Next generation characterisation of cereal genomes for marker discovery

Abstract

Cereal crops form the bulk of the world's food sources, and thus their importance cannot be understated. Crop breeding programs increasingly rely on high-resolution molecular genetic markers to accelerate the breeding process. The development of these markers is hampered by the complexity of some of the major cereal crop genomes, as well as the time and cost required. In this review, we address current and future methods available for the characterisation of cereal genomes, with an emphasis on faster and more cost effective approaches for genome sequencing and the development of markers for trait association and marker assisted selection (MAS) in crop breeding programs.

Figure 1

A schematic representation of cereal crop improvement using Next Generation Sequencing (NGS) technologies. Blue denotes main steps in the characterization of cereal genomes, brown denotes reference specific approaches while green represents applications to several cultivars or populations for variation discovery. (1) Sequencing approaches are determined by the project aims. For characterization of previously un-sequenced genomes without a closely related species, generation of a reference genome is undertaken. This may involve direct whole genome shotgun (WGS), chromosome (arm) isolation or BAC-by-BAC approaches or a combination of these. For GWAS, where a suitable reference genome is available, a large number of cultivars or populations are sequenced at low coverage. (2) Assembly strategies depend on the nature of the genome to be assembled, reads available (length, read types i.e., paired end (PE) or mate pair (MP)), coverage depth, and whether there is a high quality draft genome of a closely related species of which if absent, de-novo assembly is undertaken. (3) Characterization then follows which involves gene prediction based on orthologous genes in related species or ab-initio. (4) Variation discovery through SNPs discovery and GBS within cultivars or populations enables trait associations and the generation of molecular markers for applications in crop breeding programs.