The contribution of genomic approaches to resolving genotype x environment interactions in Brassica crops

Geneticists and breeders have conventionally relied on multi-site experiments and structured populations to partition phenotypic variation into component traits, where variation can then be assigned to genotype and environment, with recent efforts focused on resolution of quantitative trait loci (QTL) and identification of underlying genes. For Brassica genomes, which are relatively large and complex, this process requires access to interconnected sets of platform experimental resources, including ongoing determination of the complete chromosomal DNA sequences. The B. rapa genome sequence has recently been used to provide valuable information for a number of studies. In coming years, the ability to navigate between the various genome sequences and trait genetics will contribute to understanding Genotype x Environment (GxE) interactions at the molecular level and benefit pre-breeding activities. Exploitation of the genome sequence for trait resolution is benefiting from recent integration of genetic maps for Brassica napus, as well as development of advanced recombinant and diversity populations. There is particular value in the combined screening of diversity collections and QTL analysis which can demonstrate the extent of variation and genetic basis for traits as diverse as oil composition and mineral nutrition. The availability of genome sequences provide the opportunity to understand GxE interactions at the molecular level, using genetical genomic techniques such as expression QTL (eQTL) analysis. Although the role that epigenetic regulation plays in GxE interactions is currently poorly understood, we are now starting to determine the distribution of heritable epigenetic marks superimposed on Brassica genomes, and to explore the scope for epigenetic intervention as contribution to crop improvement. The need for integrated data management that allows navigation from trait to underlying genes is discussed.