Bud dormancy is a complex physiological process of perennial woody plants living in temperate regions,and it can be affected by various phytohormones.Cytokinin oxidase/dehydrogenases(CKXs)are a group of enzymes essent...Bud dormancy is a complex physiological process of perennial woody plants living in temperate regions,and it can be affected by various phytohormones.Cytokinin oxidase/dehydrogenases(CKXs)are a group of enzymes essential for maintaining cytokinin homeostasis,yet a comprehensive analysis of these enzymes in peach remains lacking.Here,a total of 51 CKX members from different species,including six from peach,eleven from apple,nine from poplar,seven from Arabidopsis,eight from strawberry,and ten from rice,were identified using the Simple HMM Search tool of TBtools and a BLASTP program and classified into four groups using phylogenetic analysis.Conserved motif and gene structure analysis of these 51 CKX members showed that 10 conserved motifs were identified,and each CKX gene contained at least two introns.Cis-element analysis of PpCKXs showed that all PpCKX genes have light-responsive elements and at least one hormone-responsive element.The changed relative expression levels of six PpCKX genes in peach buds from endodormancy to bud-break were observed by qRT-PCR.Among them,the expression trend of PpCKX6 was almost opposite that of PpEBB1,a positive bud-break regulator in woody plants,around the bud-break stage.Y1H,EMSA,and dual-luciferase assays indicated that PpEBB1negatively regulated PpCKX6 through direct binding to a GCC box-like element located in the promoter region of PpCKX6.In addition,a transient assay showed that overexpression of PpCKX6 delayed the bud-break of peach.These results indicate that the PpCKX genes play an essential role in the dormancy-regrowth process,and Pp CKX6may act downstream of PpEBB1 directly to regulate the bud-break process,which further improves the hormoneregulatory network of dormancy-regrowth of woody plants,and provides new insights for molecular breeding and genetic engineering of peach.展开更多
Prunus species include many important perennial fruit crops,such as peach,plum,apricot,and related wild species.Here,we report de novo genome assemblies for five species,including the cultivated species peach(Prunus p...Prunus species include many important perennial fruit crops,such as peach,plum,apricot,and related wild species.Here,we report de novo genome assemblies for five species,including the cultivated species peach(Prunus persica),plum(Prunus salicina),and apricot(Prunus armeniaca),and the wild peach species Tibetan peach(Prunus mira)and Chinese wild peach(Prunus davidiana).The genomes ranged from 240 to 276 Mb in size,with contig N50 values of 2.27−8.30Mb and 25,333−27,826 protein-coding gene models.As the phylogenetic tree shows,plum diverged from its common ancestor with peach,wild peach species,and apricot~7 million years ago(MYA).We analyzed whole-genome resequencing data of 417 peach accessions,called 3,749,618 high-quality SNPs,577,154 small indels,31,800 deletions,duplications,and inversions,and 32,338 insertions,and performed a structural variant-based genome-wide association study(GWAS)of key agricultural traits.From our GWAS data,we identified a locus associated with a fruit shape corresponding to the OVATE transcription factor,where a large inversion event correlates with higher OVATE expression in flat-shaped accessions.Furthermore,a GWAS revealed a NAC transcription factor associated with fruit developmental timing that is linked to a tandem repeat variant and elevated NAC expression in early-ripening accessions.We also identified a locus encoding microRNA172d,where insertion of a transposable element into its promoter was found in double-flower accessions.Thus,our efforts have suggested roles for OVATE,a NAC transcription factor,and microRNA172d in fruit shape,fruit development period,and floral morphology,respectively,that can be connected to traits in other crops,thereby demonstrating the importance of parallel evolution in the diversification of several commercially important domesticated species.In general,these genomic resources will facilitate functional genomics,evolutionary research,and agronomic improvement of these five and other Prunus species.We believe that structural variant-based GWASs can also be used in other plants,animal species,and humans and be combined with deep sequencing GWASs to precisely identify candidate genes and genetic architecture components.展开更多
Bud endodormancy represents an ecological adaptation mechanism in perennial deciduous fruit trees to endure winter cold conditions.Sucrose serves a crucial role in bud endodormancy as both an energy metabolizer and si...Bud endodormancy represents an ecological adaptation mechanism in perennial deciduous fruit trees to endure winter cold conditions.Sucrose serves a crucial role in bud endodormancy as both an energy metabolizer and signaling molecule.Sugars Will Eventually be Exported Transporters(SWEETs)function as sugar-efflux transporters that respond to environmental stimuli and contribute to plant growth and development.While SWEET gene families have been identified in various plant species for sugar transport regulation,their mechanism in regulating peach bud endodormancy remains undefined.In this study,we identified 15 SWEET genes in peach.The nomenclature was established through homologous alignment with the Arabidopsis SWEET gene family,resulting in four distinct clades through phylogenetic analysis.Covariance correlation analysis revealed 6 and 12 collinear SWEET genes in peach and Arabidopsis,respectively,forming 13 collinear gene pairs.Real-time quantitative polymerase chain reaction(RT-qPCR)analysis demonstrated significantly elevated expression of PpSWEET6 during peach bud endodormancy release,correlating positively with sucrose content.Transient overexpression of PpSWEET6 enhanced peach bud endodormancy release,while overexpressing PpSWEET6 in Arabidopsis enhanced seed germination and flowering.Y2H and luciferase complementation imaging(LCI)assays confirmed PpSWEET6 interacted with PpABF2.Additionally,dual luciferase reporter(DLR)assays showed that PpSWEET6 significantly decreased the activation of PpDAM6(key dormancy-inducing gene)through PpABF2,thereby modulating peach bud endodormancy release.These findings advance our understanding of SWEET genes in peach bud endodormancy regulation.展开更多
基金supported by the National Natural Science Foundation of China(32302509)the Weifang University Doctoral Research Launch Fund,China(2022BS18)the National Natural Science Foundation of China(32072518)。
文摘Bud dormancy is a complex physiological process of perennial woody plants living in temperate regions,and it can be affected by various phytohormones.Cytokinin oxidase/dehydrogenases(CKXs)are a group of enzymes essential for maintaining cytokinin homeostasis,yet a comprehensive analysis of these enzymes in peach remains lacking.Here,a total of 51 CKX members from different species,including six from peach,eleven from apple,nine from poplar,seven from Arabidopsis,eight from strawberry,and ten from rice,were identified using the Simple HMM Search tool of TBtools and a BLASTP program and classified into four groups using phylogenetic analysis.Conserved motif and gene structure analysis of these 51 CKX members showed that 10 conserved motifs were identified,and each CKX gene contained at least two introns.Cis-element analysis of PpCKXs showed that all PpCKX genes have light-responsive elements and at least one hormone-responsive element.The changed relative expression levels of six PpCKX genes in peach buds from endodormancy to bud-break were observed by qRT-PCR.Among them,the expression trend of PpCKX6 was almost opposite that of PpEBB1,a positive bud-break regulator in woody plants,around the bud-break stage.Y1H,EMSA,and dual-luciferase assays indicated that PpEBB1negatively regulated PpCKX6 through direct binding to a GCC box-like element located in the promoter region of PpCKX6.In addition,a transient assay showed that overexpression of PpCKX6 delayed the bud-break of peach.These results indicate that the PpCKX genes play an essential role in the dormancy-regrowth process,and Pp CKX6may act downstream of PpEBB1 directly to regulate the bud-break process,which further improves the hormoneregulatory network of dormancy-regrowth of woody plants,and provides new insights for molecular breeding and genetic engineering of peach.
基金This work was supported byNational Key Research and Development Plan,grant No.2018YFD1000104National Natural Science Foundation of China,grant No.31872041+2 种基金Provincial Natural Science Foundation of Shandong,grant No.ZR2018MC023Shandong Province Agricultural Good Seed Project grant,No.2020LZGC007 and 2020LZGC00702Funding for major agricultural application technology innovation projects in Shandong Province.
文摘Prunus species include many important perennial fruit crops,such as peach,plum,apricot,and related wild species.Here,we report de novo genome assemblies for five species,including the cultivated species peach(Prunus persica),plum(Prunus salicina),and apricot(Prunus armeniaca),and the wild peach species Tibetan peach(Prunus mira)and Chinese wild peach(Prunus davidiana).The genomes ranged from 240 to 276 Mb in size,with contig N50 values of 2.27−8.30Mb and 25,333−27,826 protein-coding gene models.As the phylogenetic tree shows,plum diverged from its common ancestor with peach,wild peach species,and apricot~7 million years ago(MYA).We analyzed whole-genome resequencing data of 417 peach accessions,called 3,749,618 high-quality SNPs,577,154 small indels,31,800 deletions,duplications,and inversions,and 32,338 insertions,and performed a structural variant-based genome-wide association study(GWAS)of key agricultural traits.From our GWAS data,we identified a locus associated with a fruit shape corresponding to the OVATE transcription factor,where a large inversion event correlates with higher OVATE expression in flat-shaped accessions.Furthermore,a GWAS revealed a NAC transcription factor associated with fruit developmental timing that is linked to a tandem repeat variant and elevated NAC expression in early-ripening accessions.We also identified a locus encoding microRNA172d,where insertion of a transposable element into its promoter was found in double-flower accessions.Thus,our efforts have suggested roles for OVATE,a NAC transcription factor,and microRNA172d in fruit shape,fruit development period,and floral morphology,respectively,that can be connected to traits in other crops,thereby demonstrating the importance of parallel evolution in the diversification of several commercially important domesticated species.In general,these genomic resources will facilitate functional genomics,evolutionary research,and agronomic improvement of these five and other Prunus species.We believe that structural variant-based GWASs can also be used in other plants,animal species,and humans and be combined with deep sequencing GWASs to precisely identify candidate genes and genetic architecture components.
基金funded by the National Key Research and Development Program of China(2018YFD1000104)the Shandong Provincial Fruit Industry Technology System Cultivation and Soil Fertilization Post,China(SDAIT-06-04)the Key R&D Program of Shandong Province(Competitive Innovation Platform),China(2022CXPT017).
文摘Bud endodormancy represents an ecological adaptation mechanism in perennial deciduous fruit trees to endure winter cold conditions.Sucrose serves a crucial role in bud endodormancy as both an energy metabolizer and signaling molecule.Sugars Will Eventually be Exported Transporters(SWEETs)function as sugar-efflux transporters that respond to environmental stimuli and contribute to plant growth and development.While SWEET gene families have been identified in various plant species for sugar transport regulation,their mechanism in regulating peach bud endodormancy remains undefined.In this study,we identified 15 SWEET genes in peach.The nomenclature was established through homologous alignment with the Arabidopsis SWEET gene family,resulting in four distinct clades through phylogenetic analysis.Covariance correlation analysis revealed 6 and 12 collinear SWEET genes in peach and Arabidopsis,respectively,forming 13 collinear gene pairs.Real-time quantitative polymerase chain reaction(RT-qPCR)analysis demonstrated significantly elevated expression of PpSWEET6 during peach bud endodormancy release,correlating positively with sucrose content.Transient overexpression of PpSWEET6 enhanced peach bud endodormancy release,while overexpressing PpSWEET6 in Arabidopsis enhanced seed germination and flowering.Y2H and luciferase complementation imaging(LCI)assays confirmed PpSWEET6 interacted with PpABF2.Additionally,dual luciferase reporter(DLR)assays showed that PpSWEET6 significantly decreased the activation of PpDAM6(key dormancy-inducing gene)through PpABF2,thereby modulating peach bud endodormancy release.These findings advance our understanding of SWEET genes in peach bud endodormancy regulation.
