Single nucleotide polymorphism genotyping and its application on mapping and marker-assisted plant breeding

Abstract

The nucleotide diversity across a genome is the source of most phenotypic variation. Such DNA polymorphism is the basis for the development of molecular markers, an indispensable tool in genetic
mapping studies. In general, the high resolution fine mapping of genes is often limited by lack of sufficient number of polymorphic molecular markers. This problem is compounded with traits controlled by multi-genes because in several such studies, QTL cannot be resolved to a workable resolution that could be feasible for predicting the candidate gene(s) associated with traits of interests. The availability of abundant, high-throughput sequence-based markers is the key for detailed genomewide trait analysis. Single-nucleotide polymorphisms (SNP) are the most common sequence variation and a significant amount of effort has been invested in re-sequencing alleles to discover SNPs. In fully sequenced small-genome model organisms, SNP discovery is relatively straight forward, although highthroughput
SNP discovery in natural populations remains both expensive and time-consuming. Here five central biochemical reaction principles that underlie SNP-genotyping methods specifically for large panel sizes and an intermediate number of SNPs are reviewed.