Insights into Doubled Haploid Breeding Programs from a Genome-Wide Transcriptome and Methylome Analysis of Brassica oleracea. Doubled Haploids Brassica oleracea

With global food insecurity on the rise and increased pressures on habitat conser- vation it is vital to pursue increased efficiencies in plant breeding. New understanding of genetics in the last five decades has provided significant advances in yield gains in most cultivated crops. However, new advances in genomics have opened the door to better design breeding programs; the major strategy to develop new cultivars, in order to exploit novel sources of genetic variation and increase selection efficiency. Many studies have focused on the efficient use of molecular markers to speed up se- lection processes, yet the use of omics studies in plant breeding programs is currently under utilised as they could be used to elucidate the mechanisms underpinning the inheritance of traits currently exploited by plant breeders. This study has generated whole-genome transcriptome and methylome data to uncover the mechanisms impli- cated in the inheritance of traits generated during a doubled haploid (DH) breeding program. Our analysis reveals the existence of a number of predictive elements that explain the molecular variation present in DH breeding. The major elements con- tributing to this variation are the level of dominance in hybrids and the contribution of each parental genome in individual DH lines. Collectively, our works demonstrate that genomic and epigenomic studies can provide insights into genome regulation and more importantly, aid the design of new plant breeding programs.