Insertion-Deletion Marker Targeting for Intron Polymorphisms

Abstract

Insertion-deletion (indel) polymorphisms are the second most frequent type of polymorphisms in genomes following single nucleotide polymorphisms (SNPs). As one of the types of indel markers to detect polymorphisms among individuals, we focus on markers targeting intron length polymorphisms (ILPs) in this chapter. Intron polymorphism (IP) markers including ILP markers are based on more abundant polymorphisms in intron regions compared to exon regions. Conserved genic sequences and structures including exon-intron junctions allow the development of IP markers for orphan crops without genomic information. Based on syntenic relationships among genomes of related species, IP markers can be developed in regions of interest based on the single-copy genes, such as for regions containing quantitative trait loci (QTL). Although introns are non-coding sequences in genes, they are suggested to have functions such as control of transcription. In some cases, ILPs are directly associated with trait variation as functional nucleotide polymorphisms (FNPs). This chapter reviews recent studies on the characteristics of IPs, especially ILPs, how to develop markers, and their application for the genetic analysis and molecular breeding of crops.