies in crops with a reference genome such as rice and maize. The WGR-based QTL mapping approach developed in soybean combines SNP discovery, SNP 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. Traditional approaches such as bulked segregant analysis (BSA) and targeting induced local lesions in genomes (TILLING) are also revolutionized by WGR. The combination of WGR with BSA and TILLING provides rapid ways to identify genes or causal mutations. Currently, DNA sequencing technologies are being improved rapidly. The third generation sequencing (TGS) platforms can overcome some inherent disadvantages of NGS and are expected to promote the applications of the WGR-based approaches and revolutionize plant breeding, genomics and genetics research.