Sequence based DNA markers and genotyping for cereal genomics and breeding

The last three decades has seen the rapid evolution of a variety of DNA-based molecular markers that are powerful tools for genome analysis and marker-trait association (MTA) studies. Recently, high-throughput sequence-based methods have been developed for use in plant breeding. Sequence-based markers include simple sequence repeats (SSRs; also known as microsatellites) and single nucleotide polymorphisms (SNPs), which now dominate applications in modern genetic analysis. Insertion site-based polymorphisms (ISBPs), copy number variations (CNVs) and presence and absence variations (PAVs) constitute another group of markers that are being applied in a variety of plant systems. Markers may be used for a variety of purposes including diversity analysis, linkage-based QTL mapping, LD-based association mapping and marker assisted selection (MAS). Large sequence datasets (including both, genomic sequences and expressed sequences) are available for many cereals, enabling the mining for large numbers of SSRs, SNPs, ISBPs and CNVs/PAVs. Recombination bins are being used as markers for genotyping mapping populations and QTL analysis in crops such as rice, where reference genome sequences are available. In this chapter we describe the discovery and application of molecular markers using automated sequencing platforms including those based on next generation sequencing (NGS).