Prospects and Limitations for Development and Application of Functional Markers in Plants

The discovery of sequence variants and their functionality has been increasing with new genotyping technologies and mapping studies across plant species. Sequence polymorphisms associated with trait variation can be converted into Functional Markers (FMs), which are derived from polymorphic sites within genes or regulatory sequences causally affecting phenotypic trait variation. The effects of FMs on the phenotypic variation of complex inherited traits, however, are usually dependent on epistatic and environment interactions. In this review, we propose the term “potential” to define effects of FMs. The potential of a FM is based on distribution of allelic effects across environments and backgrounds, and the probability of achieving a phenotype of interest. The use of FM in plant breeding programs and how FMs may be combined with Genomic Selection to increase genetic gain are also discussed.