Black raspberry(Rubus occidentalis L.)is a niche fruit crop valued for its flavor and potential health benefits.The improvement of fruit and cane characteristics via molecular breeding technologies has been hindered b...Black raspberry(Rubus occidentalis L.)is a niche fruit crop valued for its flavor and potential health benefits.The improvement of fruit and cane characteristics via molecular breeding technologies has been hindered by the lack of a high-quality reference genome.The recently released draft genome for black raspberry(ORUS 4115-3)lacks assembly of scaffolds to chromosome scale.We used high-throughput chromatin conformation capture(Hi-C)and Proximity-Guided Assembly(PGA)to cluster and order 9650 out of 11,936 contigs of this draft genome assembly into seven pseudo-chromosomes.The seven pseudo-chromosomes cover~97.2%of the total contig length(~223.8 Mb).Locating existing genetic markers on the physical map resolved multiple discrepancies in marker order on the genetic map.Centromeric regions were inferred from recombination frequencies of genetic markers,alignment of 303 bp centromeric sequence with the PGA,and heat map showing the physical contact matrix over the entire genome.We demonstrate a high degree of synteny between each of the seven chromosomes of black raspberry and a high-quality reference genome for strawberry(Fragaria vesca L.)assembled using only PacBio long-read sequences.We conclude that PGA is a cost-effective and rapid method of generating chromosome-scale assemblies from Illumina short-read sequencing data.展开更多
The cultivated strawberry(Fragaria×ananassa)is an allo-octoploid species,originating nearly 300 years ago from wild progenitors from the Americas.Since that time the strawberry has become the most widely cultivat...The cultivated strawberry(Fragaria×ananassa)is an allo-octoploid species,originating nearly 300 years ago from wild progenitors from the Americas.Since that time the strawberry has become the most widely cultivated fruit crop in the world,universally appealing due to its sensory qualities and health benefits.The recent publication of the first highquality chromosome-scale octoploid strawberry genome(cv.Camarosa)is enabling rapid advances in genetics,stimulating scientific debate and provoking new research questions.In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture.Among these are the origins of the genome,characterization of genetic variants,and big data approaches to breeding.Key areas of research in molecular biology will include the control of flowering,fruit development,fruit quality,and plant–pathogen interactions.In order to realize this potential as a global community,investments in genome resources must be continually augmented.展开更多
The molecular mechanism underlying dormancy release and the induction of flowering remains poorly understood in woody plants.Mu-legacy is a valuable blueberry mutant,in which a transgene insertion caused increased exp...The molecular mechanism underlying dormancy release and the induction of flowering remains poorly understood in woody plants.Mu-legacy is a valuable blueberry mutant,in which a transgene insertion caused increased expression of a RESPONSE REGULATOR 2-like gene(VcRR2).Mu-legacy plants,compared with nontransgenic‘Legacy’plants,show dwarfing,promotion of flower bud formation,and can flower under nonchilling conditions.We conducted transcriptomic comparisons in leaves,chilled and nonchilled flowering buds,and late-pink buds,and analyzed a total of 41 metabolites of six groups of hormones in leaf tissues of both Mu-legacy and‘Legacy’plants.These analyses uncovered that increased VcRR2 expression promotes the expression of a homolog of Arabidopsis thaliana ENTCOPALYL DIPHOSPHATE SYNTHETASE 1(VcGA1),which induces new homeostasis of hormones,including increased gibberellin 4(GA4)levels in Mu-legacy leaves.Consequently,increased expression of VcRR2 and VcGA1,which function in cytokinin responses and gibberellin synthesis,respectively,initiated the reduction in plant height and the enhancement of flower bud formation of the Mu-legacy plants through interactions of multiple approaches.In nonchilled flower buds,29 differentially expressed transcripts of 17 genes of five groups of hormones were identified in transcriptome comparisons between Mu-legacy and‘Legacy’plants,of which 22 were chilling responsive.Thus,these analyses suggest that increased expression of VcRR2 was collectively responsible for promoting flower bud formation in highbush blueberry under nonchilling conditions.We report here for the first time the importance of VcRR2 to induce a suite of downstream hormones that promote flowering in woody plants.展开更多
Anthracnose fruit rot(AFR),caused by the fungal pathogen Colletotrichum fioriniae,is among the most destructive and widespread fruit disease of blueberry,impacting both yield and overall fruit quality.Blueberry cultiv...Anthracnose fruit rot(AFR),caused by the fungal pathogen Colletotrichum fioriniae,is among the most destructive and widespread fruit disease of blueberry,impacting both yield and overall fruit quality.Blueberry cultivars have highly variable resistance against AFR.To date,this pathogen is largely controlled by applying various fungicides;thus,a more cost-effective and environmentally conscious solution for AFR is needed.Here we report three quantitative trait loci associated with AFR resistance in northern highbush blueberry(Vaccinium corymbosum).Candidate genes within these genomic regions are associated with the biosynthesis of flavonoids(e.g.anthocyanins)and resistance against pathogens.Furthermore,we examined gene expression changes in fruits following inoculation with Colletotrichum in a resistant cultivar,which revealed an enrichment of significantly differentially expressed genes associated with certain specialized metabolic pathways(e.g.flavonol biosynthesis)and pathogen resistance.Using non-targeted metabolite profiling,we identified a flavonol glycoside with properties consistent with a quercetin rhamnoside as a compound exhibiting significant abundance differences among the most resistant and susceptible individuals from the genetic mapping population.Further analysis revealed that this compound exhibits significant abundance differences among the most resistant and susceptible individuals when analyzed as two groups.However,individuals within each group displayed considerable overlapping variation in this compound,suggesting that its abundance may only be partially associated with resistance against C.fioriniae.These findings should serve as a powerful resource that will enable breeding programs to more easily develop new cultivars with superior resistance to AFR and as the basis of future research studies.展开更多
Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s,respectively,and in part owing to their f lavors and health-promoting benefits are now cultivated and consumed worldwide...Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s,respectively,and in part owing to their f lavors and health-promoting benefits are now cultivated and consumed worldwide.The industry continues to face a wide variety of production challenges(e.g.disease pressures),as well as a demand for higher-yielding cultivars with improved fruit quality characteristics.Unfortunately,molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops.Here,we describe the construction and analysis of the first pangenome for both blueberry and cranberry.Our analysis of these pangenomes revealed both crops exhibit great genetic diversity,including the presence-absence variation of 48.4%genes in highbush blueberry and 47.0%genes in cranberry.Auxiliary genes,those not shared by all cultivars,are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites,including compounds previously associated with improving fruit quality traits.The discovery of thousands of genes,not present in the previous reference genomes for blueberry and cranberry,will serve as the basis of future research and as potential targets for future breeding efforts.The pangenome,as a multiple-sequence alignment,as well as individual annotated genomes,are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational database.Lastly,the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.展开更多
The assembly of chromosome-scale and haplotype-resolved reference genomes is now more easily attainable,largely due to various improvements in both assembly algorithms and long-read sequencing technologies(see recent ...The assembly of chromosome-scale and haplotype-resolved reference genomes is now more easily attainable,largely due to various improvements in both assembly algorithms and long-read sequencing technologies(see recent review by Michael and VanBuren,2020).Due to these technological advancements,there has been a shift away from using highly inbred accessions,in some instances double haploids,to instead assembling the genomes of important reference genotypes.For example,a haplotype-resolved genome was recently assembled for an important cultivated garden strawberry(Fragaria x ananassa)cultivar Royal Royce.展开更多
文摘Black raspberry(Rubus occidentalis L.)is a niche fruit crop valued for its flavor and potential health benefits.The improvement of fruit and cane characteristics via molecular breeding technologies has been hindered by the lack of a high-quality reference genome.The recently released draft genome for black raspberry(ORUS 4115-3)lacks assembly of scaffolds to chromosome scale.We used high-throughput chromatin conformation capture(Hi-C)and Proximity-Guided Assembly(PGA)to cluster and order 9650 out of 11,936 contigs of this draft genome assembly into seven pseudo-chromosomes.The seven pseudo-chromosomes cover~97.2%of the total contig length(~223.8 Mb).Locating existing genetic markers on the physical map resolved multiple discrepancies in marker order on the genetic map.Centromeric regions were inferred from recombination frequencies of genetic markers,alignment of 303 bp centromeric sequence with the PGA,and heat map showing the physical contact matrix over the entire genome.We demonstrate a high degree of synteny between each of the seven chromosomes of black raspberry and a high-quality reference genome for strawberry(Fragaria vesca L.)assembled using only PacBio long-read sequences.We conclude that PGA is a cost-effective and rapid method of generating chromosome-scale assemblies from Illumina short-read sequencing data.
基金funding from USDA National Institute of Food and Agriculture Specialty Crop Research Initiative projects[2014-51181-22376,2014-51181-22378]USDA National Institute of Food and Agriculture National Research Support Project 10+1 种基金NSF Plant Genome Research Program award#444573,NSF CIF21 Data infrastructure Building Blocks award#1443040USDA Hatch project 1014919,California Strawberry Commission,Florida Strawberry Growers Association,Washington Tree Fruit Research Commission,and Washington State University.
文摘The cultivated strawberry(Fragaria×ananassa)is an allo-octoploid species,originating nearly 300 years ago from wild progenitors from the Americas.Since that time the strawberry has become the most widely cultivated fruit crop in the world,universally appealing due to its sensory qualities and health benefits.The recent publication of the first highquality chromosome-scale octoploid strawberry genome(cv.Camarosa)is enabling rapid advances in genetics,stimulating scientific debate and provoking new research questions.In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture.Among these are the origins of the genome,characterization of genetic variants,and big data approaches to breeding.Key areas of research in molecular biology will include the control of flowering,fruit development,fruit quality,and plant–pathogen interactions.In order to realize this potential as a global community,investments in genome resources must be continually augmented.
基金supported by AgBioResearch of Michigan State University(http://www.canr.msu.edu/research/agbioresearch/)and USDA-NIFA AFRI 1015241 to P.P.E.and G.S.
文摘The molecular mechanism underlying dormancy release and the induction of flowering remains poorly understood in woody plants.Mu-legacy is a valuable blueberry mutant,in which a transgene insertion caused increased expression of a RESPONSE REGULATOR 2-like gene(VcRR2).Mu-legacy plants,compared with nontransgenic‘Legacy’plants,show dwarfing,promotion of flower bud formation,and can flower under nonchilling conditions.We conducted transcriptomic comparisons in leaves,chilled and nonchilled flowering buds,and late-pink buds,and analyzed a total of 41 metabolites of six groups of hormones in leaf tissues of both Mu-legacy and‘Legacy’plants.These analyses uncovered that increased VcRR2 expression promotes the expression of a homolog of Arabidopsis thaliana ENTCOPALYL DIPHOSPHATE SYNTHETASE 1(VcGA1),which induces new homeostasis of hormones,including increased gibberellin 4(GA4)levels in Mu-legacy leaves.Consequently,increased expression of VcRR2 and VcGA1,which function in cytokinin responses and gibberellin synthesis,respectively,initiated the reduction in plant height and the enhancement of flower bud formation of the Mu-legacy plants through interactions of multiple approaches.In nonchilled flower buds,29 differentially expressed transcripts of 17 genes of five groups of hormones were identified in transcriptome comparisons between Mu-legacy and‘Legacy’plants,of which 22 were chilling responsive.Thus,these analyses suggest that increased expression of VcRR2 was collectively responsible for promoting flower bud formation in highbush blueberry under nonchilling conditions.We report here for the first time the importance of VcRR2 to induce a suite of downstream hormones that promote flowering in woody plants.
基金This work was supported by United States Department of Agriculture-Agriculture and Food Research Initiative(USDA-AFRI)#2018-67013-27592 to G.S.,T.M.and P.P.E.United States Department of Agriculture-Specialty Crop Research Initiative(USDASCRI)#2019-51181-30015 to P.P.E.+2 种基金National Institute of Health(NIH)Training Grant#T32-GM110523National Science Foundation(NSF)Training Grant DGE-1828149 to M.J.and P.P.EThis work was also supported by Michigan State University AgBioRe search and United States Department of Agriculture-HATCH MICL02742 to P.P.E.
文摘Anthracnose fruit rot(AFR),caused by the fungal pathogen Colletotrichum fioriniae,is among the most destructive and widespread fruit disease of blueberry,impacting both yield and overall fruit quality.Blueberry cultivars have highly variable resistance against AFR.To date,this pathogen is largely controlled by applying various fungicides;thus,a more cost-effective and environmentally conscious solution for AFR is needed.Here we report three quantitative trait loci associated with AFR resistance in northern highbush blueberry(Vaccinium corymbosum).Candidate genes within these genomic regions are associated with the biosynthesis of flavonoids(e.g.anthocyanins)and resistance against pathogens.Furthermore,we examined gene expression changes in fruits following inoculation with Colletotrichum in a resistant cultivar,which revealed an enrichment of significantly differentially expressed genes associated with certain specialized metabolic pathways(e.g.flavonol biosynthesis)and pathogen resistance.Using non-targeted metabolite profiling,we identified a flavonol glycoside with properties consistent with a quercetin rhamnoside as a compound exhibiting significant abundance differences among the most resistant and susceptible individuals from the genetic mapping population.Further analysis revealed that this compound exhibits significant abundance differences among the most resistant and susceptible individuals when analyzed as two groups.However,individuals within each group displayed considerable overlapping variation in this compound,suggesting that its abundance may only be partially associated with resistance against C.fioriniae.These findings should serve as a powerful resource that will enable breeding programs to more easily develop new cultivars with superior resistance to AFR and as the basis of future research studies.
基金supported by Michigan State University AgBioResearch,Michigan State University Institute for Cyber-Enabled Research,NIH 5T32GM110523-10,NSF NRT-HDR 1828149 USDANIFA HATCH MICL02742,USDA-NIFA AFRI 1015241,and USDANIFA SCRI award 2019-51181-30015supported in part by the National Science Foundation Research Traineeship Program(DGE-1828149)to M.J.
文摘Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s,respectively,and in part owing to their f lavors and health-promoting benefits are now cultivated and consumed worldwide.The industry continues to face a wide variety of production challenges(e.g.disease pressures),as well as a demand for higher-yielding cultivars with improved fruit quality characteristics.Unfortunately,molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops.Here,we describe the construction and analysis of the first pangenome for both blueberry and cranberry.Our analysis of these pangenomes revealed both crops exhibit great genetic diversity,including the presence-absence variation of 48.4%genes in highbush blueberry and 47.0%genes in cranberry.Auxiliary genes,those not shared by all cultivars,are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites,including compounds previously associated with improving fruit quality traits.The discovery of thousands of genes,not present in the previous reference genomes for blueberry and cranberry,will serve as the basis of future research and as potential targets for future breeding efforts.The pangenome,as a multiple-sequence alignment,as well as individual annotated genomes,are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational database.Lastly,the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.
基金This work was supported by Michigan State University AgBioResearch,USDA-HATCH 1009804,USDA-AFRI 2019-51181-30015,and NSF-PGRP 2029959.
文摘The assembly of chromosome-scale and haplotype-resolved reference genomes is now more easily attainable,largely due to various improvements in both assembly algorithms and long-read sequencing technologies(see recent review by Michael and VanBuren,2020).Due to these technological advancements,there has been a shift away from using highly inbred accessions,in some instances double haploids,to instead assembling the genomes of important reference genotypes.For example,a haplotype-resolved genome was recently assembled for an important cultivated garden strawberry(Fragaria x ananassa)cultivar Royal Royce.
