Figure 2.

The impact of whole genome sequencing on breeding. (a) Initial genetic maps consisted of few and sparse markers, many of which were anonymous markers (simple sequence repeats (SSR)) or markers based on restriction fragment length polymorphisms (RFLP). For example, if a phenotype of interest was affected by genetic variation within the SSR1-SSR2 interval, the complete region would be selected with little information about its gene content or allelic variation. (b) Whole genome sequencing of a closely related species enabled projection of gene content onto the target genetic map. This allowed breeders to postulate the presence of specific genes on the basis of conserved gene order across species (synteny), although this varies between species and regions. (c) Complete genome sequence in the target species provides breeders with an unprecedented wealth of information that allows them to access and identify variation that is useful for crop improvement. In addition to providing immediate access to gene content, putative gene function and precise genomic positions, the whole genome sequence facilitates the identification of both natural and induced (by TILLING) variation in germplasm collections and copy number variation between varieties. Promoter sequences allow epigenetic states to be surveyed, and expression levels can be monitored in different tissues or environments and in specific genetic backgrounds using RNAseq or microarrays. Integration of these layers of information can create gene networks, from which epistasis and target pathways can be identified. Furthermore, re-sequencing of varieties identifies a high density of SNP markers across genomic intervals, which enable genome-wide association studies (GWAS), genomic selection (GS) and more defined marker-assisted selection (MAS) strategies.