Sequence-Based Markers

Abstract

Marker-assisted selection (MAS) has revolutionized plant and animal breeding activities. MAS is based on DNA markers, which facilitate gene/QTL identification and mapping and gene/QTL transfer, and has many other applications. Some of the important issues concerning marker systems relate to their abundance, genome-wide distribution, cost and effort for marker development, ease of use, automated high-throughput genotyping, and cost per data point. Sequencing of the genome has facilitated the discovery of single nucleotide polymorphism (SNP) markers, which are abundant, almost evenly distributed throughout the genome, highly reproducible, and are amenable to ultra-high-throughput genotyping at relatively very low cost per data point. Next-generation sequencing (NGS) and third-generation sequencing (TGS) are of high throughput, simpler, cheaper, and much faster than the Sanger-Coulson sequencing. NGS and TGS technologies have allowed rapid sequencing of genomes and transcriptomes. NGS-based transcriptome sequencing (RNAseq) enables identification of thousands of SNPs located in the coding regions of the genomes. The development of SNP markers involves the discovery of SNPs, either through whole-genome/transcriptome sequencing, sequencing of the targeted genomic region, or in silico SNP mining, and validation of the discovered SNPs through various genotyping techniques. Genome sequencing also made it possible to discover and develop insertion and deletion (Indel) and epigenetic markers. This chapter describes the various DNA sequencing technologies, the strategies for discovery of SNP markers, and the low-to-medium-throughput approaches for SNP genotyping. The concept of polymorphic information content (PIC) of a marker system is explained in some details, and the selection of a marker system suitable for a given study is also discussed. The choice of the marker system for a study depends on the objectives of the project, financial resources, availability of the desired marker system in the target species, and reproducibility of the marker system.