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
Dear Editor,Sugarcane mosaic virus （SCMV） causes severe viral diseases in maize worldwide （Fuchs and Gruntzig, 1995）, resulting in significant losses in grain and forage yield in susceptible cultivars of maize and...Dear Editor,Sugarcane mosaic virus （SCMV） causes severe viral diseases in maize worldwide （Fuchs and Gruntzig, 1995）, resulting in significant losses in grain and forage yield in susceptible cultivars of maize and related crops. The most promising solution is to cultivate resistant varieties, which contribute to sustainable crop production. Two epistatically interacting major SCMV resistance loci （Scmvl and Scmv2） are required to confer complete resistance against SCMV in the resistant nearisogenic line F7RPJRR （the letters left of the slash refer to the genotype at Scmv2 on chromosome 3 and those on the right refer to the genotype at Scmvl on chromosome 6, with R indicating a resistance allele and S a susceptibility allele） （Xing et al., 2006）.展开更多
Common buckwheat(Fagopyrum esculentum)is an ancient crop with a world-wide distribution.Due to its excellent nutritional quality and high economic and ecological value,common buckwheat is becoming increasingly importa...Common buckwheat(Fagopyrum esculentum)is an ancient crop with a world-wide distribution.Due to its excellent nutritional quality and high economic and ecological value,common buckwheat is becoming increasingly important throughout the world.The availability of a high-quality reference genome sequence and population genomic data will accelerate the breeding of common buckwheat,but the high heterozygosity due to the outcrossing nature has greatly hindered the genome assembly.Here we report the assembly of a chromosome-scale high-quality reference genome of F.esculentum var.homotropicum,a homozygous self-pollinating variant of common buckwheat.Comparative genomics revealed that two cultivated buckwheat species,common buckwheat(F.esculentum)and Tartary buckwheat(F.tataricum),underwent metabolomic divergence and ecotype differentiation.The expansion of several gene families in common buckwheat,including FhFAR genes,is associated with its wider distribution than Tartary buckwheat.Copy number variation of genes involved in the metabolism of flavonoids is associated with the difference of rutin content between common and Tartary buckwheat.Furthermore,we present a comprehensive atlas of genomic variation based on whole-genome resequencing of 572 accessions of common buckwheat.Population and evolutionary genomics reveal genetic variation associated with environmental adaptability and floral development between Chinese and non-Chinese cultivated groups.Genome-wide association analyses of multi-year agronomic traits with the content of flavonoids revealed that Fh05G014970 is a potential major regulator of flowering period,a key agronomic trait controlling the yield of outcrossing crops,and that Fh06G015130 is a crucial gene underlying flavor-associated flavonoids.Intriguingly,we found that the gene translocation and sequence variation of FhS-ELF3 contribute to the homomorphic self-compatibility of common buckwheat.Collectively,our results elucidate the genetic basis of speciation,ecological adaptation,fertility,and unique flavor of common buckwheat,and provide new resources for future genomics-assisted breeding of this economically important crop.展开更多
Accurate,high-throughput phenotyping for quantitative traits is a limiting factor for progress in plant breeding.We developed an automated image analysis to measure quantitative resistance to septoria tritici blotch(S...Accurate,high-throughput phenotyping for quantitative traits is a limiting factor for progress in plant breeding.We developed an automated image analysis to measure quantitative resistance to septoria tritici blotch(STB),a globally important wheat disease,enabling identification of small chromosome intervals containing plausible candidate genes for STB resistance.335 winter wheat cultivars were included in a replicated field experiment that experienced natural epidemic development by a highly diverse but fungicide-resistant pathogen population.More than 5.4 million automatically generated phenotypes were associated with 13,648 SNP markers to perform the GWAS.We identified 26 chromosome intervals explaining 1.9-10.6%of the variance associated with four independent resistance traits.Sixteen of the intervals overlapped with known STB resistance intervals,suggesting that our phenotyping approach can identify simultaneously(i.e.,in a single experiment)many previously defined STB resistance intervals.Seventeen of the intervals were less than 5 Mbp in size and encoded only 173 genes,including many genes associated with disease resistance.Five intervals contained four or fewer genes,providing high priority targets for functional validation.Ten chromosome intervals were not previously associated with STB resistance,perhaps representing resistance to pathogen strains that had not been tested in earlier experiments.The SNP markers associated with these chromosome intervals can be used to recombine different forms of quantitative STB resistance that are likely to be more durable than pyramids of major resistance genes.Our experiment illustrates how high-throughput automated phenotyping can accelerate breeding for quantitative disease resistance.展开更多
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Dear Editor,Sugarcane mosaic virus （SCMV） causes severe viral diseases in maize worldwide （Fuchs and Gruntzig, 1995）, resulting in significant losses in grain and forage yield in susceptible cultivars of maize and related crops. The most promising solution is to cultivate resistant varieties, which contribute to sustainable crop production. Two epistatically interacting major SCMV resistance loci （Scmvl and Scmv2） are required to confer complete resistance against SCMV in the resistant nearisogenic line F7RPJRR （the letters left of the slash refer to the genotype at Scmv2 on chromosome 3 and those on the right refer to the genotype at Scmvl on chromosome 6, with R indicating a resistance allele and S a susceptibility allele） （Xing et al., 2006）.
基金the National Key R&D Program of China(2022YFE0140800)the European Union Horizon 2020 project ECOBREED(771367)+4 种基金the Youth Innovation Program of Chinese Academy of Agricultural Sciences(No.Y2022QC02)Project of Sanya Yazhou Bay Science and Technology City(SCKJ-JYRC-2022-22)National Natural Science Foundation of China(32161143005,31911530772,32111540258)PlantaSYST(SGA No 739582 under FPA No.664620)the BG05M2OP001-1.003-001-C01 project,financed by the European Regional Development Fund through the“Science and Education for Smart Growth”Operational Programme and Slovenian Research Agency,program P4-0077“Genetics and Modern Technologies of Crops”.
文摘Common buckwheat(Fagopyrum esculentum)is an ancient crop with a world-wide distribution.Due to its excellent nutritional quality and high economic and ecological value,common buckwheat is becoming increasingly important throughout the world.The availability of a high-quality reference genome sequence and population genomic data will accelerate the breeding of common buckwheat,but the high heterozygosity due to the outcrossing nature has greatly hindered the genome assembly.Here we report the assembly of a chromosome-scale high-quality reference genome of F.esculentum var.homotropicum,a homozygous self-pollinating variant of common buckwheat.Comparative genomics revealed that two cultivated buckwheat species,common buckwheat(F.esculentum)and Tartary buckwheat(F.tataricum),underwent metabolomic divergence and ecotype differentiation.The expansion of several gene families in common buckwheat,including FhFAR genes,is associated with its wider distribution than Tartary buckwheat.Copy number variation of genes involved in the metabolism of flavonoids is associated with the difference of rutin content between common and Tartary buckwheat.Furthermore,we present a comprehensive atlas of genomic variation based on whole-genome resequencing of 572 accessions of common buckwheat.Population and evolutionary genomics reveal genetic variation associated with environmental adaptability and floral development between Chinese and non-Chinese cultivated groups.Genome-wide association analyses of multi-year agronomic traits with the content of flavonoids revealed that Fh05G014970 is a potential major regulator of flowering period,a key agronomic trait controlling the yield of outcrossing crops,and that Fh06G015130 is a crucial gene underlying flavor-associated flavonoids.Intriguingly,we found that the gene translocation and sequence variation of FhS-ELF3 contribute to the homomorphic self-compatibility of common buckwheat.Collectively,our results elucidate the genetic basis of speciation,ecological adaptation,fertility,and unique flavor of common buckwheat,and provide new resources for future genomics-assisted breeding of this economically important crop.
基金STB research in BAM's lab wassupported by the Swiss National Science Foundation(grants155955,134755,104145,and 56874)the ETH ZurichResearch Commission(grants 12-03 and 15-02)AM and PK were supported by the Swiss National Science Foundationthrough Ambizione grant PZ00P3_161453.
文摘Accurate,high-throughput phenotyping for quantitative traits is a limiting factor for progress in plant breeding.We developed an automated image analysis to measure quantitative resistance to septoria tritici blotch(STB),a globally important wheat disease,enabling identification of small chromosome intervals containing plausible candidate genes for STB resistance.335 winter wheat cultivars were included in a replicated field experiment that experienced natural epidemic development by a highly diverse but fungicide-resistant pathogen population.More than 5.4 million automatically generated phenotypes were associated with 13,648 SNP markers to perform the GWAS.We identified 26 chromosome intervals explaining 1.9-10.6%of the variance associated with four independent resistance traits.Sixteen of the intervals overlapped with known STB resistance intervals,suggesting that our phenotyping approach can identify simultaneously(i.e.,in a single experiment)many previously defined STB resistance intervals.Seventeen of the intervals were less than 5 Mbp in size and encoded only 173 genes,including many genes associated with disease resistance.Five intervals contained four or fewer genes,providing high priority targets for functional validation.Ten chromosome intervals were not previously associated with STB resistance,perhaps representing resistance to pathogen strains that had not been tested in earlier experiments.The SNP markers associated with these chromosome intervals can be used to recombine different forms of quantitative STB resistance that are likely to be more durable than pyramids of major resistance genes.Our experiment illustrates how high-throughput automated phenotyping can accelerate breeding for quantitative disease resistance.
