[Objective] This study was to investigate the in vitro culture of unfertilized ovary of strawberry.[Methods] Employing single factor experiment,we investigated six key factors including genotype,extrinsic hormone,sucr...[Objective] This study was to investigate the in vitro culture of unfertilized ovary of strawberry.[Methods] Employing single factor experiment,we investigated six key factors including genotype,extrinsic hormone,sucrose concentration,low temperature pretreatment,growth environment and development status,and illumination condition on induction of gynogenesis in vitro of unfertilized ovary,on the induction of gynogenesis in vitro of unfertilized ovary.[Results] The optimal conditions for in vitro culture of unfertilized ovary of strawberry were as follows：the primary flower buds cultured on bare land as explants,selection of appropriate genotype,2,4-D as external hormone,sucrose at the concentration of 6%,low temperature pretreatment for 48 hours and dark culture under alternated temperature.[Conclusion] The research provided reference for ploidy breeding in strawberry.展开更多
Cultivated strawberry(Fragaria×ananassa)originated from four diploid ancestors:F.vesca,F.viridis,F.iinumae and F.nipponica.Among them,F.vesca is the dominant subgenome for cultivated strawberry.It is not well und...Cultivated strawberry(Fragaria×ananassa)originated from four diploid ancestors:F.vesca,F.viridis,F.iinumae and F.nipponica.Among them,F.vesca is the dominant subgenome for cultivated strawberry.It is not well understood how differences in gene expression between diploid and octoploid strawberry contribute to differences during fruit development.In this study,we used comprehensive transcriptomic analyses of F.vesca and F.×ananassa to investigate gene expression at the different stages of fruit development.In total,we obtained 3508(turning stage)and 3958(red stage)differentially expressed genes with pairwise comparisons between diploid and octoploid.The genes involved in flavonoid biosynthesis were almost upregulated in the turning stages of octoploid,and we also discovered a ripe fruit-specific module associated with several flavonoid biosynthetic genes,including FveMYB10,FveMYB9/11,and Fve RAP,using weighted gene coexpression network analysis(WGCNA).Furthermore,we identified the species-specific regulated networks in the octoploid and diploid fruit.Notably,we found that the WAK and F-box genes were enriched in the octoploid and diploid fruits,respectively.This study elucidates new findings on flavonoid biosynthesis and fruit size of strawberry with important implications for future molecular breeding in cultivated strawberry.展开更多
Auxin signaling plays a significant role in the whole process of plant growth and development from embryogenesis to senescence.Auxin response factors(ARFs) are reported to regulate the expression of auxin response gen...Auxin signaling plays a significant role in the whole process of plant growth and development from embryogenesis to senescence.Auxin response factors(ARFs) are reported to regulate the expression of auxin response genes by binding to auxin response elements.ARF is the most critical transcription factor family which has been released in most species,but few reports in strawberry.In this study,the structure characterization of 12 FvARF genes in strawberry,their expression patterns at different development stages,different organizations,and different indole-3-acetic acid(IAA) treatments were analyzed.The expression of 12 FvARFs was found in all experiment tissues and showed almost the same trend during fruit development.All FvARFs respond to the treatment of IAA.Our study provides comprehensive information on ARF family in strawberry,including gene structures,chromosome locations,phylogenetic relationships and expression patterns.The information on FvARF genes paves the way for future research on strawberry ARF genes.展开更多
Fragaria vesca,commonly known as wild or woodland strawberry,is the most widely distributed diploid Fragaria species and is native to Europe and Asia.Because of its small plant size,low heterozygosity,and relative eas...Fragaria vesca,commonly known as wild or woodland strawberry,is the most widely distributed diploid Fragaria species and is native to Europe and Asia.Because of its small plant size,low heterozygosity,and relative ease of genetic transformation,F.vesca has been a model plant for fruit research since the publication of its Illumina-based genome in 2011.However,its genomic contribution to octoploid cultivated strawberry remains a long-standing question.Here,we de novo assembled and annotated a telomere-to-telomere,gap-free genome of F.vesca‘Hawaii 4’,with all seven chromosomes assembled into single contigs,providing the highest completeness and assembly quality to date.The gap-free genome is 220785082 bp in length and encodes 36173 protein-coding gene models,including 1153 newly annotated genes.All 14 telomeres and seven centromeres were annotated within the seven chromosomes.Among the three previously recognized wild diploid strawberry ancestors,F.vesca,F.iinumae,and F.viridis,phylogenomic analysis showed that F.vesca and F.viridis are the ancestors of the cultivated octoploid strawberry F.×ananassa,and F.vesca is its closest relative.Three subgenomes of F.×ananassa belong to the F.vesca group,and one is sister to F.viridis.We anticipate that this high-quality,telomere-to-telomere,gap-free F.vesca genome,combined with our phylogenomic inference of the origin of cultivated strawberry,will provide insight into the genomic evolution of Fragaria and facilitate strawberry genetics and molecular breeding.展开更多
The cultivated strawberry(Fragaria×ananassa)is consumed worldwide for its flavor and nutritional benefits.Genetic analysis of commercially important traits in strawberry are important for the development of breed...The cultivated strawberry(Fragaria×ananassa)is consumed worldwide for its flavor and nutritional benefits.Genetic analysis of commercially important traits in strawberry are important for the development of breeding methods and tools for this species.Although several quantitative trait loci(QTL)have been previously detected for fruit quality and flowering traits using low-density genetic maps,clarity on the sub-genomic locations of these QTLs was missing.Recent discoveries in allo-octoploid strawberry genomics led to the development of the IStraw90 single-nucleotide polymorphism(SNP)array,enabling high-density genetic maps and finer resolution QTL analysis.In this study,breeder-specified traits were evaluated in the Eastern(Michigan)and Western(Oregon)United States for a common set of breeding populations during 2 years.Several QTLs were validated for soluble solids content(SSC),fruit weight(FWT),pH and titratable acidity(TA)using a pedigree-based QTL analysis approach.For fruit quality,a QTL for SSC on linkage group(LG)6A,a QTL for FWT on LG 2BII,a QTL for pH on LG 4CII and two QTLs for TA on LGs 2A and 5B were detected.In addition,a large-effect QTL for flowering was detected at the distal end of LG 4A,coinciding with the FaPFRU locus.Marker haplotype analysis in the FaPFRU region indicated that the homozygous recessive genotype was highly predictive of seasonal flowering.SNP probes in the FaPFRU region may help facilitate marker-assisted selection for this trait.展开更多
The diploid strawberry Fragaria vesca serves as an ideal model plant for cultivated strawberry(Fragaria×ananassa,8x)and the Rosaceae family.The F.vesca genome was initially published in 2011 using older technolog...The diploid strawberry Fragaria vesca serves as an ideal model plant for cultivated strawberry(Fragaria×ananassa,8x)and the Rosaceae family.The F.vesca genome was initially published in 2011 using older technologies.Recently,a new and greatly improved F.vesca genome,designated V4,was published.However,the number of annotated genes is remarkably reduced in V4(28,588 genes)compared to the prior annotations(32,831 to 33,673 genes).Additionally,the annotation of V4(v4.0.a1)implements a new nomenclature for gene IDs(FvH4_XgXXXXX),rather than the previous nomenclature(geneXXXXX).Hence,further improvement of the V4 genome annotation and assigning gene expression levels under the new gene IDs with existing transcriptome data are necessary to facilitate the utility of this high-quality F.vesca genome V4.Here,we built a new and improved annotation,v4.0.a2,for F.vesca genome V4.The new annotation has a total of 34,007 gene models with 98.1%complete Benchmarking Universal Single-Copy Orthologs(BUSCOs).In this v4.0.a2 annotation,gene models of 8,342 existing genes are modified,9,029 new genes are added,and 10,176 genes possess alternatively spliced isoforms with an average of 1.90 transcripts per locus.Transcription factors/regulators and protein kinases are globally identified.Interestingly,the transcription factor family FAr-red-impaired Response 1(FAR1)contains 82 genes in v4.0.a2 but only two members in v4.0.a1.Additionally,the expression levels of all genes in the new annotation across a total of 46 different tissues and stages are provided.Finally,miRNAs and their targets are reanalyzed and presented.Altogether,this work provides an updated genome annotation of the F.vesca V4 genome as well as a comprehensive gene expression atlas with the new gene ID nomenclature,which will greatly facilitate gene functional studies in strawberry and other evolutionarily related plant species.展开更多
Based on the recently published whole-genome sequence of cultivated strawberry ’Camarosa’, in this study, 222FaWRKY genes were identified in the ’Camarosa’ genome. Phylogenetic analysis showed that the 222 FaWRKY ...Based on the recently published whole-genome sequence of cultivated strawberry ’Camarosa’, in this study, 222FaWRKY genes were identified in the ’Camarosa’ genome. Phylogenetic analysis showed that the 222 FaWRKY candidate genes were classified into three groups, of which 41 were in group Ⅰ, 142 were in group Ⅱ, and 39 were in group Ⅲ. The 222 FaWRKY genes were evenly distributed among the seven chromosomes. The exon–intron structures and motifs of the WRKY genes had evolutionary diversity in different cultivated strawberry genomes. Regarding differential expression, the expression of FaWRKY133 was relatively high in leaves, while FaWRKY63 was specifically expressed in roots. FaWRKY207, 59, 46, 182, 156, 58, 39, 62 and 115 were up-regulated during achene development from the green to red fruit transition. FaWRK181, 166 and 211 were highly expressed in receptacles at the ripe fruit stage. One interesting finding was that Fa WRKY179 and 205 were significantly repressed after Colletotrichum fructicola inoculation in both ’Benihoppe’ and ’Sweet Charlie’ compared with Mock. The data reported here provide a foundation for further comparative genomics and analyses of the distinct expression patterns of FaWRKY genes in various tissues and in response to C. fructicola inoculation.展开更多
Since the publication of this article,the authors have noticed that the GeneIDs from new and original genome annotations don’t match in Table S6,the correct Table S6 is given here.The authors would like to apologize ...Since the publication of this article,the authors have noticed that the GeneIDs from new and original genome annotations don’t match in Table S6,the correct Table S6 is given here.The authors would like to apologize for this error.展开更多
A biparental cross of octoploid strawberry segregating for resistance to Verticillium dahliae,the causative agent of Verticillium wilt,was screened under field conditions for three seasons.Average wilt scores were sig...A biparental cross of octoploid strawberry segregating for resistance to Verticillium dahliae,the causative agent of Verticillium wilt,was screened under field conditions for three seasons.Average wilt scores were significantly associated with multiple QTL,which were mostly significant across all years.Markers significantly associated with the traits were used to screen material with known wilt resistance and susceptibility phenotypes.A clear and statistically significant relationship was observed between resistant,tolerant and susceptible material and the total number of markers present in the different resistance classes.In field situations resistance QTL appear to behave in an additive manner.These markers are abundant in the cultivated strawberry germplasm indicating that,despite the large number of markers,clear genetic gain is possible through marker-assisted breeding.展开更多
Strawberry(Fragaria spp.)is a member of the Rosoideae subfamily in the family Rosaceae.The self-incompatibility(SI)of some diploid species is a key agronomic trait that acts as a basic pollination barrier;however,the ...Strawberry(Fragaria spp.)is a member of the Rosoideae subfamily in the family Rosaceae.The self-incompatibility(SI)of some diploid species is a key agronomic trait that acts as a basic pollination barrier;however,the genetic mechanism underlying SI control in strawberry remains unclear.Two candidate S-RNases(S a-and S^-RNase)identi fi ed in the transcriptome of the styles of the self-incompatible Fragaria viridis 42 were con fi rmed to be SI determinants at the S locus following genotype identi fi cation and intraspeci fi c hybridization using sel fi ng progenies.Whole-genome collinearity and RNase T2 family analysis revealed that only an S locus exists in Fragaria;however,none of the compatible species contained S-RNase.Although the results of interspeci fi c hybridization experiments showed that F.viridis(SI)styles could accept pollen from F.mandshurica(self-compatible),the reciprocal cross was incompatible.S a and S b-RNase contain large introns,and their noncoding sequences(promotors and introns)can be transcribed into long noncoding RNAs(lncRNAs).Overall,the genus Fragaria exhibits S-RNase-based gametophytic SI,and S-RNase loss occurs at the S locus of compatible germplasms.In addition,a type of SI-independent unilateral incompatibility exists between compatible and incompatible Fragaria species.Furthermore,the large introns and neighboring lncRNAs in S-RNase in Fragaria could offer clues about S-RNase expression strategies.展开更多
Flowering time is an important trait that affects survival,reproduction and yield in both wild and cultivated plants.Therefore,many studies have focused on the identification of flowering time quantitative trait locus...Flowering time is an important trait that affects survival,reproduction and yield in both wild and cultivated plants.Therefore,many studies have focused on the identification of flowering time quantitative trait locus(QTLs)in different crops,and molecular control of this trait has been extensively investigated in model species.Here we report the mapping of QTLs for flowering time and vegetative traits in a large woodland strawberry mapping population that was phenotyped both under field conditions and in a greenhouse after flower induction in the field.The greenhouse experiment revealed additive QTLs in three linkage groups(LG),two on both LG4 and LG7,and one on LG6 that explain about half of the flowering time variance in the population.Three of the QTLs were newly identified in this study,and one co-localized with the previously characterized FvTFL1 gene.An additional strong QTL corresponding to previously mapped PFRU was detected in both field and greenhouse experiments indicating that gene(s)in this locus can control the timing of flowering in different environments in addition to the duration of flowering and axillary bud differentiation to runners and branch crowns.Several putative flowering time genes were identified in these QTL regions that await functional validation.Our results indicate that a few major QTLs may control flowering time and axillary bud differentiation in strawberries.We suggest that the identification of causal genes in the diploid strawberry may enable fine tuning of flowering time and vegetative growth in the closely related octoploid cultivated strawberry.展开更多
Apple latent spherical virus(ALSV)vector is a convenient alternative to genetic transformation in horticultural plants,especially in species recalcitrant to genetic transformation.ALSV,an RNA virus,can infect a wide v...Apple latent spherical virus(ALSV)vector is a convenient alternative to genetic transformation in horticultural plants,especially in species recalcitrant to genetic transformation.ALSV,an RNA virus,can infect a wide variety of plant species including major horticultural plants without inducing symptoms.Here,methodologies were developed for infection of ALSV vectors to strawberry seedlings and plantlets cultured in vitro.A seed-propagated F1 hybrid strawberry cultivar'Yotsuboshi'was aseptically grown on half-strength Murashige–Skoog medium for 1 month and true leaves were inoculated with an ALSV RNA preparation by particle bombardment.ALSV vector infection rates varied from 58 to 100%according to the insertion sequences,in‘Yotsuboshi’seedlings.Plantlets(‘Dover’)propagated in vitro could also be infected with ALSV vector at a similar infection rate.For virus-induced gene silencing(VIGS),we prepared an ALSV vector carrying a 201 nucleotide segment of the strawberry phytoene desaturase gene.‘Yotsuboshi’and‘Dover’plants infected by this vector generated completely white leaves at fifth or sixth true leaves and above.For virus-induced flowering(VIF),we used an ALSV vector expressing the Arabidopsis thaliana flowering locus T gene.Strawberry seedlings infected by this vector started to flower from about 2 months post inoculation and bore fruits with viable seeds.The ALSV vector was no longer detected in any of the seedlings from early-flowered strawberries.Thus,the ALSV vector may be beneficial for examination of gene functions by VIGS in strawberry,and VIF using ALSV vector constitutes an effective new plant breeding technique for the promotion of cross-breeding in strawberry.展开更多
Powdery mildew(PM)caused by Podosphaera aphanis is a major fungal disease of cultivated strawberry.Mildew Resistance Locus O(MLO)is a gene family described for having conserved seven-transmembrane domains.Induced loss...Powdery mildew(PM)caused by Podosphaera aphanis is a major fungal disease of cultivated strawberry.Mildew Resistance Locus O(MLO)is a gene family described for having conserved seven-transmembrane domains.Induced loss-of-function in specific MLO genes can confer durable and broad resistance against PM pathogens.However,the genomic structure and potential role of MLO genes for PM resistance have not been characterized yet in the octoploid cultivated strawberry.In the present study,MLO gene families were characterized in four diploid progenitor species(Fragaria vesca,F.iinumae,F.viridis,and F.nipponica)and octoploid cultivated(Fragaria×ananassa)strawberry,and potential sources of MLO-mediated susceptibility were identified.Twenty MLO sequences were identified in F.vesca and 68 identified in F.×ananassa.Phylogenetic analysis divided diploid and octoploid strawberry MLO genes into eight different clades,in which three FveMLO(MLO10,MLO17,and MLO20)and their twelve orthologs of FaMLO were grouped together with functionally characterized MLO genes conferring PM susceptibility.Copy number variations revealed differences in MLO composition among homoeologous chromosomes,supporting the distinct origin of each subgenome during the evolution of octoploid strawberry.Dissecting genomic sequence and structural variations in candidate FaMLO genes revealed their potential role associated with genetic controls and functionality in strawberry against PM pathogen.Furthermore,the gene expression profiling and RNAi silencing of putative FaMLO genes in response to the pathogen indicate the function in PM resistance.These results are a critical first step in understanding the function of strawberry MLO genes and will facilitate further genetic studies of PM resistance in cultivated strawberry.展开更多
基金Supported by Program from Beijing Municipal Science & Technology Commission (Z080005032508017)~~
文摘[Objective] This study was to investigate the in vitro culture of unfertilized ovary of strawberry.[Methods] Employing single factor experiment,we investigated six key factors including genotype,extrinsic hormone,sucrose concentration,low temperature pretreatment,growth environment and development status,and illumination condition on induction of gynogenesis in vitro of unfertilized ovary,on the induction of gynogenesis in vitro of unfertilized ovary.[Results] The optimal conditions for in vitro culture of unfertilized ovary of strawberry were as follows：the primary flower buds cultured on bare land as explants,selection of appropriate genotype,2,4-D as external hormone,sucrose at the concentration of 6%,low temperature pretreatment for 48 hours and dark culture under alternated temperature.[Conclusion] The research provided reference for ploidy breeding in strawberry.
基金the Program for High-level University Construction of the Fujian Agriculture and Forestry University,China(612014028)the Natural Science Foundation of Fujian Province,China(2018J01700)Rural Revitalization Service Team of Fujian Agriculture and Forestry University,China(11899170125)。
文摘Cultivated strawberry(Fragaria×ananassa)originated from four diploid ancestors:F.vesca,F.viridis,F.iinumae and F.nipponica.Among them,F.vesca is the dominant subgenome for cultivated strawberry.It is not well understood how differences in gene expression between diploid and octoploid strawberry contribute to differences during fruit development.In this study,we used comprehensive transcriptomic analyses of F.vesca and F.×ananassa to investigate gene expression at the different stages of fruit development.In total,we obtained 3508(turning stage)and 3958(red stage)differentially expressed genes with pairwise comparisons between diploid and octoploid.The genes involved in flavonoid biosynthesis were almost upregulated in the turning stages of octoploid,and we also discovered a ripe fruit-specific module associated with several flavonoid biosynthetic genes,including FveMYB10,FveMYB9/11,and Fve RAP,using weighted gene coexpression network analysis(WGCNA).Furthermore,we identified the species-specific regulated networks in the octoploid and diploid fruit.Notably,we found that the WAK and F-box genes were enriched in the octoploid and diploid fruits,respectively.This study elucidates new findings on flavonoid biosynthesis and fruit size of strawberry with important implications for future molecular breeding in cultivated strawberry.
基金financially supported by the National Natural Science Foundation of China(31872069)the Natural Science Foundation of Liaoning Province,China(201602659)+1 种基金the Liaoning BaiQianWan Talents Program,China(2016921067)the Program for Excellent Talents in University of Liaoning Province,China(LJQ2014069)
文摘Auxin signaling plays a significant role in the whole process of plant growth and development from embryogenesis to senescence.Auxin response factors(ARFs) are reported to regulate the expression of auxin response genes by binding to auxin response elements.ARF is the most critical transcription factor family which has been released in most species,but few reports in strawberry.In this study,the structure characterization of 12 FvARF genes in strawberry,their expression patterns at different development stages,different organizations,and different indole-3-acetic acid(IAA) treatments were analyzed.The expression of 12 FvARFs was found in all experiment tissues and showed almost the same trend during fruit development.All FvARFs respond to the treatment of IAA.Our study provides comprehensive information on ARF family in strawberry,including gene structures,chromosome locations,phylogenetic relationships and expression patterns.The information on FvARF genes paves the way for future research on strawberry ARF genes.
基金funding from the National Natural Science Foundation of China(32172614)a startup fund fromHainan University and a Hainan Province Science and Technology Special Fund(ZDYF2023XDNY050).
文摘Fragaria vesca,commonly known as wild or woodland strawberry,is the most widely distributed diploid Fragaria species and is native to Europe and Asia.Because of its small plant size,low heterozygosity,and relative ease of genetic transformation,F.vesca has been a model plant for fruit research since the publication of its Illumina-based genome in 2011.However,its genomic contribution to octoploid cultivated strawberry remains a long-standing question.Here,we de novo assembled and annotated a telomere-to-telomere,gap-free genome of F.vesca‘Hawaii 4’,with all seven chromosomes assembled into single contigs,providing the highest completeness and assembly quality to date.The gap-free genome is 220785082 bp in length and encodes 36173 protein-coding gene models,including 1153 newly annotated genes.All 14 telomeres and seven centromeres were annotated within the seven chromosomes.Among the three previously recognized wild diploid strawberry ancestors,F.vesca,F.iinumae,and F.viridis,phylogenomic analysis showed that F.vesca and F.viridis are the ancestors of the cultivated octoploid strawberry F.×ananassa,and F.vesca is its closest relative.Three subgenomes of F.×ananassa belong to the F.vesca group,and one is sister to F.viridis.We anticipate that this high-quality,telomere-to-telomere,gap-free F.vesca genome,combined with our phylogenomic inference of the origin of cultivated strawberry,will provide insight into the genomic evolution of Fragaria and facilitate strawberry genetics and molecular breeding.
基金This research was funded through the USDA’s National Institute of Food and Agriculture—Specialty Crop Research Initiative project,‘RosBREED:Enabling Marker-Assisted Breeding in Rosaceae’(2009-51181-05808)‘RosBREED:Combining Disease Resistance and Horticultural Quality in New Rosaceous Cultivars’(2014-51181-22378).
文摘The cultivated strawberry(Fragaria×ananassa)is consumed worldwide for its flavor and nutritional benefits.Genetic analysis of commercially important traits in strawberry are important for the development of breeding methods and tools for this species.Although several quantitative trait loci(QTL)have been previously detected for fruit quality and flowering traits using low-density genetic maps,clarity on the sub-genomic locations of these QTLs was missing.Recent discoveries in allo-octoploid strawberry genomics led to the development of the IStraw90 single-nucleotide polymorphism(SNP)array,enabling high-density genetic maps and finer resolution QTL analysis.In this study,breeder-specified traits were evaluated in the Eastern(Michigan)and Western(Oregon)United States for a common set of breeding populations during 2 years.Several QTLs were validated for soluble solids content(SSC),fruit weight(FWT),pH and titratable acidity(TA)using a pedigree-based QTL analysis approach.For fruit quality,a QTL for SSC on linkage group(LG)6A,a QTL for FWT on LG 2BII,a QTL for pH on LG 4CII and two QTLs for TA on LGs 2A and 5B were detected.In addition,a large-effect QTL for flowering was detected at the distal end of LG 4A,coinciding with the FaPFRU locus.Marker haplotype analysis in the FaPFRU region indicated that the homozygous recessive genotype was highly predictive of seasonal flowering.SNP probes in the FaPFRU region may help facilitate marker-assisted selection for this trait.
基金supported by the National Key Research and Development Program of China(2018YFD1000102)National Natural Science Foundation of China(31772274 and 31822044)Huazhong Agricultural University Scientific&Technological Self-innovation Foundation(2014RC005 and 2014RC017).
文摘The diploid strawberry Fragaria vesca serves as an ideal model plant for cultivated strawberry(Fragaria×ananassa,8x)and the Rosaceae family.The F.vesca genome was initially published in 2011 using older technologies.Recently,a new and greatly improved F.vesca genome,designated V4,was published.However,the number of annotated genes is remarkably reduced in V4(28,588 genes)compared to the prior annotations(32,831 to 33,673 genes).Additionally,the annotation of V4(v4.0.a1)implements a new nomenclature for gene IDs(FvH4_XgXXXXX),rather than the previous nomenclature(geneXXXXX).Hence,further improvement of the V4 genome annotation and assigning gene expression levels under the new gene IDs with existing transcriptome data are necessary to facilitate the utility of this high-quality F.vesca genome V4.Here,we built a new and improved annotation,v4.0.a2,for F.vesca genome V4.The new annotation has a total of 34,007 gene models with 98.1%complete Benchmarking Universal Single-Copy Orthologs(BUSCOs).In this v4.0.a2 annotation,gene models of 8,342 existing genes are modified,9,029 new genes are added,and 10,176 genes possess alternatively spliced isoforms with an average of 1.90 transcripts per locus.Transcription factors/regulators and protein kinases are globally identified.Interestingly,the transcription factor family FAr-red-impaired Response 1(FAR1)contains 82 genes in v4.0.a2 but only two members in v4.0.a1.Additionally,the expression levels of all genes in the new annotation across a total of 46 different tissues and stages are provided.Finally,miRNAs and their targets are reanalyzed and presented.Altogether,this work provides an updated genome annotation of the F.vesca V4 genome as well as a comprehensive gene expression atlas with the new gene ID nomenclature,which will greatly facilitate gene functional studies in strawberry and other evolutionarily related plant species.
基金supported by the National Natural Science Foundation of China (31601731)
文摘Based on the recently published whole-genome sequence of cultivated strawberry ’Camarosa’, in this study, 222FaWRKY genes were identified in the ’Camarosa’ genome. Phylogenetic analysis showed that the 222 FaWRKY candidate genes were classified into three groups, of which 41 were in group Ⅰ, 142 were in group Ⅱ, and 39 were in group Ⅲ. The 222 FaWRKY genes were evenly distributed among the seven chromosomes. The exon–intron structures and motifs of the WRKY genes had evolutionary diversity in different cultivated strawberry genomes. Regarding differential expression, the expression of FaWRKY133 was relatively high in leaves, while FaWRKY63 was specifically expressed in roots. FaWRKY207, 59, 46, 182, 156, 58, 39, 62 and 115 were up-regulated during achene development from the green to red fruit transition. FaWRK181, 166 and 211 were highly expressed in receptacles at the ripe fruit stage. One interesting finding was that Fa WRKY179 and 205 were significantly repressed after Colletotrichum fructicola inoculation in both ’Benihoppe’ and ’Sweet Charlie’ compared with Mock. The data reported here provide a foundation for further comparative genomics and analyses of the distinct expression patterns of FaWRKY genes in various tissues and in response to C. fructicola inoculation.
文摘Since the publication of this article,the authors have noticed that the GeneIDs from new and original genome annotations don’t match in Table S6,the correct Table S6 is given here.The authors would like to apologize for this error.
基金This work was funded by BBSRC grants,BB/K017071/1 and BB/E007074/1.
文摘A biparental cross of octoploid strawberry segregating for resistance to Verticillium dahliae,the causative agent of Verticillium wilt,was screened under field conditions for three seasons.Average wilt scores were significantly associated with multiple QTL,which were mostly significant across all years.Markers significantly associated with the traits were used to screen material with known wilt resistance and susceptibility phenotypes.A clear and statistically significant relationship was observed between resistant,tolerant and susceptible material and the total number of markers present in the different resistance classes.In field situations resistance QTL appear to behave in an additive manner.These markers are abundant in the cultivated strawberry germplasm indicating that,despite the large number of markers,clear genetic gain is possible through marker-assisted breeding.
基金This work was supported by the National Natural Science Foundation of Chi na(Gr ant no.32072540,31872056)the Fun dame ntal Research Fun ds for the Central Universities(Grant no.KYZZ2021002)a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD).
文摘Strawberry(Fragaria spp.)is a member of the Rosoideae subfamily in the family Rosaceae.The self-incompatibility(SI)of some diploid species is a key agronomic trait that acts as a basic pollination barrier;however,the genetic mechanism underlying SI control in strawberry remains unclear.Two candidate S-RNases(S a-and S^-RNase)identi fi ed in the transcriptome of the styles of the self-incompatible Fragaria viridis 42 were con fi rmed to be SI determinants at the S locus following genotype identi fi cation and intraspeci fi c hybridization using sel fi ng progenies.Whole-genome collinearity and RNase T2 family analysis revealed that only an S locus exists in Fragaria;however,none of the compatible species contained S-RNase.Although the results of interspeci fi c hybridization experiments showed that F.viridis(SI)styles could accept pollen from F.mandshurica(self-compatible),the reciprocal cross was incompatible.S a and S b-RNase contain large introns,and their noncoding sequences(promotors and introns)can be transcribed into long noncoding RNAs(lncRNAs).Overall,the genus Fragaria exhibits S-RNase-based gametophytic SI,and S-RNase loss occurs at the S locus of compatible germplasms.In addition,a type of SI-independent unilateral incompatibility exists between compatible and incompatible Fragaria species.Furthermore,the large introns and neighboring lncRNAs in S-RNase in Fragaria could offer clues about S-RNase expression strategies.
基金The project was funded by the Academy of Finland(Grant 278475 to TH)the University of Helsinki(Grant DW-4881545211 to TH)SS received a personal grant from the Fondazione Edmund Mach(GMPF PhD Fellowship).SS and EK belong to the Doctoral Program in Plant Sciences.
文摘Flowering time is an important trait that affects survival,reproduction and yield in both wild and cultivated plants.Therefore,many studies have focused on the identification of flowering time quantitative trait locus(QTLs)in different crops,and molecular control of this trait has been extensively investigated in model species.Here we report the mapping of QTLs for flowering time and vegetative traits in a large woodland strawberry mapping population that was phenotyped both under field conditions and in a greenhouse after flower induction in the field.The greenhouse experiment revealed additive QTLs in three linkage groups(LG),two on both LG4 and LG7,and one on LG6 that explain about half of the flowering time variance in the population.Three of the QTLs were newly identified in this study,and one co-localized with the previously characterized FvTFL1 gene.An additional strong QTL corresponding to previously mapped PFRU was detected in both field and greenhouse experiments indicating that gene(s)in this locus can control the timing of flowering in different environments in addition to the duration of flowering and axillary bud differentiation to runners and branch crowns.Several putative flowering time genes were identified in these QTL regions that await functional validation.Our results indicate that a few major QTLs may control flowering time and axillary bud differentiation in strawberries.We suggest that the identification of causal genes in the diploid strawberry may enable fine tuning of flowering time and vegetative growth in the closely related octoploid cultivated strawberry.
文摘Apple latent spherical virus(ALSV)vector is a convenient alternative to genetic transformation in horticultural plants,especially in species recalcitrant to genetic transformation.ALSV,an RNA virus,can infect a wide variety of plant species including major horticultural plants without inducing symptoms.Here,methodologies were developed for infection of ALSV vectors to strawberry seedlings and plantlets cultured in vitro.A seed-propagated F1 hybrid strawberry cultivar'Yotsuboshi'was aseptically grown on half-strength Murashige–Skoog medium for 1 month and true leaves were inoculated with an ALSV RNA preparation by particle bombardment.ALSV vector infection rates varied from 58 to 100%according to the insertion sequences,in‘Yotsuboshi’seedlings.Plantlets(‘Dover’)propagated in vitro could also be infected with ALSV vector at a similar infection rate.For virus-induced gene silencing(VIGS),we prepared an ALSV vector carrying a 201 nucleotide segment of the strawberry phytoene desaturase gene.‘Yotsuboshi’and‘Dover’plants infected by this vector generated completely white leaves at fifth or sixth true leaves and above.For virus-induced flowering(VIF),we used an ALSV vector expressing the Arabidopsis thaliana flowering locus T gene.Strawberry seedlings infected by this vector started to flower from about 2 months post inoculation and bore fruits with viable seeds.The ALSV vector was no longer detected in any of the seedlings from early-flowered strawberries.Thus,the ALSV vector may be beneficial for examination of gene functions by VIGS in strawberry,and VIF using ALSV vector constitutes an effective new plant breeding technique for the promotion of cross-breeding in strawberry.
基金This work was supported by the Florida Strawberry Research and Education Foundation(FSREF)the“Next-generation Disease Resistance Breeding and Management Solutions for Strawberry”under award no.2017-51181-26833.
文摘Powdery mildew(PM)caused by Podosphaera aphanis is a major fungal disease of cultivated strawberry.Mildew Resistance Locus O(MLO)is a gene family described for having conserved seven-transmembrane domains.Induced loss-of-function in specific MLO genes can confer durable and broad resistance against PM pathogens.However,the genomic structure and potential role of MLO genes for PM resistance have not been characterized yet in the octoploid cultivated strawberry.In the present study,MLO gene families were characterized in four diploid progenitor species(Fragaria vesca,F.iinumae,F.viridis,and F.nipponica)and octoploid cultivated(Fragaria×ananassa)strawberry,and potential sources of MLO-mediated susceptibility were identified.Twenty MLO sequences were identified in F.vesca and 68 identified in F.×ananassa.Phylogenetic analysis divided diploid and octoploid strawberry MLO genes into eight different clades,in which three FveMLO(MLO10,MLO17,and MLO20)and their twelve orthologs of FaMLO were grouped together with functionally characterized MLO genes conferring PM susceptibility.Copy number variations revealed differences in MLO composition among homoeologous chromosomes,supporting the distinct origin of each subgenome during the evolution of octoploid strawberry.Dissecting genomic sequence and structural variations in candidate FaMLO genes revealed their potential role associated with genetic controls and functionality in strawberry against PM pathogen.Furthermore,the gene expression profiling and RNAi silencing of putative FaMLO genes in response to the pathogen indicate the function in PM resistance.These results are a critical first step in understanding the function of strawberry MLO genes and will facilitate further genetic studies of PM resistance in cultivated strawberry.
