Almond[Prunus dulcis Miller(D.A.Webb)]is the main tree nut species worldwide.Here,genotyping-by-sequencing(GBS)was applied to 149 almond cultivars from the ex situ collections of the Italian Council for Agricultural R...Almond[Prunus dulcis Miller(D.A.Webb)]is the main tree nut species worldwide.Here,genotyping-by-sequencing(GBS)was applied to 149 almond cultivars from the ex situ collections of the Italian Council for Agricultural Research(CREA)and the Spanish National Research Council(CSIC),leading to the detection of 93,119 single-nucleotide polymorphisms(SNPs).The study of population structure outlined four distinct genetic groups and highlighted diversification between the Mediterranean and Californian gene pools.Data on SNP diversity and runs of homozygosity(ROHs)allowed the definition of kinship,inbreeding,and linkage disequilibrium(LD)decay in almond cultivated germplasm.Four-year phenotypic observations,gathered on 98 cultivars of the CREA collection,were used to perform a genome-wide association study(GWAS)and,for the first time in a crop species,homozygosity mapping(HM),resulting in the identification of genomic associations with nut,shell,and seed weight.Both GWAS and HM suggested that loci controlling nut and seed weight are mostly independent.Overall,this study provides insights on the almond cultivation history and delivers information of major interest for almond genetics and breeding.In a broader perspective,our results encourage the use of ROHs in crop science to estimate inbreeding,choose parental combinations minimizing the risk of inbreeding depression,and identify genomic footprints of selection for specific traits.展开更多
Bulked segregant analysis(BSA)is a widely used method for identifying genomic loci associated with traits of interest in crops.However,conventional BSA is limited by its reliance on phenotype-driven bulk sampling,whic...Bulked segregant analysis(BSA)is a widely used method for identifying genomic loci associated with traits of interest in crops.However,conventional BSA is limited by its reliance on phenotype-driven bulk sampling,which restricts its scalability and confines its applicability to single-trait analysis.This study introduces a novel method,reverse BSA-QTLseq,which uses genotype-driven bulk reconstruction through bioinformatics,enabling the simultaneous mapping of multiple traits from the same genotypic dataset.Reverse BSA-QTLseq uses a two-step strategy-low-resolution genotyping of the entire population followed by high-resolution sequencing of selected bulks-enabling cost-effective identification of genetically divergent lines to enhance the discovery of quantitative trait loci(QTLs).Using a bread wheat recombinant inbred line(RIL)population as a case study,we mapped loci associated with heading date and plant height,confirming approximately 95%of known QTLs,including both dwarfing genes(e.g.,Rht-B1 and Rht-5)and flowering-time regulators(e.g.,Vrn-A1),and identified novel QTLs and candidate loci with strong phenotypic effects.The phased genotyping strategy maximized genetic distance in the initial sampling,facilitating the in silico reconstruction of trait-specific contrasting bulks.Integration of transcriptional profiles from the parental lines of the RIL population,from which the bulks were derived,aided in identifying candidate genes and regulatory networks underlying the variation of traits such as photoperiod response,nutrient transport,and stress adaptation.The versatility and potential for data reuse offered by the proposed method represent a significant advancement in QTL mapping,with broad implications for marker-assisted breeding and selection programs.Future integration of transcriptomic and epigenomic data is expected to further enhance the power of reverse BSA-QTLseq,accelerating genetic improvement in crops.展开更多
文摘Almond[Prunus dulcis Miller(D.A.Webb)]is the main tree nut species worldwide.Here,genotyping-by-sequencing(GBS)was applied to 149 almond cultivars from the ex situ collections of the Italian Council for Agricultural Research(CREA)and the Spanish National Research Council(CSIC),leading to the detection of 93,119 single-nucleotide polymorphisms(SNPs).The study of population structure outlined four distinct genetic groups and highlighted diversification between the Mediterranean and Californian gene pools.Data on SNP diversity and runs of homozygosity(ROHs)allowed the definition of kinship,inbreeding,and linkage disequilibrium(LD)decay in almond cultivated germplasm.Four-year phenotypic observations,gathered on 98 cultivars of the CREA collection,were used to perform a genome-wide association study(GWAS)and,for the first time in a crop species,homozygosity mapping(HM),resulting in the identification of genomic associations with nut,shell,and seed weight.Both GWAS and HM suggested that loci controlling nut and seed weight are mostly independent.Overall,this study provides insights on the almond cultivation history and delivers information of major interest for almond genetics and breeding.In a broader perspective,our results encourage the use of ROHs in crop science to estimate inbreeding,choose parental combinations minimizing the risk of inbreeding depression,and identify genomic footprints of selection for specific traits.
基金supported by the Italian Ministry of Enterprises and Made in Italy-Mimit(MIMIT)in the framework of a project entitled"GRANO.IT Nr.F/360091/01-02/X75"(CUP B19J24000140005)within the Agritech National Research Center,funded by MIUR-European Union PNRR-MISSIONE 4 COMPONENTE 2,INVESTIMENTO 1.4-SPOKE 1 INVESTIMENTO 1.4(D.D.103217/06/2022,CN00000022).
文摘Bulked segregant analysis(BSA)is a widely used method for identifying genomic loci associated with traits of interest in crops.However,conventional BSA is limited by its reliance on phenotype-driven bulk sampling,which restricts its scalability and confines its applicability to single-trait analysis.This study introduces a novel method,reverse BSA-QTLseq,which uses genotype-driven bulk reconstruction through bioinformatics,enabling the simultaneous mapping of multiple traits from the same genotypic dataset.Reverse BSA-QTLseq uses a two-step strategy-low-resolution genotyping of the entire population followed by high-resolution sequencing of selected bulks-enabling cost-effective identification of genetically divergent lines to enhance the discovery of quantitative trait loci(QTLs).Using a bread wheat recombinant inbred line(RIL)population as a case study,we mapped loci associated with heading date and plant height,confirming approximately 95%of known QTLs,including both dwarfing genes(e.g.,Rht-B1 and Rht-5)and flowering-time regulators(e.g.,Vrn-A1),and identified novel QTLs and candidate loci with strong phenotypic effects.The phased genotyping strategy maximized genetic distance in the initial sampling,facilitating the in silico reconstruction of trait-specific contrasting bulks.Integration of transcriptional profiles from the parental lines of the RIL population,from which the bulks were derived,aided in identifying candidate genes and regulatory networks underlying the variation of traits such as photoperiod response,nutrient transport,and stress adaptation.The versatility and potential for data reuse offered by the proposed method represent a significant advancement in QTL mapping,with broad implications for marker-assisted breeding and selection programs.Future integration of transcriptomic and epigenomic data is expected to further enhance the power of reverse BSA-QTLseq,accelerating genetic improvement in crops.
