Functional diversi?cations of Gh ERF1 duplicate genes after the formation of allotetraploid cotton

Whole genome duplication, a prevalent force of evolution in plants, results in massive genome restructuring in different organisms. Roles of the resultant duplicated genes are poorly understood both functionally and evolutionarily. In the present study, differentially expressed ethylene responsive factors(GhERF1 s), anchored on Chr-A07 and Chr-D07 were isolated from a high-yielding cotton hybrid(XZM2)and its parents. The GhERF1 was located in the B3 subgroup of the ethylene responsive factors subfamily involved in conferring tolerance to abiotic stress Nucleotide sequence analysis of 524 diverse accessions together with quantitative real-time polymerase chain reaction analysis, elucidated that de-functionalization of GhERF1-7 A occurred due to one base insertion following formation of the allotetraploid cotton. Our quantitative trait loci and association mapping analyses highlighted a role for GhERF1-7 A in conferring high boll number per plant in modern cotton cultivars. Overexpression of GhERF1-7 A in transgenic Arabidopsis resulted in a substantial increase in the number of siliques and total seed yield. Neo-functionalization of GhERF1-7 A was also observed in modern cultivars rather than in races and/or landraces, further supporting its role in the development of high-yielding cotton cultivars. Both de-and neofunctionalization occurred in one of the duplicate genes,thus providing new genomic insight into the evolution of allotetraploid cotton species.     

Functional diversifications of GhERF1 duplicate genes after the formation of allotetraploid cotton

Whole genome duplication, a prevalent force of evolution in plants, results in massive genome restructuring in different organisms. Roles of the resultant duplicated genes are poorly understood both functionally and evolutionarily. In the present study, differentially expressed ethylene responsive factors(GhERF1 s), anchored on Chr-A07 and Chr-D07 were isolated from a high-yielding cotton hybrid(XZM2)and its parents. The GhERF1 was located in the B3 subgroup of the ethylene responsive factors subfamily involved in conferring tolerance to abiotic stress Nucleotide sequence analysis of 524 diverse accessions together with quantitative real-time polymerase chain reaction analysis, elucidated that de-functionalization of GhERF1-7 A occurred due to one base insertion following formation of the allotetraploid cotton. Our quantitative trait loci and association mapping analyses highlighted a role for GhERF1-7 A in conferring high boll number per plant in modern cotton cultivars. Overexpression of GhERF1-7 A in transgenic Arabidopsis resulted in a substantial increase in the number of siliques and total seed yield. Neo-functionalization of GhERF1-7 A was also observed in modern cultivars rather than in races and/or landraces, further supporting its role in the development of high-yielding cotton cultivars. Both de-and neofunctionalization occurred in one of the duplicate genes,thus providing new genomic insight into the evolution of allotetraploid cotton species.     

大豆转录因子GmERF5的克隆、表达及功能分析

ERF转录因子是植物中特有的转录因子家族之一, 在植物响应生物和非生物胁迫过程中发挥重要的调控作用。通过对大豆(Glycine max)吉林32未成熟胚的表达谱分析, 利用RT-PCR技术从大豆中克隆了1个新的ERF转录因子GmERF5。GmERF5具有237个氨基酸残基, 分子量为26.09 kDa, 等电点为6.85, 其开放阅读框长714 bp。该转录因子蛋白与Gh-ERF2蛋白的同源性最高, 它们同属ERF亚家族的第IV亚类。实时荧光定量PCR分析表明, 该蛋白基因在大豆的根中表达量最高, 且受干旱、高盐、低温及乙烯、脱落酸和茉莉酸甲酯的诱导上调表达。亚细胞定位实验结果表明, GmERF5蛋白定位于细胞核中。转录激活能力分析结果显示, GmERF5可以激活报告基因的表达, 为转录激活子。综合以上结果, 认为GmERF5可能作为转录调控因子参与大豆生物和非生物胁迫的应答。     

Developmental and pathogen-induced expression of three barley genes encoding lipid transfer proteins

Clones for three barley non-specific lipid transfer proteins (LTP2, LTP3, and LTP4; formerly Cw18, Cw20 and Cw21, respectively) which had been previously shown to inhibit growth of plant pathogens, were selected and characterized from a cDNA library derived from young etiolated leaves. Genes Ltp2 and Ltp4 were located in chromosome 3H and gene Ltp3 was assigned to chromosome 7H by Southern blot analysis of wheat—barley disomic addition lines, using gene-specific probes (3'-ends of cDNAs). These assignments were confirmed by the polymerase chain reaction, using specific primers. The three genes were expressed in stem, shoot apex, leaves and roots (at low levels) throughout development. Genes Ltp3 and Ltp4 were expressed at high levels, and Lpt2 at low levels, in the spike (rachis, lemma plus palea and grain coats). Neither of the mRNAs was detected in endosperm. The proteins were localized by tissue-printing with polyclonal antibodies in the outer cell layer of the exposed surfaces of the plant, throughout the embryo, and in vascular tissues. Expression levels in leaves were moderately increased by 0.34 M NaCl and by 0.1 mM abscisic acid and were not affected by cold, drought, salicylate, 2,6-dichloro-isonicotinic acid, ethylene or ethephon. Methyl Jasmonate (10 µM) switched off all three genes. Inoculation with Av6 or vir6 isolates of the fungal pathogen Erysiphe graminis increased the three mRNAs, especially that of LTP4, which reached a maximum nine-fold increase 12–16 h after infection.     

利用阵列分析水稻AP2/EREBP 家族基因的表达特性

AP2/EREBP蛋白是广泛存在于高等植物中的且包含AP2/EREBP功能域的重要转录因子家族, 通常可分为包含单功能域的EREBP类蛋白和包含两个功能域的AP2类蛋白, 它们的功能涉及植物生长发育调控和对逆境应答等许多方面。据预测,水稻基因组编码150个左右的AP2/EREBP 家族成员, 但目前绝大多数蛋白的功能仍不清楚。为了解这些基因在水稻不同器官中的表达特性, 我们以AP2/EREBP功能域的氨基酸序列为基础, 从水稻基因组数据库中搜索到12个AP2类以及20个EREBP类预测基因, 利用PCR扩增的编码区序列制备了这些预测基因的macro-array。 以幼芽、幼根、幼叶、颖花和灌浆期成熟叶的 cDNA为探针, 杂交分析结果显示: 不同AP2类预测基因之间的表达量差别较大, 但同一个基因在不同器官中表达量基本一致; 与此不同的是, 大部分EREBP类预测基因在幼根和成熟叶片中表达量较高, 而在幼芽和幼叶中表达量较低。这些预测基因的表达模式可能与它们的功能密切相关。     

Genome- Wide Analysis and Characterization of the TRX Gene Family in Upland Cotton

Thioredoxins (TRX) are small molecules of proteins that are present in all organisms. TRXs play an important role in diverse functions of plant growth and development. In this study, we performed genome-wide, characterization and expression levels of TRX gene family in cotton. A total of 150 GhTRX proteins were identified in upland cotton and classified into five subfamilies based on their domain compositions. Phylogenetic tree analysis divided TRX genes into seven subgroups. GhTRX genes covered all upland cotton chromosomes, with duplicated gene events. Ka/Ks ratio of three gene pairs was less than 1, suggesting purifying selection. The functions of GhTRX genes were studied using gene ontology, protein localization, and promoter analysis. Furthermore, six GhTRX genes were randomly selected to examine their expression level in cotton development and under various exogenous treatments. The genes showed high expressions in various tissues and at different stages of leaf senescence, also showed high expression under abscisic acid, ethylene, drought, and salinity. This study reveals the first report of TRX family genes in upland cotton. However further studies are needed to elucidate their specific functions in cotton plant.     

Transcriptome Analysis of Plant Hormone-Related Tomato (Solanum lycopersicum) Genes in a Sunlight-Type Plant Factory

In plant factories, measurements of plant conditions are necessary at an early stage of growth to predict harvest times of high value-added crops. Moreover, harvest qualities depend largely on environmental stresses that elicit plant hormone responses. However, the complexities of plant hormone networks have not been characterized under nonstress conditions. In the present study, we determined temporal expression profiles of all genes and then focused on plant hormone pathways using RNA-Seq analyses of gene expression in tomato leaves every 2 h for 48 h. In these experiments, temporally expressed genes were found in the hormone synthesis pathways for salicylic acid, abscisic acid, ethylene, and jasmonic acid. The timing of CAB expression 1 (TOC1) and abscisic acid insensitive 1 (ABA1) and open stomata 1 (OST1) control gating stomata. In this study, compare with tomato and Arabidopsis thaliana, expression patterns of TOC1 have similarity. In contrast, expression patterns of tomato ABI1 and OST1 had expression peak at different time. These findings suggest that the regulation of gating stomata does not depend predominantly on TOC1 and significantly reflects the extracellular environment. The present data provide new insights into relationships between temporally expressed plant hormone-related genes and clock genes under normal sunlight conditions.     

Genome-Wide Functional Analysis of Cotton (Gossypium hirsutum) in Response to Drought

Cotton is one of the most important crops for its natural textile fibers in the world. However, it often suffered from drought stress during its growth and development, resulting in a drastic reduction in cotton productivity. Therefore, study on molecular mechanism of cotton drought-tolerance is very important for increasing cotton production. To investigate molecular mechanism of cotton drought-resistance, we employed RNA-Seq technology to identify differentially expressed genes in the leaves of two different cultivars (drought-resistant cultivar J-13 and drought-sensitive cultivar Lu-6) of cotton. The results indicated that there are about 13.38% to 18.75% of all the unigenes differentially expressed in drought-resistant sample and drought-sensitive control, and the number of differentially expressed genes was increased along with prolonged drought treatment. DEG (differentially expression gene) analysis showed that the normal biophysical profiles of cotton (cultivar J-13) were affected by drought stress, and some cellular metabolic processes (including photosynthesis) were inhibited in cotton under drought conditions. Furthermore, the experimental data revealed that there were significant differences in expression levels of the genes related to abscisic acid signaling, ethylene signaling and jasmonic acid signaling pathways between drought-resistant cultivar J-13 and drought-sensitive cultivar Lu-6, implying that these signaling pathways may participate in cotton response and tolerance to drought stress.     

利用阵列分析水稻AP2/EREBP家族基因的表达特性

AP2／EREBP蛋白是广泛存在于高等植物中的且包含AP2／EREBP功能域的重要转录因子家族,通常可分为包含单功能域的EREBP类蛋白和包含两个功能域的AP2类蛋白,它们的功能涉及植物生长发育调控和对逆境应答等许多方面。据预测．水稻基因组编码150个左右的AP2／EREBP家族成员,但目前绝大多数蛋白的功能仍不清楚。为了解这些基因在水稻不同器官中的表达特性,我们以AP2／EREBP功能域的氨基酸序列为基础,从水稻基因组数据库中搜索到12个AP2类以及20个EREBP类预测基因,利用PCR扩增的编码区序列制备了这些预测基因的macro—array。以幼芽、幼根、幼叶、颖花和灌浆期成熟叶的cDNA为探针,杂交分析结果显示：不同AP2类预测基因之间的表达量差别较大,但同一个基因在不同器官中表达量基本一致：与此不同的是,大部分EREBP类预测基因在幼根和成熟叶片中表达量较高,而在幼芽和幼叶中表达量较低。这些预测基因的表达模式可能与它们的功能密切相关。