盐胁迫是限制作物产量提高的一个主要非生物因素。棉花是盐碱地的先锋作物,研究棉花的耐盐性,筛选耐盐相关分子标记,对充分利用棉花的耐盐性及棉花耐盐种质鉴定有重要意义。在本研究中,我们对前期筛选到的1281个耐盐相关候选SNP即SNPr(S...盐胁迫是限制作物产量提高的一个主要非生物因素。棉花是盐碱地的先锋作物,研究棉花的耐盐性,筛选耐盐相关分子标记,对充分利用棉花的耐盐性及棉花耐盐种质鉴定有重要意义。在本研究中,我们对前期筛选到的1281个耐盐相关候选SNP即SNPr(SNP related to salt tolerance)进行分析,利用BEDTools软件获得位于基因上的SNPr,并使用AgriGO(http://bioinfo.cau.edu.cn/agriGO/)和KAAS(http://www.genome.jp/tools/kaas/)网站对这些基因进行GO和KEGG分析。借助perl编程,获得非同义SNPr。分析发现,1281个SNPr中,有353个位于基因上,其中247个位于基因外显子区,且有174个是非同义SNPr。从中选择12个非同义SNPr,使用CAPS/dCAPS引物进行验证,并结合田间耐盐鉴定的结果,最终得到1个与耐盐相关的SNPr。这个SNPr位于CHD3/CHD4家族基因上,可能与盐胁迫过程中的表观修饰有关。展开更多
ZAT(Zinc Finger of Arabidopsis thaliana)proteins are composed of a plant-specific transcription factor family,which play an important role in plant growth,development,and stress resista nee.To study the potential func...ZAT(Zinc Finger of Arabidopsis thaliana)proteins are composed of a plant-specific transcription factor family,which play an important role in plant growth,development,and stress resista nee.To study the potential function of ZAT family in cotton,the whole genome identification,expression,and structure analysis of ZAT gene family were carried out.In this study,our analysis revealed the presenee of 115Z 56,59,and 115 ZAT genes in Gossypium hirsutum,G raimondii,G.arboreum and G barbadense,respectively.According to the number of domains and phylogenetic characteristics,we divided ZAT genes of four Gossypium species into 4 different clades,and further divided them into 11 subfamilies.The results of collinearity an alysis showed that segmental duplicati on was the main method to amplify the cotton ZAT genes family.Analysis of c/s-elements of promoters indicated that most GhZAT genes contained c/5-elements related to plant hormones and abiotic stress.According to heatmap analysis,the expression patterns of GhZAT genes under different stresses indicated that GhZAT genes were significantly involved in the response to cold,heat,salt,and PEG stress,possibly through different mechanisms.Among the highly expressed genes,we cloned a G hirsutum gene GhZAT67.Through virus-induced gene silencing(VIGS),we found that its expression level decreased significantly after being sileneed.Under alkaline treatment,the wilting degree of silenced plants was even greater than the wild type,which proved that GhZAT67 gene was involved in the response to alkaline stress.展开更多
Background:DNA methylation is an important epigenetic factor that maintains and regulates gene expression.The mode and level of DNA methylation depend on the roles of DNA methyltransferase and demethylase,while DNA de...Background:DNA methylation is an important epigenetic factor that maintains and regulates gene expression.The mode and level of DNA methylation depend on the roles of DNA methyltransferase and demethylase,while DNA demethylase plays a key role in the process of DNA demethylation.The results showed that the plant’s DNA demethylase all contained conserved DNA glycosidase domain.This study identified the cotton DNA demethylase gene family and analyzed it using bioinformatics methods to lay the foundation for further study of cotton demethylase gene function.Results:This study used genomic information from diploid Gossypium raimondii JGI(D),Gossypium arboreum L.CRI(A),Gossypium hirsutum L.JGI(AD1) and Gossypium barbadebse L NAU(AD2) to Arabidopsis thaliana.Using DNA demethylase genes sequence of Arabidopsis as reference,25 DNA demethylase genes were identified in cotton by BLAST analysis.There are 4 genes in the genome D,5 genes in the genome A,10 genes in the genome AD1,and 6 genes in the genome AD2.The gene structure and evolution were analyzed by bioinformatics,and the expression patterns of DNA demethylase gene family in Gossypium hirsutum L were analyzed.From the phylogenetic tree analysis,the DNA demethylase gene family of cotton can be divided into four subfamilies:REPRESSOR of SILENCING 1(ROS1),DEMETER(DME),DEMETER-LIKE 2(DML2),and DEMETER-LIKE3(DML3).The sequence similarity of DNA demethylase genes in the same species was higher,and the genetic relationship was also relatively close.Analysis of the gene structure revealed that the DNA demethylase gene family members of the four subfamilies varied greatly.Among them,the number of introns of ROS1 and DME subfamily was larger,and the gene structure was more complex.For the analysis of the conserved domain,it was known that the DNA demethylase family gene member has an endonuclease Ⅲ(END03 c) domain.Conclusion:The genes of the DNA demethylase family are distributed differently in different cotton species,and the gene structure is very different.High expression of ROS1 genes in cotton were under abiotic stress.The expression levels of ROS1 genes were higher during the formation of cotton ovule.The transcription levels of ROS1 family genes were higher during cotton fiber development.展开更多
Background: Nucleobase-ascorbate transporters(NAT), synonymously called nucleobase-cation symporter 2(NCS2) proteins, were earlier reported to be involved in plant growth, development and resistance to stress. Previou...Background: Nucleobase-ascorbate transporters(NAT), synonymously called nucleobase-cation symporter 2(NCS2) proteins, were earlier reported to be involved in plant growth, development and resistance to stress. Previous studies concluded that s a polymorphic SNP associated with NAT12 was significant di erent between salt-tolerant and salt-sensitive materials of upland cotton. In current study, a comprehensive analysis of NAT family genes was conducted for the first time in cotton.Results: In this study, we discovered 32, 32, 18, and 16 NAT genes in Gossypium hirsutum, G. barbadense, G. raimondii and G. arboreum, respectively, which were classified into four groups(groups I–IV) based on the multiple sequence analysis. These GhNAT genes were unevenly distributed on At and Dt sub-genome in G. hirsutum. Most GhNAT members in the same group had similar gene structure characteristics and motif composition. The collinearity analysis revealed segmental duplication as well as tandem duplication contributing to the expansion of the GhNATs. The analysis of cis-acting regulatory elements of GhNATs showed that the function of GhNAT genes in cotton might be related to plant hormone and stress response. Under di erent conditions, the expression levels further suggested the GhNAT family genes were associated with plant response to various abiotic stresses. GhNAT12 was detected in the plasma membrane. And it was validated that the GhNAT12 gene played an important role in regulating cotton resistance to salt and drought stress through the virus-induced gene silencing(VIGS) analysis.Conclusions: A comprehensive analysis of NAT gene family was performed in cotton, including phylogenetic analysis, chromosomal location, collinearity analysis, motifs, gene structure and so on. Our results will further broaden the insight into the evolution and potential functions of NAT genes in cotton. Current findings could make significant contribution towards screening more candidate genes related to biotic and abiotic resistance for the improvement in cotton.展开更多
Background:Under abiotic stress conditions,cotton growth is inhibited and yield losses are severe.Identification of calnexin family members and function analysis under abiotic stress laid the foundation for the screen...Background:Under abiotic stress conditions,cotton growth is inhibited and yield losses are severe.Identification of calnexin family members and function analysis under abiotic stress laid the foundation for the screening of stressrelated candidate genes.Results:A total of 60 CNX family members have been identified in Gossypium hirsutum,G.barbadense,G.arboreum,and G.raimondii,and they were divided into two categories:CNX and CRT genes.Through the construction of a phylogenetic tree,they were subdivided into three classes.Further analysis of chromosome localization,conserved promoters,gene structure and selection under pressure showed that the family members were highly conserved in the evolution process.Analysis of cis-acting elements in the promoter regions showed that CNX family genes contain regulatory elements for growth and development,anaerobic,drought,defense and stress response,and plant hormones.Using RNA-seq data to study the expression pattern of GhCNX genes under cold,hot,salt stress and Polyethylene glycol,it was observed that the gene expression levels changed by different degrees under different stress conditions,indicating that GhCNX members were involved in the regulation of multiple biological stresses.Conclusion:This study provides an insight into the members of cotton CNX genes.The results of this study suggested that CNX family members play a role in defense against adversity and provide a foundation for the discovery of stress-related genes.展开更多
文摘盐胁迫是限制作物产量提高的一个主要非生物因素。棉花是盐碱地的先锋作物,研究棉花的耐盐性,筛选耐盐相关分子标记,对充分利用棉花的耐盐性及棉花耐盐种质鉴定有重要意义。在本研究中,我们对前期筛选到的1281个耐盐相关候选SNP即SNPr(SNP related to salt tolerance)进行分析,利用BEDTools软件获得位于基因上的SNPr,并使用AgriGO(http://bioinfo.cau.edu.cn/agriGO/)和KAAS(http://www.genome.jp/tools/kaas/)网站对这些基因进行GO和KEGG分析。借助perl编程,获得非同义SNPr。分析发现,1281个SNPr中,有353个位于基因上,其中247个位于基因外显子区,且有174个是非同义SNPr。从中选择12个非同义SNPr,使用CAPS/dCAPS引物进行验证,并结合田间耐盐鉴定的结果,最终得到1个与耐盐相关的SNPr。这个SNPr位于CHD3/CHD4家族基因上,可能与盐胁迫过程中的表观修饰有关。
基金Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences.The funding bodies provided financial support to the research projects but didn't involve in study design,data collection,analysis,or preparation of the manuscript.
文摘ZAT(Zinc Finger of Arabidopsis thaliana)proteins are composed of a plant-specific transcription factor family,which play an important role in plant growth,development,and stress resista nee.To study the potential function of ZAT family in cotton,the whole genome identification,expression,and structure analysis of ZAT gene family were carried out.In this study,our analysis revealed the presenee of 115Z 56,59,and 115 ZAT genes in Gossypium hirsutum,G raimondii,G.arboreum and G barbadense,respectively.According to the number of domains and phylogenetic characteristics,we divided ZAT genes of four Gossypium species into 4 different clades,and further divided them into 11 subfamilies.The results of collinearity an alysis showed that segmental duplicati on was the main method to amplify the cotton ZAT genes family.Analysis of c/s-elements of promoters indicated that most GhZAT genes contained c/5-elements related to plant hormones and abiotic stress.According to heatmap analysis,the expression patterns of GhZAT genes under different stresses indicated that GhZAT genes were significantly involved in the response to cold,heat,salt,and PEG stress,possibly through different mechanisms.Among the highly expressed genes,we cloned a G hirsutum gene GhZAT67.Through virus-induced gene silencing(VIGS),we found that its expression level decreased significantly after being sileneed.Under alkaline treatment,the wilting degree of silenced plants was even greater than the wild type,which proved that GhZAT67 gene was involved in the response to alkaline stress.
基金funded by the National Key Research and Development Program of China(2018YFD0100401)
文摘Background:DNA methylation is an important epigenetic factor that maintains and regulates gene expression.The mode and level of DNA methylation depend on the roles of DNA methyltransferase and demethylase,while DNA demethylase plays a key role in the process of DNA demethylation.The results showed that the plant’s DNA demethylase all contained conserved DNA glycosidase domain.This study identified the cotton DNA demethylase gene family and analyzed it using bioinformatics methods to lay the foundation for further study of cotton demethylase gene function.Results:This study used genomic information from diploid Gossypium raimondii JGI(D),Gossypium arboreum L.CRI(A),Gossypium hirsutum L.JGI(AD1) and Gossypium barbadebse L NAU(AD2) to Arabidopsis thaliana.Using DNA demethylase genes sequence of Arabidopsis as reference,25 DNA demethylase genes were identified in cotton by BLAST analysis.There are 4 genes in the genome D,5 genes in the genome A,10 genes in the genome AD1,and 6 genes in the genome AD2.The gene structure and evolution were analyzed by bioinformatics,and the expression patterns of DNA demethylase gene family in Gossypium hirsutum L were analyzed.From the phylogenetic tree analysis,the DNA demethylase gene family of cotton can be divided into four subfamilies:REPRESSOR of SILENCING 1(ROS1),DEMETER(DME),DEMETER-LIKE 2(DML2),and DEMETER-LIKE3(DML3).The sequence similarity of DNA demethylase genes in the same species was higher,and the genetic relationship was also relatively close.Analysis of the gene structure revealed that the DNA demethylase gene family members of the four subfamilies varied greatly.Among them,the number of introns of ROS1 and DME subfamily was larger,and the gene structure was more complex.For the analysis of the conserved domain,it was known that the DNA demethylase family gene member has an endonuclease Ⅲ(END03 c) domain.Conclusion:The genes of the DNA demethylase family are distributed differently in different cotton species,and the gene structure is very different.High expression of ROS1 genes in cotton were under abiotic stress.The expression levels of ROS1 genes were higher during the formation of cotton ovule.The transcription levels of ROS1 family genes were higher during cotton fiber development.
基金supported by China Agriculture Research System of MOF and MOARAAgricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Science
文摘Background: Nucleobase-ascorbate transporters(NAT), synonymously called nucleobase-cation symporter 2(NCS2) proteins, were earlier reported to be involved in plant growth, development and resistance to stress. Previous studies concluded that s a polymorphic SNP associated with NAT12 was significant di erent between salt-tolerant and salt-sensitive materials of upland cotton. In current study, a comprehensive analysis of NAT family genes was conducted for the first time in cotton.Results: In this study, we discovered 32, 32, 18, and 16 NAT genes in Gossypium hirsutum, G. barbadense, G. raimondii and G. arboreum, respectively, which were classified into four groups(groups I–IV) based on the multiple sequence analysis. These GhNAT genes were unevenly distributed on At and Dt sub-genome in G. hirsutum. Most GhNAT members in the same group had similar gene structure characteristics and motif composition. The collinearity analysis revealed segmental duplication as well as tandem duplication contributing to the expansion of the GhNATs. The analysis of cis-acting regulatory elements of GhNATs showed that the function of GhNAT genes in cotton might be related to plant hormone and stress response. Under di erent conditions, the expression levels further suggested the GhNAT family genes were associated with plant response to various abiotic stresses. GhNAT12 was detected in the plasma membrane. And it was validated that the GhNAT12 gene played an important role in regulating cotton resistance to salt and drought stress through the virus-induced gene silencing(VIGS) analysis.Conclusions: A comprehensive analysis of NAT gene family was performed in cotton, including phylogenetic analysis, chromosomal location, collinearity analysis, motifs, gene structure and so on. Our results will further broaden the insight into the evolution and potential functions of NAT genes in cotton. Current findings could make significant contribution towards screening more candidate genes related to biotic and abiotic resistance for the improvement in cotton.
基金supported by the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences,and Supported by China Agriculture Research System of MOF and MARA.
文摘Background:Under abiotic stress conditions,cotton growth is inhibited and yield losses are severe.Identification of calnexin family members and function analysis under abiotic stress laid the foundation for the screening of stressrelated candidate genes.Results:A total of 60 CNX family members have been identified in Gossypium hirsutum,G.barbadense,G.arboreum,and G.raimondii,and they were divided into two categories:CNX and CRT genes.Through the construction of a phylogenetic tree,they were subdivided into three classes.Further analysis of chromosome localization,conserved promoters,gene structure and selection under pressure showed that the family members were highly conserved in the evolution process.Analysis of cis-acting elements in the promoter regions showed that CNX family genes contain regulatory elements for growth and development,anaerobic,drought,defense and stress response,and plant hormones.Using RNA-seq data to study the expression pattern of GhCNX genes under cold,hot,salt stress and Polyethylene glycol,it was observed that the gene expression levels changed by different degrees under different stress conditions,indicating that GhCNX members were involved in the regulation of multiple biological stresses.Conclusion:This study provides an insight into the members of cotton CNX genes.The results of this study suggested that CNX family members play a role in defense against adversity and provide a foundation for the discovery of stress-related genes.
