Dear Editor,Agrobacterium-mediated transformation technology is of vital importance for functional genomics studies and precision breeding in crops due to low cost and clear genetic manifestation.A morphogenic gene pa...Dear Editor,Agrobacterium-mediated transformation technology is of vital importance for functional genomics studies and precision breeding in crops due to low cost and clear genetic manifestation.A morphogenic gene pair,BABY BOOM and WUSCHEL(BBM-WUS).展开更多
Cotton(Gossypium spp.)is one of the most important fiber crops worldwide.In the last two decades,transgenesis and genome editing have played important roles in cotton improvement.However,genotype dependence is one of ...Cotton(Gossypium spp.)is one of the most important fiber crops worldwide.In the last two decades,transgenesis and genome editing have played important roles in cotton improvement.However,genotype dependence is one of the key bottlenecks in generating transgenic and gene-edited cotton plants through either particle bombardment or Agrobacterium-mediated transformation.Here,we developed a shoot apical meristem(SAM)cell-mediated transformation system(SAMT)that allowed the transformation of recalcitrant cotton genotypes including widely grown upland cotton(Gossypium hirsutum),Sea island cotton(Gossypium barbadense),and Asiatic cotton(Gossypium arboreum).Through SAMT,we successfully introduced two foreign genes,GFP and RUBY,into SAM cells of some recalcitrant cotton genotypes.Within 2–3 months,transgenic adventitious shoots generated from the axillary meristem zone could be recovered and grown into whole cotton plants.The GFP fluorescent signal and betalain accumulation could be observed in various tissues in GFP-and RUBY-positive plants,as well as in their progenies,indicating that the transgenes were stably integrated into the genome and transmitted to the next generation.Furthermore,using SAMT,we successfully generated edited cotton plants with inheritable targeted mutagenesis in the GhPGF and GhRCD1 genes through CRISPR/Cas9-mediated genome editing.In summary,the established SAMT transformation system here in this study bypasses the embryogenesis process during tissue culture in a conventional transformation procedure and significantly accelerates the generation of transgenic and gene-edited plants for genetic improvement of recalcitrant cotton varieties.展开更多
Chromatin interactions create spatial proximity between distal regulatory elements and target genes in the genome,which has an important impact on gene expression,transcriptional regulation,and phenotypic traits.To da...Chromatin interactions create spatial proximity between distal regulatory elements and target genes in the genome,which has an important impact on gene expression,transcriptional regulation,and phenotypic traits.To date,several methods have been developed for predicting gene expression.However,existing methods do not take into consideration the effect of chromatin interactions on target gene expression,thus potentially reducing the accuracy of gene expression prediction and mining of important regulatory elements.In this study,we developed a highly accurate deep learning-based gene expression prediction model(DeepCBA)based on maize chromatin interaction data.Compared with existing models,DeepCBA exhibits higher accuracy in expression classification and expression value prediction.The average Pearson correlation coefficients(PCCs)for predicting gene expression using gene promoter proximal interactions,proximaldistal interactions,and both proximal and distal interactions were 0.818,0.625,and 0.929,respectively,representing an increase of 0.357,0.16,and 0.469 over the PCCs obtained with traditional methods that use only gene proximal sequences.Some important motifs were identified through DeepCBA;they were enriched in open chromatin regions and expression quantitative trait loci and showed clear tissue specificity.Importantly,experimental results for the maize flowering-related gene ZmRap2.7 and the tillering-related gene ZmTb1 demonstrated the feasibility of DeepCBA for exploration of regulatory elements that affect gene expression.Moreover,promoter editing and verification of two reported genes(ZmCLE7 and ZmVTE4)demonstrated the utility of DeepCBA for the precise design of gene expression and even for future intelligent breeding.DeepCBA is available at http://www.deepcba.com/or http://124.220.197.196/.展开更多
基金supported by the STI 2030-Major Projects(2023ZD04074)the National Key Laboratory of Crop Genetic Improvement Self-Research Program(ZW22A0302)。
文摘Dear Editor,Agrobacterium-mediated transformation technology is of vital importance for functional genomics studies and precision breeding in crops due to low cost and clear genetic manifestation.A morphogenic gene pair,BABY BOOM and WUSCHEL(BBM-WUS).
基金supported by the National Science Foundation of China(Grant Nos.31621005,31701476,32171996)the Hainan Yazhou Bay Seed Laboratory(Grant Nos.B21HJ0207 and B21HJ0215)+1 种基金the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciencesthe China Agriculture Research System of MOF and MARA(Grant No.CARS-15-02)。
文摘Cotton(Gossypium spp.)is one of the most important fiber crops worldwide.In the last two decades,transgenesis and genome editing have played important roles in cotton improvement.However,genotype dependence is one of the key bottlenecks in generating transgenic and gene-edited cotton plants through either particle bombardment or Agrobacterium-mediated transformation.Here,we developed a shoot apical meristem(SAM)cell-mediated transformation system(SAMT)that allowed the transformation of recalcitrant cotton genotypes including widely grown upland cotton(Gossypium hirsutum),Sea island cotton(Gossypium barbadense),and Asiatic cotton(Gossypium arboreum).Through SAMT,we successfully introduced two foreign genes,GFP and RUBY,into SAM cells of some recalcitrant cotton genotypes.Within 2–3 months,transgenic adventitious shoots generated from the axillary meristem zone could be recovered and grown into whole cotton plants.The GFP fluorescent signal and betalain accumulation could be observed in various tissues in GFP-and RUBY-positive plants,as well as in their progenies,indicating that the transgenes were stably integrated into the genome and transmitted to the next generation.Furthermore,using SAMT,we successfully generated edited cotton plants with inheritable targeted mutagenesis in the GhPGF and GhRCD1 genes through CRISPR/Cas9-mediated genome editing.In summary,the established SAMT transformation system here in this study bypasses the embryogenesis process during tissue culture in a conventional transformation procedure and significantly accelerates the generation of transgenic and gene-edited plants for genetic improvement of recalcitrant cotton varieties.
基金supported by the Biological Breeding-Major Projects(2023ZD04076)the National Key Research and Development Program of China(2022YFD1201504)+3 种基金the Fundamental Research Funds for the Central Universities(2662022YLYJ010,2021ZKPY018,2662021JC008,and SZYJY2021003)the Major Project of Hubei Hongshan Laboratory(2022HSZD031)the Major Science and Technology Project of Hubei Province(2021AFB002)the Yingzi Tech&Huazhong Agricultural University Intelligent Research Institute of Food Health(IRIFH202209).
文摘Chromatin interactions create spatial proximity between distal regulatory elements and target genes in the genome,which has an important impact on gene expression,transcriptional regulation,and phenotypic traits.To date,several methods have been developed for predicting gene expression.However,existing methods do not take into consideration the effect of chromatin interactions on target gene expression,thus potentially reducing the accuracy of gene expression prediction and mining of important regulatory elements.In this study,we developed a highly accurate deep learning-based gene expression prediction model(DeepCBA)based on maize chromatin interaction data.Compared with existing models,DeepCBA exhibits higher accuracy in expression classification and expression value prediction.The average Pearson correlation coefficients(PCCs)for predicting gene expression using gene promoter proximal interactions,proximaldistal interactions,and both proximal and distal interactions were 0.818,0.625,and 0.929,respectively,representing an increase of 0.357,0.16,and 0.469 over the PCCs obtained with traditional methods that use only gene proximal sequences.Some important motifs were identified through DeepCBA;they were enriched in open chromatin regions and expression quantitative trait loci and showed clear tissue specificity.Importantly,experimental results for the maize flowering-related gene ZmRap2.7 and the tillering-related gene ZmTb1 demonstrated the feasibility of DeepCBA for exploration of regulatory elements that affect gene expression.Moreover,promoter editing and verification of two reported genes(ZmCLE7 and ZmVTE4)demonstrated the utility of DeepCBA for the precise design of gene expression and even for future intelligent breeding.DeepCBA is available at http://www.deepcba.com/or http://124.220.197.196/.
