Marker-assisted selection(MAS)is often employed in crop breeding programs to accelerate and enhance cultivar development,via selection during the juvenile phase and parental selection prior to crossing.Next-generation...Marker-assisted selection(MAS)is often employed in crop breeding programs to accelerate and enhance cultivar development,via selection during the juvenile phase and parental selection prior to crossing.Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery.To bridge the gap between marker development and MAS implementation,this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery,low-cost genotyping through amplicon sequencing(AmpSeq)and decision making.The results document the development of a MAS package derived from genotyping-by-sequencing using three traits(flower sex,disease resistance and acylated anthocyanins)in grapevine breeding.The vast majority of sequence reads(⩾99%)were from the targeted regions.Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data,most amplicons(83 to 87%)had<10%missing data,and read depth had a median of 220–244×.Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy,flexibility,speed,high-throughput,low-cost and easily automated analysis.展开更多
Powdery mildew resistance genes restrict infection attempts at different stages of pathogenesis.Here,a strong and rapid powdery mildew resistance phenotype was discovered from Vitis amurensis‘PI 588631’that rapidly ...Powdery mildew resistance genes restrict infection attempts at different stages of pathogenesis.Here,a strong and rapid powdery mildew resistance phenotype was discovered from Vitis amurensis‘PI 588631’that rapidly stopped over 97%of Erysiphe necator conidia,before or immediately after emergence of a secondary hypha from appressoria.This resistance was effective across multiple years of vineyard evaluation on leaves,stems,rachises,and fruit and against a diverse array of E.necator laboratory isolates.Using core genome rhAmpSeq markers,resistance mapped to a single dominant locus(here named REN12)on chromosome 13 near 22.8–27.0 Mb,irrespective of tissue type,explaining up to 86.9%of the phenotypic variation observed on leaves.Shotgun sequencing of recombinant vines using skim-seq technology enabled the locus to be further resolved to a 780 kb region,from 25.15 to 25.93 Mb.RNASeq analysis indicated the allele-specific expression of four resistance genes(NLRs)from the resistant parent.REN12 is one of the strongest powdery mildew resistance loci in grapevine yet documented,and the rhAmpSeq sequences presented here can be directly used for marker-assisted selection or converted to other genotyping platforms.While no virulent isolates were identified among the genetically diverse isolates and wild populations of E.necator tested here,NLR loci like REN12 are often race-specific.Thus,stacking of multiple resistance genes and minimal use of fungicides should enhance the durability of resistance and could enable a 90%reduction in fungicides in low-rainfall climates where few other pathogens attack the foliage or fruit.展开更多
The apple(Malus domestica)is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years.Here,we genetically characterise over 1000 ...The apple(Malus domestica)is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years.Here,we genetically characterise over 1000 apple accessions from the United States Department of Agriculture(USDA)germplasm collection using over 30,000 singlenucleotide polymorphisms(SNPs).We con fi rm the close genetic relationship between modern apple cultivars and their primary progenitor species,Malus sieversii from Central Asia,and fi nd that cider apples derive more of their ancestry from the European crabapple,Malus sylvestris,than do dessert apples.We determine that most of the USDA collection is a large complex pedigree:over half of the collection is interconnected by a series of fi rst-degree relationships.In addition,15%of the accessions have a fi rst-degree relationship with one of the top 8 cultivars produced in the USA.With the exception of‘Honeycrisp',the top 8 cultivars are interconnected to each other via pedigree relationships.The cultivars‘Golden Delicious'and‘Red Delicious'were found to have over 60 fi rst-degree relatives,consistent with their repeated use by apple breeders.We detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased fi rmness.Our results suggest that Americans are eating apples largely from a single family tree and that the apple's future improvement will bene fi t from increased exploitation of its tremendous natural genetic diversity.展开更多
Acidity and tannins are among the grape berry quality traits that influence wine quality.Despite advantageous environmental tolerances of Vitis aestivalis-derived‘Norton',its acidity and tannin concentrations oft...Acidity and tannins are among the grape berry quality traits that influence wine quality.Despite advantageous environmental tolerances of Vitis aestivalis-derived‘Norton',its acidity and tannin concentrations often deviate from expectations set for V.vinifera.Identification of the genetic determinants of malic acid,tartaric acid,pH,and tannin can assist in the improvement of new hybrid cultivars.For this purpose,a‘Norton'and V.vinifera‘Cabernet Sauvignon'hybrid population containing 223 individuals was used to construct a linkage map containing 384 simple sequence repeat(SSR)and 2,084 genotyping-by-sequencing(GBS)-derived single nucleotide polymorphism(SNP)markers.The resulting map was 1,441.9 cM in length with an average inter-marker distance of 0.75 cM and spanned 19 linkage groups(LGs).Quantitative trait loci(QTLs)were detected for malic acid,tartaric acid,pH,and tannin.QTLs for malic acid(LG 8)and pH(LG 6)were observed across multiple years and explained approximately 17.7%and 18.5%of the phenotypic variation,respectively.Additionally,QTLs for tartaric acid were identified on linkage groups 1,6,7,9,and 17 and tannin on LG 2 in single-year data.The QTLs for tartaric acid explained between 8.8−14.3%and tannin explained 24.7%of the phenotypic variation.The markers linked to these QTLs can be used to improve hybrid cultivar breeding through marker-assisted selection.展开更多
基金The US Department of Agriculture National Institute of Food and Agriculture Specialty Crop Research Initiative provided funding for this project(award no.2011-51181-30635).
文摘Marker-assisted selection(MAS)is often employed in crop breeding programs to accelerate and enhance cultivar development,via selection during the juvenile phase and parental selection prior to crossing.Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery.To bridge the gap between marker development and MAS implementation,this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery,low-cost genotyping through amplicon sequencing(AmpSeq)and decision making.The results document the development of a MAS package derived from genotyping-by-sequencing using three traits(flower sex,disease resistance and acylated anthocyanins)in grapevine breeding.The vast majority of sequence reads(⩾99%)were from the targeted regions.Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data,most amplicons(83 to 87%)had<10%missing data,and read depth had a median of 220–244×.Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy,flexibility,speed,high-throughput,low-cost and easily automated analysis.
文摘Powdery mildew resistance genes restrict infection attempts at different stages of pathogenesis.Here,a strong and rapid powdery mildew resistance phenotype was discovered from Vitis amurensis‘PI 588631’that rapidly stopped over 97%of Erysiphe necator conidia,before or immediately after emergence of a secondary hypha from appressoria.This resistance was effective across multiple years of vineyard evaluation on leaves,stems,rachises,and fruit and against a diverse array of E.necator laboratory isolates.Using core genome rhAmpSeq markers,resistance mapped to a single dominant locus(here named REN12)on chromosome 13 near 22.8–27.0 Mb,irrespective of tissue type,explaining up to 86.9%of the phenotypic variation observed on leaves.Shotgun sequencing of recombinant vines using skim-seq technology enabled the locus to be further resolved to a 780 kb region,from 25.15 to 25.93 Mb.RNASeq analysis indicated the allele-specific expression of four resistance genes(NLRs)from the resistant parent.REN12 is one of the strongest powdery mildew resistance loci in grapevine yet documented,and the rhAmpSeq sequences presented here can be directly used for marker-assisted selection or converted to other genotyping platforms.While no virulent isolates were identified among the genetically diverse isolates and wild populations of E.necator tested here,NLR loci like REN12 are often race-specific.Thus,stacking of multiple resistance genes and minimal use of fungicides should enhance the durability of resistance and could enable a 90%reduction in fungicides in low-rainfall climates where few other pathogens attack the foliage or fruit.
基金funding from the National Sciences and Engineering Research Council of Canada and Canada Research Chairs programme(SM).
文摘The apple(Malus domestica)is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years.Here,we genetically characterise over 1000 apple accessions from the United States Department of Agriculture(USDA)germplasm collection using over 30,000 singlenucleotide polymorphisms(SNPs).We con fi rm the close genetic relationship between modern apple cultivars and their primary progenitor species,Malus sieversii from Central Asia,and fi nd that cider apples derive more of their ancestry from the European crabapple,Malus sylvestris,than do dessert apples.We determine that most of the USDA collection is a large complex pedigree:over half of the collection is interconnected by a series of fi rst-degree relationships.In addition,15%of the accessions have a fi rst-degree relationship with one of the top 8 cultivars produced in the USA.With the exception of‘Honeycrisp',the top 8 cultivars are interconnected to each other via pedigree relationships.The cultivars‘Golden Delicious'and‘Red Delicious'were found to have over 60 fi rst-degree relatives,consistent with their repeated use by apple breeders.We detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased fi rmness.Our results suggest that Americans are eating apples largely from a single family tree and that the apple's future improvement will bene fi t from increased exploitation of its tremendous natural genetic diversity.
基金supported by Capacity Building Grants for Non-Land Grant College of Agriculture,Award No.2016-70001-24623Specialty Crop Research Initiative Competitive Grant,Award No.2017-51181-26829,from the USDA National Institute of Food and Agriculture.
文摘Acidity and tannins are among the grape berry quality traits that influence wine quality.Despite advantageous environmental tolerances of Vitis aestivalis-derived‘Norton',its acidity and tannin concentrations often deviate from expectations set for V.vinifera.Identification of the genetic determinants of malic acid,tartaric acid,pH,and tannin can assist in the improvement of new hybrid cultivars.For this purpose,a‘Norton'and V.vinifera‘Cabernet Sauvignon'hybrid population containing 223 individuals was used to construct a linkage map containing 384 simple sequence repeat(SSR)and 2,084 genotyping-by-sequencing(GBS)-derived single nucleotide polymorphism(SNP)markers.The resulting map was 1,441.9 cM in length with an average inter-marker distance of 0.75 cM and spanned 19 linkage groups(LGs).Quantitative trait loci(QTLs)were detected for malic acid,tartaric acid,pH,and tannin.QTLs for malic acid(LG 8)and pH(LG 6)were observed across multiple years and explained approximately 17.7%and 18.5%of the phenotypic variation,respectively.Additionally,QTLs for tartaric acid were identified on linkage groups 1,6,7,9,and 17 and tannin on LG 2 in single-year data.The QTLs for tartaric acid explained between 8.8−14.3%and tannin explained 24.7%of the phenotypic variation.The markers linked to these QTLs can be used to improve hybrid cultivar breeding through marker-assisted selection.
