Most molecularly characterized plant resistance genes(R genes)belong to the nucleotide-binding-site-leucine-rich-repeat(NLR)receptor family and are prone to duplication and transposition with high sequence diversity.I...Most molecularly characterized plant resistance genes(R genes)belong to the nucleotide-binding-site-leucine-rich-repeat(NLR)receptor family and are prone to duplication and transposition with high sequence diversity.In this family,the Vat gene in melon is one of the few R genes known for conferring resistance to insect,i.e.,Aphis gossypii,but it has been misassembled and/or mispredicted in the whole genomes of Cucurbits.We examined 14 genomic regions(about 400 kb)derived from long-read assemblies spanning Vat-related genes in Cucumis melo,Cucumis sativus,Citrullus lanatus,Benincasa hispida,Cucurbita argyrosperma,and Momordica charantia.We built the phylogeny of those genes.Investigating the paleohistory of the Vat gene cluster,we revealed a step by step process beginning from a common ancestry in cucurbits older than 50 my.We highlighted Vat exclusively in the Cucumis genera,which diverged about 20 my ago.We then focused on melon,evaluating a minimum duplication rate of Vat in 80 wild and cultivated melon lines using generalist primers;our results suggested that duplication started before melon domestication.The phylogeny of 44 Vat-CDS obtained from 21 melon lines revealed gain and loss of leucine-rich-repeat domains along diversification.Altogether,we revealed the high putative recognition scale offered in melon based on a combination of SNPs,number of leucine-rich-repeat domains within each homolog and number of homologs within each cluster that might jointly confer resistance to a large pest and pathogen spectrum.Based on our findings,we propose possible avenues for breeding programs.展开更多
Texture is a complex trait and a major component of fruit quality in apple.While the major effect of MdPG1,a gene controlling firmness,has already been exploited in elite cultivars,the genetic basis of crispness remai...Texture is a complex trait and a major component of fruit quality in apple.While the major effect of MdPG1,a gene controlling firmness,has already been exploited in elite cultivars,the genetic basis of crispness remains poorly understood.To further improve fruit texture,harnessing loci with minor effects via genomic selection is therefore necessary.In this study,we measured acoustic and mechanical features in 537 genotypes to dissect the firmness and crispness components of fruit texture.Predictions of across-year phenotypic values for these components were calculated using a model calibrated with 8,294 SNP markers.The best prediction accuracies following cross-validations within the training set of 259 genotypes were obtained for the acoustic linear distance(0.64).Predictions for biparental families using the entire training set varied from low to high accuracy,depending on the family considered.While adding siblings or half-siblings into the training set did not clearly improve predictions,we performed an optimization of the training set size and composition for each validation set.This allowed us to increase prediction accuracies by 0.17 on average,with a maximal accuracy of 0.81 when predicting firmness in the‘Gala’בPink Lady’family.Our results therefore identified key genetic parameters to consider when deploying genomic selection for texture in apple.In particular,we advise to rely on a large training population,with high phenotypic variability from which a‘tailored training population’can be extracted using a priori information on genetic relatedness,in order to predict a specific target population.展开更多
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
Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates.Genomics-assisted breeding utilizes genomic and phenotypic information to increase the sele...Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates.Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs,and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic conditions.Here we present an apple reference population:the apple REFPOP,a large collection formed of 534 genotypes planted in six European countries,as a unique tool to accelerate apple breeding.The population consisted of 269 accessions and 265 progeny from 27 parental combinations,representing the diversity in cultivated apple and current European breeding material,respectively.A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of 0.95.Based on the genotypic data,linkage disequilibrium was low and population structure was weak.Two well-studied phenological traits of horticultural importance were measured.We found marker–trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date,respectively.With decreasing SNP density,the detection of significant marker–trait associations varied depending on trait architecture.Regardless of the trait,10,000 SNPs sufficed to maximize genomic prediction ability.We confirm the suitability of the apple REFPOP design for genomics-assisted breeding,especially for breeding programs using related germplasm,and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.展开更多
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...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.展开更多
Since its discovery as a bacterial adaptive immune system and its development for genome editing in eukaryotes,the CRISPR technology has revolutionized plant research and precision crop breeding.The CRISPR toolbox hol...Since its discovery as a bacterial adaptive immune system and its development for genome editing in eukaryotes,the CRISPR technology has revolutionized plant research and precision crop breeding.The CRISPR toolbox holds great promise in the production of crops with genetic disease resistance to increase agriculture resilience and reduce chemical crop protection with a strong impact on the environment and public health.In this review,we provide an extensive overviewon recent breakthroughs in CRISPR technology,including the newly developed prime editing system that allows precision gene editing in plants.We present how each CRISPR tool can be selected for optimal use in accordance with its specific strengths and limitations,and illustrate how the CRISPR toolbox can foster the development of genetically pathogen-resistant crops for sustainable agriculture.展开更多
Pepper(Capsicum spp.)is an important vegetable crop that provides a unique pungent sensation when eaten.Through construction of a pepper variome map,we examined the main groups that emerged during domestication and br...Pepper(Capsicum spp.)is an important vegetable crop that provides a unique pungent sensation when eaten.Through construction of a pepper variome map,we examined the main groups that emerged during domestication and breeding of C.annuum,their relationships and temporal succession,and the molecular events underlying the main transitions.The results showed that the initial differentiation in fruit shape and pungency,increase in fruit weight,and transition from erect to pendent fruits,as well as the recent appearance of large,blocky,sweet fruits(bell peppers),were accompanied by strong selection/fixation of key alleles and introgressions in two large genomic regions.Furthermore,we identified Up,which encodes a BIG GRAIN protein involved in auxin transport,as a key domestication gene that controls erect vs pendent fruit orientation.The up mutation gained increased expression especially in the fruit pedicel through a 579-bp sequence deletion in its 5′upstream region,resulting in the phenotype of pendent fruit.The function of Up was confirmed by virus-induced gene silencing.Taken together,these findings constitute a cornerstone for understanding the domestication and differentiation of a key horticultural crop.展开更多
基金the French Ministere de l’agriculture et de l’alimentation(Vat&Co project-CASDAR−2017-2021)。
文摘Most molecularly characterized plant resistance genes(R genes)belong to the nucleotide-binding-site-leucine-rich-repeat(NLR)receptor family and are prone to duplication and transposition with high sequence diversity.In this family,the Vat gene in melon is one of the few R genes known for conferring resistance to insect,i.e.,Aphis gossypii,but it has been misassembled and/or mispredicted in the whole genomes of Cucurbits.We examined 14 genomic regions(about 400 kb)derived from long-read assemblies spanning Vat-related genes in Cucumis melo,Cucumis sativus,Citrullus lanatus,Benincasa hispida,Cucurbita argyrosperma,and Momordica charantia.We built the phylogeny of those genes.Investigating the paleohistory of the Vat gene cluster,we revealed a step by step process beginning from a common ancestry in cucurbits older than 50 my.We highlighted Vat exclusively in the Cucumis genera,which diverged about 20 my ago.We then focused on melon,evaluating a minimum duplication rate of Vat in 80 wild and cultivated melon lines using generalist primers;our results suggested that duplication started before melon domestication.The phylogeny of 44 Vat-CDS obtained from 21 melon lines revealed gain and loss of leucine-rich-repeat domains along diversification.Altogether,we revealed the high putative recognition scale offered in melon based on a combination of SNPs,number of leucine-rich-repeat domains within each homolog and number of homologs within each cluster that might jointly confer resistance to a large pest and pathogen spectrum.Based on our findings,we propose possible avenues for breeding programs.
基金funded by the EU seventh Framework Programme by the FruitBreedomics Project No.265582。
文摘Texture is a complex trait and a major component of fruit quality in apple.While the major effect of MdPG1,a gene controlling firmness,has already been exploited in elite cultivars,the genetic basis of crispness remains poorly understood.To further improve fruit texture,harnessing loci with minor effects via genomic selection is therefore necessary.In this study,we measured acoustic and mechanical features in 537 genotypes to dissect the firmness and crispness components of fruit texture.Predictions of across-year phenotypic values for these components were calculated using a model calibrated with 8,294 SNP markers.The best prediction accuracies following cross-validations within the training set of 259 genotypes were obtained for the acoustic linear distance(0.64).Predictions for biparental families using the entire training set varied from low to high accuracy,depending on the family considered.While adding siblings or half-siblings into the training set did not clearly improve predictions,we performed an optimization of the training set size and composition for each validation set.This allowed us to increase prediction accuracies by 0.17 on average,with a maximal accuracy of 0.81 when predicting firmness in the‘Gala’בPink Lady’family.Our results therefore identified key genetic parameters to consider when deploying genomic selection for texture in apple.In particular,we advise to rely on a large training population,with high phenotypic variability from which a‘tailored training population’can be extracted using a priori information on genetic relatedness,in order to predict a specific target population.
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supported by the project RIS3CAT(COTPAFRUIT3CAT)financed by the European Regional Development Fund through the FEDER frame of Catalonia 2014–2020 and by the CERCA Program from Generalitat de Catalunya.
文摘Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates.Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs,and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic conditions.Here we present an apple reference population:the apple REFPOP,a large collection formed of 534 genotypes planted in six European countries,as a unique tool to accelerate apple breeding.The population consisted of 269 accessions and 265 progeny from 27 parental combinations,representing the diversity in cultivated apple and current European breeding material,respectively.A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of 0.95.Based on the genotypic data,linkage disequilibrium was low and population structure was weak.Two well-studied phenological traits of horticultural importance were measured.We found marker–trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date,respectively.With decreasing SNP density,the detection of significant marker–trait associations varied depending on trait architecture.Regardless of the trait,10,000 SNPs sufficed to maximize genomic prediction ability.We confirm the suitability of the apple REFPOP design for genomics-assisted breeding,especially for breeding programs using related germplasm,and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.
文摘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.
基金supported by the Investissement d’Avenir program of the French National Agency of Research for the project GENIUS(ANR-11-BTBR-0001_GENIUS)the Institut Carnot Plant2Pro program for the project POTATOCRISPsupported by the ANR project Immunereceptor(ANR-15-CE20-0007).
文摘Since its discovery as a bacterial adaptive immune system and its development for genome editing in eukaryotes,the CRISPR technology has revolutionized plant research and precision crop breeding.The CRISPR toolbox holds great promise in the production of crops with genetic disease resistance to increase agriculture resilience and reduce chemical crop protection with a strong impact on the environment and public health.In this review,we provide an extensive overviewon recent breakthroughs in CRISPR technology,including the newly developed prime editing system that allows precision gene editing in plants.We present how each CRISPR tool can be selected for optimal use in accordance with its specific strengths and limitations,and illustrate how the CRISPR toolbox can foster the development of genetically pathogen-resistant crops for sustainable agriculture.
基金China National Key Technology Research and Development Program(2016YFD0100200,2016YFD0101700,2018YFD1000800,and 2020YFD1001100)National Natural Science Foundation of China(NSFC grants 31722048,31972411,3170110879,32102382,and 32102386)+5 种基金Central Public-interest Scientific Institution Basal Research Fund(Y2022GH04,IVF-BRF2021015)Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(CAAS-ASTIP-IVFCAAS)Earmarked Fund for the China Agriculture Research System(CARS-25)CAAS-GAAS Coordinated Innovation Project of the Chinese Academy of Agricultural Sciences(2019)Key Laboratory of Biology and Genetic Improvement of Horticultural Crops,Ministry of Agriculture and Rural Affairs,P.R.ChinaHorizon 2020 G2P-SOL project(grant no.677379)from the EU.
文摘Pepper(Capsicum spp.)is an important vegetable crop that provides a unique pungent sensation when eaten.Through construction of a pepper variome map,we examined the main groups that emerged during domestication and breeding of C.annuum,their relationships and temporal succession,and the molecular events underlying the main transitions.The results showed that the initial differentiation in fruit shape and pungency,increase in fruit weight,and transition from erect to pendent fruits,as well as the recent appearance of large,blocky,sweet fruits(bell peppers),were accompanied by strong selection/fixation of key alleles and introgressions in two large genomic regions.Furthermore,we identified Up,which encodes a BIG GRAIN protein involved in auxin transport,as a key domestication gene that controls erect vs pendent fruit orientation.The up mutation gained increased expression especially in the fruit pedicel through a 579-bp sequence deletion in its 5′upstream region,resulting in the phenotype of pendent fruit.The function of Up was confirmed by virus-induced gene silencing.Taken together,these findings constitute a cornerstone for understanding the domestication and differentiation of a key horticultural crop.
