Background:The cotton crop is universally considered as protein and edible oil source besides the major contributor of natural fiber and is grown in tropical and subtropical regions around the world Unpredicted enviro...Background:The cotton crop is universally considered as protein and edible oil source besides the major contributor of natural fiber and is grown in tropical and subtropical regions around the world Unpredicted environmental stresses are becoming significant threats to sustainable cotton production,ultimately leading to a substantial irreversible economic loss.Mitogen-activated protein kinase(MAPK)is generally considered essential for recognizing environmental stresses through phosphorylating downstream signal pathways and plays a vital role in numerous biological processes.Results:We have identified 74 MAPK genes across cotton,41 from G.hirsutum,19 from G.raimondii,whereas 14 have been identified from G.arboreum.The MAPK gene-proteins have been further studied to determine their physicochemical characteristics and other essential features.In this perspective,characterization,phylogenetic relationship,chromosomal mapping,gene motif,cis-regulatory element,and subcellular localization were carried out.Based on phylogenetic analysis,the MAPK family in cotton is usually categorized as A,B,C,D,and E clade.According to the results of the phylogenic relationship,cotton has more MAPKS genes in Clade A than Clade B.The cis-elements identified were classified into five groups(hormone responsiveness,light responsiveness,stress responsiveness,cellular development,and binding site).The prevalence of such elements across the promoter region of these genes signifies their role in the growth and development of plants.Seven GHMAPK genes(GH_A07G1527,GH_D02G1138,GH_D03G0121,GH_D03G1517,GH_D05G1003,GH_D11G0040,and GH_D12G2528)were selected,and specific tissue expression and profiling were performed across drought and salt stresses.Results expressed that six genes were upregulated under drought treatment except for GH_D11G0040 which is downregulated.Whereas all the seven genes have been upregulated at various hours of salt stress treatment.Conclusions:RNA sequence and qPCR results showed that genes as differentially expressed across both vegetative and reproductive plant parts.Similarly,the qPCR analysis showed that six genes had been upregulated substantially through drought treatment while all the seven genes were upregulated across salt treatments.The results of this study showed that cotton GHMPK3 genes play an important role in improving cotton resistance to drought and salt stresses.MAPKs are thought to play a significant regulatory function in plants’responses to abiotic stresses according to various studies.MAPKs’involvement in abiotic stress signaling and innovation is a key goal for crop species research,especially in crop breeding.展开更多
Background: Cotton is an important commercial crop for being a valuable source of natural fiber.Its production has undergone a sharp decline because of abiotic stresses,etc.Drought is one of the major abiotic stress c...Background: Cotton is an important commercial crop for being a valuable source of natural fiber.Its production has undergone a sharp decline because of abiotic stresses,etc.Drought is one of the major abiotic stress causing significant yield losses in cotton.However,plants have evolved self-defense mechanisms to cope abiotic factors like drought,salt,cold,etc.The evolution of stress responsive transcription factors such as the trihelix,a nodule-inception-like protein(NLP),and the late embryogenesis abundant proteins have shown positive response in the resistance improvement to several abiotic stresses.Results: Genome wide identification and characterization of the effects of Light-Harvesting Chloro a/b binding(LHC)genes were carried out in cotton under drought stress conditions.A hundred and nine proteins encoded by the LHC genes were found in the cotton genome,with 55,27,and 27 genes found to be distributed in Gossypium hirsutum,G.arboreum,and G.raimondii,respectively.The proteins encoded by the genes were unevenly distributed on various chromosomes.The Ka/Ks(Non-synonymous substitution rate/Synonymous substitution rate)values were less than one,an indication of negative selection of the gene family.Differential expressions of genes showed that majority of the genes are being highly upregulated in the roots as compared with leaves and stem tissues.Most genes were found to be highly expressed in MR-85,a relative drought tolerant germplasm.Conclusion: The results provide proofs of the possible role of the LHC genes in improving drought stress tolerance,and can be explored by cotton breeders in releasing a more drought tolerant cotton varieties.展开更多
In order to unravel the biochemical pathways and understand the molecular mechanisms involved in leaf senescence, suppression subtractive hybridization (SSH) was used to generate a cDNA library enriched for transcript...In order to unravel the biochemical pathways and understand the molecular mechanisms involved in leaf senescence, suppression subtractive hybridization (SSH) was used to generate a cDNA library enriched for transcripts differentially expressed in developmental senescence cotyledons of upland cotton. After differential screening by membrane- based hybridization and subsequent confirmation by reverse Northern blot analysis, selected 678 clones were sequenced and analyzed. Sequencing of these cDNA fragments reveals that 216 of expressed se- quence tags (ESTs) represented unique genes. Of these 216 cDNAs, 151 clones (69.9%) show signifi- cant homologies to previously known genes, while the remaining 65 do not match any known sequences. 151 unique ESTs are assigned to twelve different categories based on their putative functions gener- ated by BLAST analysis. These SAG-encoded pro- teins are likely to participate in macromolecule deg- radation, nutrient recycling, detoxification of oxidative metabolites, and signaling and regulatory events. The expression pattern of selection of genes was confirmed using northern hybridization. Northern hybridization confirmed several distinct patterns, from expression at a very early stage to the terminal phase of the senescence syndrome. Clones encod- ing proteases and proteins involved in macromole- cule degradation and gluconeogenesis, as well as stress-related genes, are up regulated in senescence cotyledons.展开更多
A promising way to uncover the genetic architectures underlying complex traits may lie in the ability to recognize the genetic variants and expression transcripts that are responsible for the traits' inheritance.H...A promising way to uncover the genetic architectures underlying complex traits may lie in the ability to recognize the genetic variants and expression transcripts that are responsible for the traits' inheritance.However,statistical methods capable of investigating the association between the inheritance of a quantitative trait and expression transcripts are still limited.In this study,we described a two-step approach that we developed to evaluate the contribution of expression transcripts to the inheritance of a complex trait.First,a mixed linear model approach was applied to detect significant trait-associated differentially expressed transcripts.Then,conditional analysis were used to predict the contribution of the differentially expressed genes to a target trait.Diallel cross data of cotton was used to test the application of the approach.We proposed that the detected differentially expressed transcripts with a strong impact on the target trait could be used as intermediates for screening lines to improve the traits in plant and animal breeding programs.It can benefit the discovery of the genetic mechanisms underlying complex traits.展开更多
基金funded by National Key R&D Program of China(2020YFD1001004).
文摘Background:The cotton crop is universally considered as protein and edible oil source besides the major contributor of natural fiber and is grown in tropical and subtropical regions around the world Unpredicted environmental stresses are becoming significant threats to sustainable cotton production,ultimately leading to a substantial irreversible economic loss.Mitogen-activated protein kinase(MAPK)is generally considered essential for recognizing environmental stresses through phosphorylating downstream signal pathways and plays a vital role in numerous biological processes.Results:We have identified 74 MAPK genes across cotton,41 from G.hirsutum,19 from G.raimondii,whereas 14 have been identified from G.arboreum.The MAPK gene-proteins have been further studied to determine their physicochemical characteristics and other essential features.In this perspective,characterization,phylogenetic relationship,chromosomal mapping,gene motif,cis-regulatory element,and subcellular localization were carried out.Based on phylogenetic analysis,the MAPK family in cotton is usually categorized as A,B,C,D,and E clade.According to the results of the phylogenic relationship,cotton has more MAPKS genes in Clade A than Clade B.The cis-elements identified were classified into five groups(hormone responsiveness,light responsiveness,stress responsiveness,cellular development,and binding site).The prevalence of such elements across the promoter region of these genes signifies their role in the growth and development of plants.Seven GHMAPK genes(GH_A07G1527,GH_D02G1138,GH_D03G0121,GH_D03G1517,GH_D05G1003,GH_D11G0040,and GH_D12G2528)were selected,and specific tissue expression and profiling were performed across drought and salt stresses.Results expressed that six genes were upregulated under drought treatment except for GH_D11G0040 which is downregulated.Whereas all the seven genes have been upregulated at various hours of salt stress treatment.Conclusions:RNA sequence and qPCR results showed that genes as differentially expressed across both vegetative and reproductive plant parts.Similarly,the qPCR analysis showed that six genes had been upregulated substantially through drought treatment while all the seven genes were upregulated across salt treatments.The results of this study showed that cotton GHMPK3 genes play an important role in improving cotton resistance to drought and salt stresses.MAPKs are thought to play a significant regulatory function in plants’responses to abiotic stresses according to various studies.MAPKs’involvement in abiotic stress signaling and innovation is a key goal for crop species research,especially in crop breeding.
基金This research was funded by the National Natural Science Foundation of China,grant number 31621005,31530053,31671745The National Key R&D Program of China(2021YFE0101200),PSF/CRP/18thProtocol(07).
文摘Background: Cotton is an important commercial crop for being a valuable source of natural fiber.Its production has undergone a sharp decline because of abiotic stresses,etc.Drought is one of the major abiotic stress causing significant yield losses in cotton.However,plants have evolved self-defense mechanisms to cope abiotic factors like drought,salt,cold,etc.The evolution of stress responsive transcription factors such as the trihelix,a nodule-inception-like protein(NLP),and the late embryogenesis abundant proteins have shown positive response in the resistance improvement to several abiotic stresses.Results: Genome wide identification and characterization of the effects of Light-Harvesting Chloro a/b binding(LHC)genes were carried out in cotton under drought stress conditions.A hundred and nine proteins encoded by the LHC genes were found in the cotton genome,with 55,27,and 27 genes found to be distributed in Gossypium hirsutum,G.arboreum,and G.raimondii,respectively.The proteins encoded by the genes were unevenly distributed on various chromosomes.The Ka/Ks(Non-synonymous substitution rate/Synonymous substitution rate)values were less than one,an indication of negative selection of the gene family.Differential expressions of genes showed that majority of the genes are being highly upregulated in the roots as compared with leaves and stem tissues.Most genes were found to be highly expressed in MR-85,a relative drought tolerant germplasm.Conclusion: The results provide proofs of the possible role of the LHC genes in improving drought stress tolerance,and can be explored by cotton breeders in releasing a more drought tolerant cotton varieties.
文摘In order to unravel the biochemical pathways and understand the molecular mechanisms involved in leaf senescence, suppression subtractive hybridization (SSH) was used to generate a cDNA library enriched for transcripts differentially expressed in developmental senescence cotyledons of upland cotton. After differential screening by membrane- based hybridization and subsequent confirmation by reverse Northern blot analysis, selected 678 clones were sequenced and analyzed. Sequencing of these cDNA fragments reveals that 216 of expressed se- quence tags (ESTs) represented unique genes. Of these 216 cDNAs, 151 clones (69.9%) show signifi- cant homologies to previously known genes, while the remaining 65 do not match any known sequences. 151 unique ESTs are assigned to twelve different categories based on their putative functions gener- ated by BLAST analysis. These SAG-encoded pro- teins are likely to participate in macromolecule deg- radation, nutrient recycling, detoxification of oxidative metabolites, and signaling and regulatory events. The expression pattern of selection of genes was confirmed using northern hybridization. Northern hybridization confirmed several distinct patterns, from expression at a very early stage to the terminal phase of the senescence syndrome. Clones encod- ing proteases and proteins involved in macromole- cule degradation and gluconeogenesis, as well as stress-related genes, are up regulated in senescence cotyledons.
基金supported by the National Basic Research Program of China(2011CB109306)the National High Technology Research and Development Program of China(2009ZX08009-004B,2011AA10A102)+2 种基金the CNTC(110200701023)the YNTC(08A05)the earmearked fund for Modern Agro-industry Technology Reasearch System(CARS-18-05)
文摘A promising way to uncover the genetic architectures underlying complex traits may lie in the ability to recognize the genetic variants and expression transcripts that are responsible for the traits' inheritance.However,statistical methods capable of investigating the association between the inheritance of a quantitative trait and expression transcripts are still limited.In this study,we described a two-step approach that we developed to evaluate the contribution of expression transcripts to the inheritance of a complex trait.First,a mixed linear model approach was applied to detect significant trait-associated differentially expressed transcripts.Then,conditional analysis were used to predict the contribution of the differentially expressed genes to a target trait.Diallel cross data of cotton was used to test the application of the approach.We proposed that the detected differentially expressed transcripts with a strong impact on the target trait could be used as intermediates for screening lines to improve the traits in plant and animal breeding programs.It can benefit the discovery of the genetic mechanisms underlying complex traits.