An integrated approach for increasing breeding efficiency in apple and peach in Europe

Despite the availability of whole genome sequences of apple and peach,there has been a considerable gap between genomics and breeding.To bridge the gap,the European Union funded the FruitBreedomics project(March 2011 to August 2015)involving 28 research institutes and private companies.Three complementary approaches were pursued:(i)tool and software development,(ii)deciphering genetic control of main horticultural traits taking into account allelic diversity and(iii)developing plant materials,tools and methodologies for breeders.Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding,development of new,dense SNP arrays in apple and peach,new phenotypic methods for some complex traits,software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis(PBA).This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies(GWAS)on several European genebank collections.FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities.Through FruitBreedomics,significant progresses were made in the field of apple and peach breeding,genetics,genomics and bioinformatics of which advantage will be made by breeders,germplasm curators and scientists.A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public.This review covers the scientific discoveries made in this major endeavour,and perspective in the apple and peach breeding and genomics in Europe and beyond.

Sugars in peach fruit: a breeding perspective

The last decade has been characterized by a decrease in peach(Prunus persica)fruit consumption in many countries,foremost due to unsatisfactory quality.The sugar content is one of the most important quality traits perceived by consumers,and the development of novel peach cultivars with sugar-enhanced content is a primary objective of breeding programs to revert the market inertia.Nevertheless,the progress reachable through classical phenotypic selection is limited by the narrow genetic bases of peach breeding material and by the complex quantitative nature of the trait,which is deeply affected by environmental conditions and agronomical management.The development of molecular markers applicable in MAS or MAB has become an essential strategy to boost the selection efficiency.Despite the enormous advances in‘omics’sciences,providing powerful tools for plant genotyping,the identification of the genetic bases of sugar-related traits is hindered by the lack of adequate phenotyping methods that are able to address strong within-plant variability.This review provides an overview of the current knowledge of the metabolic pathways and physiological mechanisms regulating sugar accumulation in peach fruit,the main advances in phenotyping approaches and genetic background,and finally addressing new research priorities and prospective for breeders.

<i>Endopolygalacturonase</i>Gene Polymorphisms: Asset of the Locus in Different Peach Accessions

Endopolygalacturonase (endoPG) plays a pivotal role in determining peach [Prunus persica L. (Batsch)] fruit characteristics. Different Pp-endoPG genes or allelic variants have been described, characterized by different polymorphisms: insertions-deletions (InDels) and single nucleotide polymorphisms (SNPs). Eighty-five peach accessions (comprising commercial cultivars, F1 progenies of selected crosses, and three haploid seedlings) with different flesh softening patterns (Non Melting: NM;Melting: M;Slow Softening: SS;Stony Hard: SH) were screened by exploiting specific polymorphisms, with the aim to characterize their asset at the endoPG locus and evaluate a potential relationship with fruit flesh texture phenotype. The results of InDel analysis allowed to distinguish, by a simple genotyping procedure, NM flesh phenotypes from the others. Further information arose from this analysis, showing that two Pp-endoPG genes, i.e., Pp-endoPGm (Ppa006839m), involved in the determination of the Melting/Non Melting trait, and Pp-endoPG_M (Ppa006857m), involved in the determination of the Clingstone/Freestone trait, always co-segregate, and that SS Big Top possesses a “null” Pp-endoPG allele. Cleaved Amplified Polymorphic Sequence (CAPS) analysis allowed to preliminarily discriminate the Pp-endoPG variants of the SS and SH accessions considered. The integrated use of the considered polymorphisms in a high number of peach accessions proved useful, by individuating the different gene variants and their combinations, to describe the structure of the endoPG locus in different genotypes.