Where are we now as we merge genomics into plant breeding and what are our limitations? Experiences from RosBREED

The complete genome sequences of apple, peach, and diploid strawberry - one member of each of the three main fruit-producing branches of the Rosaceae tree - were available in 2010. Despite this achievement, virtually none of this genomics knowledge was being used to assist breeding efforts of these crops. Four years later, this gap has been bridged, with genetic information routinely used in many US apple, peach, and cherry breeding programs. For example, DNA tests predict apple crispness, peach maturity date, and cherry fruit size, enabling breeders to determine the best parents to combine and the best seedlings to advance. This application significantly reduces the wasted effort to eliminate entirely poor families and reduces the costs to grow and evaluate thousands of seedlings genetically destined to have unacceptable fruit quality or maturity date. This achievement was enabled by international community efforts, including the RosBREED project, funded by the USDA-National Institute of Food and Agriculture Specialty Crop Research Initiative (SCRI). DNA tests are now applied for high-value attributes where the targeted loci explain a large proportion of the trait variation. However, limitations to widespread adoption of these predictive tests still exist. Some limitations are due to lack of knowledge, such as an understanding of genotype by environment (GxE) interactions and loci associated with variation for other valuable attributes. Technical limitations include streamlined phasing of alleles from multiple families of pedigree-connected breeding germplasm and access to suitable commercial service providers.