Prior to the availability of whole-genome sequences,our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development...Prior to the availability of whole-genome sequences,our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources.With public release of the peach genome and others that followed,significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits ensued.In this review,we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome sequences.Within the structural and evolutionary contexts,we summarize:(1)the current status of Prunus whole-genome sequences;(2)preliminary and ongoing work on the sequence structure and diversity of the genomes;(3)the analyses of Prunus genome evolution driven by natural and man-made selection;and(4)provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide.Functionally,we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits.These include phenology,fruit quality,allergens,disease resistance,tree architecture,and self-incompatibility.Translationally,we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop improvement.Finally,we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae(GDR)and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry.展开更多
The Rosaceae crop family(including almond,apple,apricot,blackberry,peach,pear,plum,raspberry,rose,strawberry,sweet cherry,and sour cherry)provides vital contributions to human well-being and is economically significan...The Rosaceae crop family(including almond,apple,apricot,blackberry,peach,pear,plum,raspberry,rose,strawberry,sweet cherry,and sour cherry)provides vital contributions to human well-being and is economically significant across the U.S.In 2003,industry stakeholder initiatives prioritized the utilization of genomics,genetics,and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural quality.However,rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding—a“chasm”existed between existing genomics and genetic information and the application of this knowledge in breeding.The RosBREED project(“Ros”signifying a Rosaceae genomics,genetics,and breeding community initiative,and“BREED”,indicating the core focus on breeding programs),addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research Initiative.RosBREED was designed to enable the routine application of modern genomics and genetics technologies in U.S.rosaceous crop breeding programs,thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural quality.This review presents a synopsis of the approach,deliverables,and impacts of RosBREED,highlighting synergistic global collaborations and future needs.Enabling technologies and tools developed are described,including genome-wide scanning platforms and DNA diagnostic tests.Examples of DNA-informed breeding use by project participants are presented for all breeding stages,including pre-breeding for disease resistance,parental and seedling selection,and elite selection advancement.The chasm is now bridged,accelerating rosaceous crop genetic improvement.展开更多
Breeding apple cultivars with resistance offers a potential solution to fire blight,a damaging bacterial disease caused by Erwinia amylovora.Most resistance alleles at quantitative trait loci(QTLs)were previously char...Breeding apple cultivars with resistance offers a potential solution to fire blight,a damaging bacterial disease caused by Erwinia amylovora.Most resistance alleles at quantitative trait loci(QTLs)were previously characterized in diverse Malus germplasm with poor fruit quality,which reduces breeding utility.This study utilized a pedigree-based QTL analysis approach to elucidate the genetic basis of resistance/susceptibility to fire blight from multiple genetic sources in germplasm relevant to U.S.apple breeding programs.Twenty-seven important breeding parents(IBPs)were represented by 314 offspring from 32 full-sib families,with‘Honeycrisp’being the most highly represented IBP.Analyzing resistance/susceptibility data from a two-year replicated field inoculation study and previously curated genome-wide single nucleotide polymorphism data,QTLs were consistently mapped on chromosomes(Chrs.)6,7,and 15.These QTLs together explained~28% of phenotypic variation.The Chr.6 and Chr.15 QTLs colocalized with previously reported QTLs,while the Chr.7 QTL is possibly novel.‘Honeycrisp’inherited a rare reduced-susceptibility allele at the Chr.6 QTL from its grandparent‘Frostbite’.The highly resistant IBP‘Enterprise’had at least one putative reduced-susceptibility allele at all three QTLs.In general,lower susceptibility was observed for individuals with higher numbers of reduced-susceptibility alleles across QTLs.This study highlighted QTL mapping and allele characterization of resistance/susceptibility to fire blight in complex pedigree-connected apple breeding germplasm.Knowledge gained will enable more informed parental selection and development of trait-predictive DNA tests for pyramiding favorable alleles and selection of superior apple cultivars with resistance to fire blight.展开更多
Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of interest.Traditionally,genetic potential is determined by phenotypic evaluation.With the avail...Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of interest.Traditionally,genetic potential is determined by phenotypic evaluation.With the availability of DNA tests for some agronomically important traits,breeders have the opportunity to include DNA information in their seedling selection operations—known as marker-assisted seedling selection.A major challenge in deploying marker-assisted seedling selection in clonally propagated crops is a lack of knowledge in genetic gain achievable from alternative strategies.Existing models based on additive effects considering seed-propagated crops are not directly relevant for seedling selection of clonally propagated crops,as clonal propagation captures all genetic effects,not just additive.This study modeled genetic gain from traditional and various marker-based seedling selection strategies on a single trait basis through analytical derivation and stochastic simulation,based on a generalized seedling selection scheme of clonally propagated crops.Various trait-test scenarios with a range of broad-sense heritability and proportion of genotypic variance explained by DNA markers were simulated for two populations with different segregation patterns.Both derived and simulated results indicated that marker-based strategies tended to achieve higher genetic gain than phenotypic seedling selection for a trait where the proportion of genotypic variance explained by marker information was greater than the broad-sense heritability.Results from this study provides guidance in optimizing genetic gain from seedling selection for single traits where DNA tests providing marker information are available.展开更多
Pedigree information is of fundamental importance in breeding programs and related genetics efforts.However,many individuals have unknown pedigrees.While methods to identify and confirm direct parent–offspring relati...Pedigree information is of fundamental importance in breeding programs and related genetics efforts.However,many individuals have unknown pedigrees.While methods to identify and confirm direct parent–offspring relationships are routine,those for other types of close relationships have yet to be effectively and widely implemented with plants,due to complications such as asexual propagation and extensive inbreeding.The objective of this study was to develop and demonstrate methods that support complex pedigree reconstruction via the total length of identical by state haplotypes(referred to in this study as“summed potential lengths of shared haplotypes”,SPLoSH).A custom Python script,HapShared,was developed to generate SPLoSH data in apple and sweet cherry.HapShared was used to establish empirical distributions of SPLoSH data for known relationships in these crops.These distributions were then used to estimate previously unknown relationships.Case studies in each crop demonstrated various pedigree reconstruction scenarios using SPLoSH data.For cherry,a full-sib relationship was deduced for‘Emperor Francis,and‘Schmidt’,a half-sib relationship for‘Van’and‘Windsor’,and the paternal grandparents of‘Stella’were confirmed.For apple,29 cultivars were found to share an unknown parent,the pedigree of the unknown parent of‘Cox’s Pomona’was reconstructed,and‘Fameuse’was deduced to be a likely grandparent of‘McIntosh’.Key genetic resources that enabled this empirical study were large genome-wide SNP array datasets,integrated genetic maps,and previously identified pedigree relationships.Crops with similar resources are also expected to benefit from using HapShared for empowering pedigree reconstruction.展开更多
One application of DNA-informed breeding,which has potential to increase the effectiveness of traditional breeding methods,is the use of DNAbased diagnostic tests to estimate genetic potential of breeding individuals....One application of DNA-informed breeding,which has potential to increase the effectiveness of traditional breeding methods,is the use of DNAbased diagnostic tests to estimate genetic potential of breeding individuals.In sweet cherry(Prunus avium L.),cracked or soft fruit are major industry challenges.Recent research detected two quantitative trait loci(QTLs)for fruit cracking and firmness differing in trait levels associated with QTL haplotypic variation.Also,a DNA test for cracking(Pav-G5Crack-SSR),using two simple sequence repeat(SSR)markers,was previously developed but not yet validated on breeding germplasm.In addition to SSR markers,single nucleotide polymorphism(SNP)markers can be used for developing locus-specific DNA tests and run as simple assays such as high-resolution melting(HRM).The objective of this research was to develop and evaluate the predictiveness of DNA tests for fruit cracking and firmness in sweet cherry.Unselected seedlings from pedigreeconnected families were screened with the Pav-G5Crack-SSR DNA test.DNA tests were also created from four SNP markers with HRM assays,using two years of cracking and firmness data for evaluation.Pav-G5Crack-SSR explained 12–15%of the cracking phenotypic variance,while Pav-G1Crack-SNP and Pav-G5Crack-SNP(which targeted the same QTL as Pav-G5Crack-SSR)together explained 16%–30%of the cracking phenotypic variance.Pav-G1Firm-SNP and Pav-G3Firm-SNP together explained 22%–28%of the firmness phenotypic variance.All three DNA tests can be implemented in breeding programs to enhance effectiveness in breeding for decreased cracking incidence and increased fruit firmness in sweet cherry.展开更多
Only when all contribute their firewood can they build up a big fire(众人拾柴火焰高).Horticultural crops are a major source of high value nutritious food,and new improved cultivars developed through breeding are requi...Only when all contribute their firewood can they build up a big fire(众人拾柴火焰高).Horticultural crops are a major source of high value nutritious food,and new improved cultivars developed through breeding are required for sustainable production in the face of abiotic and biotic stresses,and to deliver novel,premium products to consumers.However,grower confidence in the performance of new germplasm,particularly across environmental variability,is important for commercial adoption and germplasm-environ-ment matching to optimize production.展开更多
基金supported in part by grants from the Ministry of Economy and Competitiveness(MINECO/FEDER projects AGL2015-68329-R and RTA2015-00050-00-00,Severo Ochoa Program for Centres of Excellence in R&D 201-2019 SEV-2015-0533 and CERCA Programme-Generalitat de Catalunya)from SpainUSDA-NIFA-Specialty Crop Research Initiative project,RosBREED:“Enabling marker-assisted breeding in Rosaceae”(2009-51181-05808)and RosBREED 2:“Combining disease resistance with horticultural quality in new rosaceous cultivars”(2014-51181-22378)and USDA NIFA Hatch project 1014919 from USAKey Project for New Agricultural Cultivar Breeding in Zhejiang Province(2016C02052-5)from China.
文摘Prior to the availability of whole-genome sequences,our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources.With public release of the peach genome and others that followed,significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits ensued.In this review,we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome sequences.Within the structural and evolutionary contexts,we summarize:(1)the current status of Prunus whole-genome sequences;(2)preliminary and ongoing work on the sequence structure and diversity of the genomes;(3)the analyses of Prunus genome evolution driven by natural and man-made selection;and(4)provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide.Functionally,we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits.These include phenology,fruit quality,allergens,disease resistance,tree architecture,and self-incompatibility.Translationally,we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop improvement.Finally,we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae(GDR)and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry.
基金funded by USDA National Institute of Food and Agriculture-Specialty Crop Research Initiative Projects,“RosBREED:Enabling marker-assisted breeding in Rosaceae”(2009-51181-05858)“RosBREED:Combining disease resistance and horticultural quality in new rosaceous cultivars”(2014-51181-22378)+2 种基金USDA National Institute of Food and Agriculture Specialty Crop Research Initiative projects 2014-51181-22376 and 2014-51181-22378USDA National Institute of Food and Agriculture National Research Support Project 10the NSF Plant Genome Research Program award#444573.
文摘The Rosaceae crop family(including almond,apple,apricot,blackberry,peach,pear,plum,raspberry,rose,strawberry,sweet cherry,and sour cherry)provides vital contributions to human well-being and is economically significant across the U.S.In 2003,industry stakeholder initiatives prioritized the utilization of genomics,genetics,and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural quality.However,rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding—a“chasm”existed between existing genomics and genetic information and the application of this knowledge in breeding.The RosBREED project(“Ros”signifying a Rosaceae genomics,genetics,and breeding community initiative,and“BREED”,indicating the core focus on breeding programs),addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research Initiative.RosBREED was designed to enable the routine application of modern genomics and genetics technologies in U.S.rosaceous crop breeding programs,thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural quality.This review presents a synopsis of the approach,deliverables,and impacts of RosBREED,highlighting synergistic global collaborations and future needs.Enabling technologies and tools developed are described,including genome-wide scanning platforms and DNA diagnostic tests.Examples of DNA-informed breeding use by project participants are presented for all breeding stages,including pre-breeding for disease resistance,parental and seedling selection,and elite selection advancement.The chasm is now bridged,accelerating rosaceous crop genetic improvement.
基金Washington Tree Fruit Research Commission projects CP-15-100 and CP-12-104,United States Department of Agriculture(USDA)-National Institute of Food and Agriculture(NIFA)award 2016-68004-24770,USDA-NIFA project‘Integrating genetics,genomics,and physiology to inform breeding for fire blight resistance in apple’(2020-67034-31887)USDA-NIFA Specialty Crop Research Initiative project‘RosBREED:combining disease resistance and horticultural quality in new rosaceous cultivars’(2014-51181-22378)USDA-NIFA Hatch project 1014919.
文摘Breeding apple cultivars with resistance offers a potential solution to fire blight,a damaging bacterial disease caused by Erwinia amylovora.Most resistance alleles at quantitative trait loci(QTLs)were previously characterized in diverse Malus germplasm with poor fruit quality,which reduces breeding utility.This study utilized a pedigree-based QTL analysis approach to elucidate the genetic basis of resistance/susceptibility to fire blight from multiple genetic sources in germplasm relevant to U.S.apple breeding programs.Twenty-seven important breeding parents(IBPs)were represented by 314 offspring from 32 full-sib families,with‘Honeycrisp’being the most highly represented IBP.Analyzing resistance/susceptibility data from a two-year replicated field inoculation study and previously curated genome-wide single nucleotide polymorphism data,QTLs were consistently mapped on chromosomes(Chrs.)6,7,and 15.These QTLs together explained~28% of phenotypic variation.The Chr.6 and Chr.15 QTLs colocalized with previously reported QTLs,while the Chr.7 QTL is possibly novel.‘Honeycrisp’inherited a rare reduced-susceptibility allele at the Chr.6 QTL from its grandparent‘Frostbite’.The highly resistant IBP‘Enterprise’had at least one putative reduced-susceptibility allele at all three QTLs.In general,lower susceptibility was observed for individuals with higher numbers of reduced-susceptibility alleles across QTLs.This study highlighted QTL mapping and allele characterization of resistance/susceptibility to fire blight in complex pedigree-connected apple breeding germplasm.Knowledge gained will enable more informed parental selection and development of trait-predictive DNA tests for pyramiding favorable alleles and selection of superior apple cultivars with resistance to fire blight.
基金This work was funded by USDA’s National Institute of Food and Agriculture-Specialty Crop Research Initiative project,‘RosBREED:Enabling Marker-Assisted Breeding in Rosaceae’(2009-51181-05808)‘Tree Fruit GDR:Translating Genomics into Advances in Horticulture’(2009-51181-06036)+2 种基金‘RosBREED:Combining Disease Resistance and Horticultural Quality in New Rosaceous Cultivars’(2014-51181-22378)‘GDR:Empowering Specialty Crop Research through Big-Data Driven Discovery and Application in Breeding’(2014-51181-223760)USDA Hatch funds provided to the Department of Horticulture,Washington State University.
文摘Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of interest.Traditionally,genetic potential is determined by phenotypic evaluation.With the availability of DNA tests for some agronomically important traits,breeders have the opportunity to include DNA information in their seedling selection operations—known as marker-assisted seedling selection.A major challenge in deploying marker-assisted seedling selection in clonally propagated crops is a lack of knowledge in genetic gain achievable from alternative strategies.Existing models based on additive effects considering seed-propagated crops are not directly relevant for seedling selection of clonally propagated crops,as clonal propagation captures all genetic effects,not just additive.This study modeled genetic gain from traditional and various marker-based seedling selection strategies on a single trait basis through analytical derivation and stochastic simulation,based on a generalized seedling selection scheme of clonally propagated crops.Various trait-test scenarios with a range of broad-sense heritability and proportion of genotypic variance explained by DNA markers were simulated for two populations with different segregation patterns.Both derived and simulated results indicated that marker-based strategies tended to achieve higher genetic gain than phenotypic seedling selection for a trait where the proportion of genotypic variance explained by marker information was greater than the broad-sense heritability.Results from this study provides guidance in optimizing genetic gain from seedling selection for single traits where DNA tests providing marker information are available.
基金Funding for this research was in part provided by the Niedersächsisches Ministerium für Wissenschaft und Kultur through the EGON project:“Research for a sustainable agricultural production:Development of organically bred fruit cultivars in creative commons initiatives”,the USDA NIFA Specialty Crop Research Initiative projects,“RosBREED:Enabling marker-assisted breeding in Rosaceae”(2009-51181-05808)“RosBREED 2:Combining disease resistance with horticultural quality in new rosaceous cultivars”(2014-51181-22378),USDA NIFA Hatch project 1014919,and State Agricultural Experiment Station-University of Minnesota Project MIN-21-040.Part of the 20K Infinium SNP data came from the FruitBreedomics project no 265582:“Integrated approach for increasing breeding efficiency in fruit tree crops”50,which was co-funded by the EU seventh Framework Programme.
文摘Pedigree information is of fundamental importance in breeding programs and related genetics efforts.However,many individuals have unknown pedigrees.While methods to identify and confirm direct parent–offspring relationships are routine,those for other types of close relationships have yet to be effectively and widely implemented with plants,due to complications such as asexual propagation and extensive inbreeding.The objective of this study was to develop and demonstrate methods that support complex pedigree reconstruction via the total length of identical by state haplotypes(referred to in this study as“summed potential lengths of shared haplotypes”,SPLoSH).A custom Python script,HapShared,was developed to generate SPLoSH data in apple and sweet cherry.HapShared was used to establish empirical distributions of SPLoSH data for known relationships in these crops.These distributions were then used to estimate previously unknown relationships.Case studies in each crop demonstrated various pedigree reconstruction scenarios using SPLoSH data.For cherry,a full-sib relationship was deduced for‘Emperor Francis,and‘Schmidt’,a half-sib relationship for‘Van’and‘Windsor’,and the paternal grandparents of‘Stella’were confirmed.For apple,29 cultivars were found to share an unknown parent,the pedigree of the unknown parent of‘Cox’s Pomona’was reconstructed,and‘Fameuse’was deduced to be a likely grandparent of‘McIntosh’.Key genetic resources that enabled this empirical study were large genome-wide SNP array datasets,integrated genetic maps,and previously identified pedigree relationships.Crops with similar resources are also expected to benefit from using HapShared for empowering pedigree reconstruction.
基金Funding was provided from start-up and royalty funds of the Pacific Northwest Sweet Cherry Breeding Program at WSU(USDA NIFA Hatch project 1014919)partially supported by the Washington State Tree Fruit Research Commission and the Oregon Sweet Cherry Commission.WWC thanks Stijn Vanderzande for supplying part of the genotypic dataset as well as for his help and guidance in data curation.
文摘One application of DNA-informed breeding,which has potential to increase the effectiveness of traditional breeding methods,is the use of DNAbased diagnostic tests to estimate genetic potential of breeding individuals.In sweet cherry(Prunus avium L.),cracked or soft fruit are major industry challenges.Recent research detected two quantitative trait loci(QTLs)for fruit cracking and firmness differing in trait levels associated with QTL haplotypic variation.Also,a DNA test for cracking(Pav-G5Crack-SSR),using two simple sequence repeat(SSR)markers,was previously developed but not yet validated on breeding germplasm.In addition to SSR markers,single nucleotide polymorphism(SNP)markers can be used for developing locus-specific DNA tests and run as simple assays such as high-resolution melting(HRM).The objective of this research was to develop and evaluate the predictiveness of DNA tests for fruit cracking and firmness in sweet cherry.Unselected seedlings from pedigreeconnected families were screened with the Pav-G5Crack-SSR DNA test.DNA tests were also created from four SNP markers with HRM assays,using two years of cracking and firmness data for evaluation.Pav-G5Crack-SSR explained 12–15%of the cracking phenotypic variance,while Pav-G1Crack-SNP and Pav-G5Crack-SNP(which targeted the same QTL as Pav-G5Crack-SSR)together explained 16%–30%of the cracking phenotypic variance.Pav-G1Firm-SNP and Pav-G3Firm-SNP together explained 22%–28%of the firmness phenotypic variance.All three DNA tests can be implemented in breeding programs to enhance effectiveness in breeding for decreased cracking incidence and increased fruit firmness in sweet cherry.
基金the USDA NIFA Specialty Crop Research Initiative project uRosBREED 2:Combining disease resistance with horticultural quality in new rosaceous cultivars"(2014-51181-22378)National Tree Genomics Program-Phenotype Prediction(AS 17000)funded by the Hort Frontiers Advanced Production Systems Fund,part of the Hort Frontiers strategic partnership initiative developed by Hort Innovation,with co-investment from The University of Queensland,Queensland State Government,and contributions from the Australian Government is acknowledged.
文摘Only when all contribute their firewood can they build up a big fire(众人拾柴火焰高).Horticultural crops are a major source of high value nutritious food,and new improved cultivars developed through breeding are required for sustainable production in the face of abiotic and biotic stresses,and to deliver novel,premium products to consumers.However,grower confidence in the performance of new germplasm,particularly across environmental variability,is important for commercial adoption and germplasm-environ-ment matching to optimize production.
