Prunus genetics and applications after de novo genome sequencing: achievements and prospects

Prior to the availability of whole-genome sequences, our understanding of the structural and functional aspects of Prunustree genomeswas limited mostly to molecular genetic mapping of important traits and development of EST resources. With public release of the peach genomeand others that followed, significant advances in our knowledge of Prunus genomesand the genetic underpinnings of important traits ensued. In this review, we highlight key achievements in Prunusgenetics and breeding driven by the availability of these whole-genome sequences. Within the structural and evolutionary contexts, we summarize: (1) the current status of Prunus whole-genome sequences; (2) preliminary and ongoing work on the sequence structure and diversity of the genomes; (3) the analyses of Prunus genome evolutiondriven by natural and man-made selection; and (4) provide insight into haploblocking genomesas a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breedingprograms worldwide. Functionally, we summarize recent and ongoing work that leverages whole-genome sequencesto identify and characterize genes controlling 22 agronomically important Prunustraits. These include phenology, fruit quality, allergens, disease resistance, tree architecture, and self-incompatibility. Translationally, we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunuscrop improvement. Finally, we present the current status of publically available Prunus genomicsand genetics data housed mainly in the GenomeDatabase for Rosaceae(GDR) and its updated functionalities for future bioinformatics-based Prunusgenetics and genomicsinquiry.