Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time

Domestication drastically changed crop genomes,fixing alleles of interest and creating different genetic populations.Genome-wide association studies(GWASs)are a powerful tool to detect these alleles of interest(and so QTLs).In this study,we explored the genetic structure as well as additive and non-additive genotype-phenotype associations in a collection of 243 almond accessions.Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups,all formed by accessions with a common origin.One of these groups was formed exclusively by Spanish accessions,while the rest were mainly formed by accessions from China,Italy,France,and the USA.These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases:Asiatic,Mediterranean,Californian,and southern hemisphere.In total,we found 13 independent QTLs for nut weight,crack-out percentage,double kernels percentage,and blooming time.Of the 13 QTLs found,only one had an additive effect.Through candidate gene analysis,we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage,Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage,and Prudul26A000954 as a candidate gene for the QTL found in blooming time.Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.

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.