Opportunity and Challenges for Whole‐Genome Resequencing‐based Genotyping in Plants

Genotyping techniques have been redesigned with the advent of next-generation sequencing technology, allowing for more effective genome mapping and analysis. Among NGS, whole-genome resequencing (WGR) is a powerful method to address evolutionary relationship that has not been completely resolved by traditional methods. WGR identifies a wide range of genetic variations through single nucleotide polymorphism. It further acts as a tool to identify the genetic basis of disease and phenotypic traits. Several megaprojects such as 1K Arabidopsis and 3K rice genome resequencing projects have been undertaken to determine the population-specific genetic variation. The recent advancement in whole-genome sequencing includes Pool-Seq which provides an alternative to individual sequencing and a cost-effective method for genome-wide association studies (GWAS). WGR has also been implemented in the identification of the target gene responsible for a particular agronomic trait with the help of QTL. Various online resources of WGR are available for SNP identification, haplotyping, and genetic variation analysis. In recent years, WGR has become a routine strategy to analyze insertion-deletion (InDels) and structural variation detection. Further, WGR showed a wide range of applications in identifying evolutionary relationships, genetic variation, haplotyping, GWAS, and conservation breeding.