Benefits of Whole-Genome Profiling

Initially, molecular markers were used in a linear, reductionist manner as a replacement for physical trait evaluation. This approach is based on a simplified concept of marker/trait associations. There are indeed cases, such as "simply"-inherited disease resistance, where such an approach works well.

Yet most of the traits that breeders are selecting for do not conform to this simple model because they are determined by multiple genetic factors. In addition, most breeders are confronted with multiple breeding targets, including yield, quality traits, disease resistance, tolerance to abiotic stresses, etc. Assuming that a breeder has to deal with a dozen characters, most of them with complex inheritance, there may be several dozens, if not hundreds of genes with significant influence on the final performance of a cultivar.

A growing body of evidence shows the complexity of interactions among genes and gene variants (alleles) within breeding populations. The contribution of specific genes, or chromosomal regions delineated by markers (QTL), usually needs to be established in several genetic backgrounds before marker-trait associations can be productively exploited by breeders.

Whole-genome profiling, when fast and cheap, can rapidly determine the associations in genetic backgrounds relevant to breeding programs. In addition, careful genome profiling of a program's breeding materials can reveal the contribution of a gene (allele) or a QTL in the breeding populations without making a cross ("mapping as you go"). In the long run, genomic profiles will undoubtedly reduce the number of crosses that breeders need to make and increase the likelihood that a particular cross will result in a new cultivar.