Browse Articles

Review Article|05 Apr 2019|OPEN
Prunus genetics and applications after de novo genome sequencing: achievements and prospects
María José Aranzana1 , Véronique Decroocq2 , Elisabeth Dirlewanger2 , Iban Eduardo1 , Zhong Shan Gao3 , Ksenija Gasic4 , Amy Iezzoni5 , Sook Jung6 , Cameron Peace6 , Humberto Prieto7 , Ryutaro Tao8 , Ignazio Verde9 , Albert G. Abbott10 and Pere Arús,1 ,
1IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
2UMR 1332 BFP, INRA, University of Bordeaux, A3C and Virology Teams, 33882 Villenave-d’Ornon Cedex, France
3Allergy Research Center, Zhejiang University, 310058 Hangzhou, China
4Clemson University, Clemson, SC 29634, USA
5Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824-1325, USA
6Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
7Biotechnology Laboratory, La Platina Research Station, Instituto de Investigaciones Agropecuarias, Santa Rosa, 11610 La Pintana, Santiago, Chile
8Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
9Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) – Centro di ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Rome, Italy
10University of Kentucky, 106 T. P. Cooper Hall, Lexington, KY 40546-0073, USA
*Corresponding author. E-mail: pere.arus@irta.cat

Horticulture Research 6,
Article number: 58 (2019)
doi: https://doi.org/10.1038/s41438-019-0140-8
Views: 1002

Received: 31 Jan 2019
Revised: 10 Mar 2019
Accepted: 13 Mar 2019
Published online: 05 Apr 2019

Abstract

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.