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 ...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.展开更多
Loss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes.However,in almond,little is known about the genetic variability in curr...Loss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes.However,in almond,little is known about the genetic variability in current breeding stocks,although several cases of inbreeding depression have been reported.To gain insights into the genetic structure in modern breeding programs worldwide,marker-verified pedigree data of 220 almond cultivars and breeding selections were analyzed.Inbreeding coefficients,pairwise relatedness,and genetic contribution were calculated for these genotypes.The results reveal two mainstream breeding lines based on three cultivars:“Tuono”,“Cristomorto”,and“Nonpareil”.Descendants from“Tuono”or“Cristomorto”number 76(sharing 34 descendants),while“Nonpareil”has 71 descendants.The mean inbreeding coefficient of the analyzed genotypes was 0.041,with 14 genotypes presenting a high inbreeding coefficient,over 0.250.Breeding programs from France,the USA,and Spain showed inbreeding coefficients of 0.075,0.070,and 0.037,respectively.According to their genetic contribution,modern cultivars from Israel,France,the USA,Spain,and Australia trace back to a maximum of six main founding genotypes.Among the group of 65 genotypes carrying the S f allele for self-compatibility,the mean relatedness coefficient was 0.125,with“Tuono”as the main founding genotype(24.7%of total genetic contribution).The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process worldwide.Increasing current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress.展开更多
Natural variations are the foundation of crop improvement.However,genomic variability remains largely understudied.Here,we present the full-spectrum integrated panvariome and pangenome of 1,020 peach accessions,includ...Natural variations are the foundation of crop improvement.However,genomic variability remains largely understudied.Here,we present the full-spectrum integrated panvariome and pangenome of 1,020 peach accessions,including 10.5 million single-nucleotide polymorphisms,insertions,deletions,duplications,inversions,translocations,copy-number variations,transposon-insertion polymorphisms,and presence-absence variations,uncovering 70.6%novel variants and 3,289 novel genes.Analysis of the panvariome recapitulated the global evolutionary history of the peach and identified several novel trait-causally rare variants.We found that landraces and improved accessions encode more genes than the wild accessions,implying gene gains during peach domestication and improvement.Analysis of global introgression patterns revealed their value in phenotype prediction and gene mining,and suggested that the most likely wild progenitor of the domesticated peach is Prunus mira and that almond was involved in the origin of Prunus davidiana.Furthermore,we developed a novel panvariome-based one-step solution for association study,GWASPV,which was used to identify several trait-conferring genes and over 2,000 novel associations..Collectively,our study reveals new insights into peach evolution and genomic variations,providing a novel method for plant gene mining and important targets for peach breeding.展开更多
基金This work has been funded under the EU seventh Framework Programme by the FruitBreedomics project No.265582:Integrated Approach for increasing breeding efficiency in fruit tree crops(http://www.fruitbreedomics.com/).
文摘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.
基金This research was supported in part by grants from the Ministry of Economy and Competitiveness MINECO/FEDER Projects RTA 2017-00084-00-00 and CERCA Program Generalitat of Catalonia.
文摘Loss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes.However,in almond,little is known about the genetic variability in current breeding stocks,although several cases of inbreeding depression have been reported.To gain insights into the genetic structure in modern breeding programs worldwide,marker-verified pedigree data of 220 almond cultivars and breeding selections were analyzed.Inbreeding coefficients,pairwise relatedness,and genetic contribution were calculated for these genotypes.The results reveal two mainstream breeding lines based on three cultivars:“Tuono”,“Cristomorto”,and“Nonpareil”.Descendants from“Tuono”or“Cristomorto”number 76(sharing 34 descendants),while“Nonpareil”has 71 descendants.The mean inbreeding coefficient of the analyzed genotypes was 0.041,with 14 genotypes presenting a high inbreeding coefficient,over 0.250.Breeding programs from France,the USA,and Spain showed inbreeding coefficients of 0.075,0.070,and 0.037,respectively.According to their genetic contribution,modern cultivars from Israel,France,the USA,Spain,and Australia trace back to a maximum of six main founding genotypes.Among the group of 65 genotypes carrying the S f allele for self-compatibility,the mean relatedness coefficient was 0.125,with“Tuono”as the main founding genotype(24.7%of total genetic contribution).The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process worldwide.Increasing current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress.
基金supported by the National Key Research and Development Program(2023YFE0105400)National Natural Science Foundation of China(32341042)+4 种基金Central Public-Interest Scientific Institution Basal Research Fund(Y2022QC23)National Key Laboratory&Zhongyuan Research Center‘Xinyi’Project(ZYZX20240304)Agricultural Science and Technology Innovation Program(CAAS-ASTIP-2024-ZFRI-01)Natural Science Foundation of Henan(232300421042)National Science and Technology Major Project of Yunan(202302AE090005-3).
文摘Natural variations are the foundation of crop improvement.However,genomic variability remains largely understudied.Here,we present the full-spectrum integrated panvariome and pangenome of 1,020 peach accessions,including 10.5 million single-nucleotide polymorphisms,insertions,deletions,duplications,inversions,translocations,copy-number variations,transposon-insertion polymorphisms,and presence-absence variations,uncovering 70.6%novel variants and 3,289 novel genes.Analysis of the panvariome recapitulated the global evolutionary history of the peach and identified several novel trait-causally rare variants.We found that landraces and improved accessions encode more genes than the wild accessions,implying gene gains during peach domestication and improvement.Analysis of global introgression patterns revealed their value in phenotype prediction and gene mining,and suggested that the most likely wild progenitor of the domesticated peach is Prunus mira and that almond was involved in the origin of Prunus davidiana.Furthermore,we developed a novel panvariome-based one-step solution for association study,GWASPV,which was used to identify several trait-conferring genes and over 2,000 novel associations..Collectively,our study reveals new insights into peach evolution and genomic variations,providing a novel method for plant gene mining and important targets for peach breeding.
