Accuracy and responses of genomic selection on key traits in apple breeding

The application of genomic selection in fruit tree crops is expected to enhance breeding eficiency by increasing prediction accuracy,increasing selection intensity and decreasing generation interval.The objectives of this study were to assess the accuracy of prediction and selection response in commercial apple breeding programmes for key traits.The training population comprised 977 individuals derived from 20 pedigreed fllsib families.Historic phenotypic data were available on 10 traits related to productivity and fruit external appearance and genotypic data for 7829 SNPs obtained with an llumina 20K SNP array.From these data,a genome-wide prediction model was built and subsequently used to calculate genomic breeding values of five application fllsib families.The application families had genotypes at 364 SNPs from a dedicated 512 SNP array,and these genotypic data were extended to the high-density level by imputation.These five families were phenotyped for 1 year and their phenotypes were compared to the predicted breeding values.Accuracy of genomic prediction across the 10 traits reached a maximum value of 0.5 and had a median value of 0.19.The accuracies were strongly affected by the phenotypic distribution and heritability of traits.In the largest family,significant selection response was observed for traits with high heritability and symmetric phenotypic distribution.Traits that showed non-significant response often had reduced and skewed phenotypic variation or low heritability.Among the five application families the accuracies were uncorrelated to the degree of relatedness to the training population.The results underline the potential of genomic prediction to accelerate breeding progress in outbred fruit tree crops that still need to overcome long generation intervals and extensive phenotyping costs.

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.

Knockdown of MLO genes reduces susceptibility to powdery mildew in grapevine

Erysiphe necator is the causal agent of powdery mildew(PM),one of the most destructive diseases of grapevine.PM is controlled by sulfur-based and synthetic fungicides,which every year are dispersed into the environment.This is why PM-resistant varieties should become a priority for sustainable grapevine and wine production.PM resistance can be achieved in other crops by knocking out susceptibility S-genes,such as those residing at genetic loci known as MLO(Mildew Locus O).All MLO S-genes of dicots belong to the phylogenetic clade V,including grapevine genes VvMLO7,11 and 13,which are upregulated during PM infection,and VvMLO6,which is not upregulated.Before adopting a gene-editing approach to knockout candidate S-genes,the evidence that loss of function of MLO genes can reduce PM susceptibility is necessary.This paper reports the knockdown through RNA interference of VvMLO6,7,11 and 13.The knockdown of VvMLO6,11 and 13 did not decrease PM severity,whereas the knockdown of VvMLO7 in combination with VvMLO6 and VvMLO11 reduced PM severity up to 77%.The knockdown of VvMLO7 and VvMLO6 seemed to be important for PM resistance,whereas a role for VvMLO11 does not seem likely.Cell wall appositions(papillae)were present in both resistant and susceptible lines in response to PM attack.Thirteen genes involved in defense were less upregulated in infected mlo plants,highlighting the early mlo-dependent disruption of PM invasion.

Molecular genetics and genomics of the Rosoideae: state of theart and future perspectives

The Rosoideae is a subfamily of the Rosaceae that contains a number of species of economic importance,including the soft fruit species strawberry(Fragaria 3ananassa),red(Rubus idaeus)and black(Rubus occidentalis)raspberries,blackberries(Rubus spp.)and one of the most economically important cut flower genera,the roses(Rosa spp.).Molecular genetics and genomics resources for the Rosoideae have developed rapidly over the past two decades,beginning with the development and application of a number of molecular marker types including restriction fragment length polymorphisms,amplified fragment length polymorphisms and microsatellites,and culminating in the recent publication of the genome sequence of the woodland strawberry,Fragaria vesca,and the development of high throughput single nucleotide polymorphism(SNP)-genotyping resources for Fragaria,Rosa and Rubus.These tools have been used to identify genes and other functional elements that control traits of economic importance,to study the evolution of plant genome structure within the subfamily,and are beginning to facilitate genomic-assisted breeding through the development and deployment of markers linked to traits such as aspects of fruit quality,disease resistance and the timing of flowering.In this review,we report on the developments that have been made over the last 20 years in the field of molecular genetics and structural genomics within the Rosoideae,comment on how the knowledge gained will improve the efficiency of cultivar development and discuss how these advances will enhance our understanding of the biological processes determining agronomically important traits in all Rosoideae species.

A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

Quantitative trait loci(QTL)mapping approaches rely on the correct ordering of molecular markers along the chromosomes,which can be obtained from genetic linkage maps or a reference genome sequence.For apple(Malus domestica Borkh),the genome sequence v1 and v2 could not meet this need;therefore,a novel approach was devised to develop a dense genetic linkage map,providing the most reliable marker-loci order for the highest possible number of markers.The approach was based on four strategies:(i)the use of multiple full-sib families,(ii)the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism(SNP)markers,(iii)the construction of a single backcross-type data set including all families,and(iv)a two-step map generation procedure based on the sequential inclusion of markers.The map comprises 15417 SNP markers,clustered in 3 K HaploBlock markers spanning 1267 cM,with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM.Moreover,chromosome 5 was oriented according to its homoeologous chromosome 10.This map was useful to improve the apple genome sequence,design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies.Its collinearity with the genome sequences v1 and v3 are reported.To our knowledge,this is the shortest published SNP map in apple,while including the largest number of markers,families and individuals.This result validates our methodology,proving its value for the construction of integrated linkage maps for any outbreeding species.

Genome mapping of postzygotic hybrid necrosis in an interspecific pear population

Deleterious epistatic interactions in plant inter-and intraspecific hybrids can cause a phenomenon known as hybrid necrosis,characterized by a typical seedling phenotype whose main distinguishing features are dwarfism,tissue necrosis and in some cases lethality.Identification of the chromosome regions associated with this type of incompatibility is important not only to increase our understanding of the evolutionary diversification that led to speciation but also for breeding purposes.Development of molecular markers linked to the lethal genes will allow breeders to avoid incompatible inbred combinations that could affect the expression of important agronomic tratis co-segregating with these genes.Although hybrid necrosis has been reported in several plant taxa,including Rosaceae species,this phenomenon has not been described previously in pear.In the interspecific pear population resulting from a cross between PEAR3(Pyrus bretschneideri×Pyrus communis)and‘Moonglow’(P.communis),we observed two types of hybrid necrosis,expressed at different stages of plant development.Using a combination of previously mapped and newly developed genetic markers,we identified three chromosome regions associated with these two types of lethality,which were genetically independent.One type resulted from a negative epistatic interaction between a locus on linkage group 5(LG5)of PEAR3 and a locus on LG1 of‘Moonglow’,while the second type was due to a gene that maps to LG2 of PEAR3 and which either acts alone or more probably interacts with another gene of unknown location inherited from‘Moonglow’.