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

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.

Fig. 1. Dividing a crop’s genome into qualitative, cognitively manageable segments by haploblocking adjacent sets of loci can be done in several ways, such as the pedigree-based approach, in which loci within haploblocks have not recombined throughout the pedigree of known progenitors of cultivars.

Haplotypes are the variants of haploblocks—sets of co-inherited alleles. To each haplotype can be assigned trait influences, ancestry, and other genetic features. If a breeding parent does not have coupling-phase linkage for desirable alleles within a haploblock containing multiple quantitative trait loci, such tight linkage might be targeted for recombination in the next generation

Fig. 2. Flat fruit shape in peach.

a Manhattan plot from Micheletti et al. data. Chromosomes are marked with different colors on the horizontal axis. The horizontal green line represents the significance threshold for the association. b Images of flowers, pistils, and fruits of a round (left) and a flat (right) fruit cultivar where it can be seen that the flat vs. round character is determined early in flower formation

Fig. 3. Haplotype mosaic of “Rainier”, a classic Washington-bred sweet cherry cultivar.

Segments that “Rainier” inherited via its parents from its three specified ancestors are displayed across the eight chromosomes of sweet cherry. In some cases, these ancestral segments are homozygous, highlighting consequences of inbreeding and signifying common ancestry in generations behind known ancestors. Trait locus alleles are indicated with phenotypic effects and ancestral origins; despite the commercial success of “Rainier,” it can be seen that there is still much to be improved. These results were obtained from single-nucleotide polymorphism (SNP) data curation and pedigree ascertainment by L. Cai and C. Peace using the RosBREED cherry 6K SNP array v1 on a U.S. breeding germplasm set (n ~ 500). Diagram is from Peace et al.