The Use of SNP Genotyping for QTL/ Candidate Gene Discovery in Plants

Abstract

Many plant species have been sequenced, which has enabled the identification of genetic variation such as novel single-nucleotide polymorphisms (SNPs). SNP-based genotyping technologies have been developed over the last decade and play important roles in detecting SNPs in a cost and time effective manner, thereby facilitating plant genetic and genomic studies. The availability of genome and genetics resources and increase in sequencing data has led to SNPs discovery and array development using various approaches in many plant species. The development of SNP arrays for genotyping requires three steps: identification of a large number of SNPs, validation, and final selection. The discovery of SNPs and array development at various densities have been successfully developed and utilized in many diploid and polyploid plant species. SNP genotyping arrays have been useful for many applications such as cloning, association mapping, analyses of species diversity, evolution, genomic selection, and comparative genomics. The assaying of large segregating or mutant populations with an SNP array allows the accurate, efficient, and rapid determination of the genotypes of many individuals and genetic variations. Genotyping assays are an efficient way of generating a vast amount of genotypic data in crop species to produce highly informative SNPs for marker-assisted selection in breeding programs as well as functional genomic studies. This review highlights the SNP genotyping in the application of identification of SNPs in the discovery of quantitative trait locus (QTL) or candidate genes for important crop traits and dissection of other complex traits.