Journal
HORTICULTURE RESEARCH
Volume 6, Issue -, Pages -Publisher
OXFORD UNIV PRESS INC
DOI: 10.1038/s41438-019-0140-8
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Funding
- Ministry of Economy and Competitiveness (MINECO/FEDER) from Spain [AGL2015-68329-R, RTA2015-00050-00-00]
- Ministry of Economy and Competitiveness (Severo Ochoa Program for Centres of Excellence in R&D 201-2019) from Spain [SEV-2015-0533]
- Ministry of Economy and Competitiveness (CERCA Programme-Generalitat de Catalunya) from Spain
- USDA-NIFA-Specialty Crop Research Initiative project, RosBREED: Enabling marker-assisted breeding in Rosaceae from USA [2009-51181-05808]
- USDA-NIFA-Specialty Crop Research Initiative project, RosBREED 2: Combining disease resistance with horticultural quality in new rosaceous cultivars from USA [2014-51181-22378]
- USDA NIFA from USA [1014919]
- Key Project for New Agricultural Cultivar Breeding in Zhejiang Province from China [2016C02052-5]
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Prior to the availability of whole-genome sequences, our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources. With public release of the peach genome and others that followed, significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits ensued. In this review, we highlight key achievements in Prunus genetics 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 evolution driven by natural and man-made selection; and (4) provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide. Functionally, we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits. 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 Prunus crop improvement. Finally, we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae (GDR) and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry.
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