scholarly journals Genome-wide identification and characterization of TALE superfamily genes in cotton reveals their functions in regulating secondary cell wall biosynthesis

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Qiang Ma ◽  
Nuohan Wang ◽  
Pengbo Hao ◽  
Huiru Sun ◽  
Congcong Wang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Cotton Fiber ◽  
Secondary Cell Wall ◽  
Fiber Strength ◽  
Fiber Quality ◽  
Expression Patterns ◽  
Evolutionary Analysis ◽  
Regulatory Relationship ◽  
Genome Wide ◽  
Regulation Functions

Abstract Background Cotton fiber length and strength are both key traits of fiber quality, and fiber strength (FS) is tightly correlated with secondary cell wall (SCW) biosynthesis. The three-amino-acid-loop-extension (TALE) superclass homeoproteins are involved in regulating diverse biological processes in plants, and some TALE members has been identified to play a key role in regulating SCW formation. However, little is known about the functions of TALE members in cotton (Gossypium spp.). Results In the present study, based on gene homology, 46, 47, 88 and 94 TALE superfamily genes were identified in G. arboreum, G. raimondii, G. barbadense and G. hirsutum, respectively. Phylogenetic and evolutionary analysis showed the evolutionary conservation of two cotton TALE families (including BEL1-like and KNOX families). Gene structure analysis also indicated the conservation of GhTALE members under selection. The analysis of promoter cis-elements and expression patterns suggested potential transcriptional regulation functions in fiber SCW biosynthesis and responses to some phytohormones for GhTALE proteins. Genome-wide analysis of colocalization of TALE transcription factors with SCW-related QTLs revealed that some BEL1-like genes and KNAT7 homologs may participate in the regulation of cotton fiber strength formation. Overexpression of GhKNAT7-A03 and GhBLH6-A13 significantly inhibited the synthesis of lignocellulose in interfascicular fibers of Arabidopsis. Yeast two-hybrid (Y2H) experiments showed extensive heteromeric interactions between GhKNAT7 homologs and some GhBEL1-like proteins. Yeast one-hybrid (Y1H) experiments identified the upstream GhMYB46 binding sites in the promoter region of GhTALE members and defined the downstream genes that can be directly bound and regulated by GhTALE heterodimers. Conclusion We comprehensively identified TALE superfamily genes in cotton. Some GhTALE members are predominantly expressed during the cotton fiber SCW thicking stage, and may genetically correlated with the formation of FS. Class II KNOX member GhKNAT7 can interact with some GhBEL1-like members to form the heterodimers to regulate the downstream targets, and this regulatory relationship is partially conserved with Arabidopsis. In summary, this study provides important clues for further elucidating the functions of TALE genes in regulating cotton growth and development, especially in the fiber SCW biosynthesis network, and it also contributes genetic resources to the improvement of cotton fiber quality.

scholarly journals Transcriptome analysis revealed the possible contribution of chromosome introgression fragments from Sea Island cotton (Gossypium barbadense) to fiber strength in Upland cotton (Gossypium hirsutum)

2016 ◽  
Author(s):  
Quanwei Lu ◽  
Yuzhen Shi ◽  
Xianghui Xiao ◽  
Pengtao Li ◽  
Juwu Gong ◽  
...  
Keyword(s):  
Cell Wall ◽  
Cotton Fiber ◽  
Cellular Response ◽  
Fiber Strength ◽  
Fiber Quality ◽  
Introgression Lines ◽  
Recurrent Parent ◽  
Single Organism ◽  
Cell Wall Development ◽  
Cotton Fiber Quality

AbstractCotton fiber strength is a critical property determining fiber qualities, and determined by the secondary cell wall development. Understanding the mechanism of fiber development will provide a way to improvement of fiber strength. In this study, the introgression lines of upland and sea island cotton, and have experience of four generations of backcross with upland parent, and have significant higher fiber strength than their upland parent, and the transcriptome were analyzed and compared between the introgression lines and their upland parent. There were 2201 differentially expressed genes (DEG) identified by comparing two introgression lines with their recurrent parent CCRI45, in different development stages from 15 days post-anthesis (DPA) to 28 DPA. The up-regulated genes regulated the polysaccharide metabolic process, single-organism localization, cell wall organization or biogenesis and so on. The down-regulated genes involved in the microtubule-based process, cellular response to stress, cell cycle process and so on. Further functional analysis revealed three significant functional genes, XLOC_036333 (mannosyl-oligosaccharide-alpha-mannosidase mns1), XLOC_029945 (FLA8) and XLOC_075372 (snakin-1), playing important roles in the regulation of cotton fiber strength. Our results provide important candidates genes and inspirations for the future investigation of the molecular mechanism of fiber quality formation, and improvement of cotton fiber quality in breeding.

scholarly journals Genome-Wide Investigation of the NAC Gene Family and Its Potential Association with the Secondary Cell Wall in Moso Bamboo

Biomolecules ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 609 ◽  
Author(s):  
Shan ◽  
Yang ◽  
Xu ◽  
Zhu ◽  
Gao
Keyword(s):  
Cell Wall ◽  
Gene Family ◽  
Secondary Cell Wall ◽  
Expression Patterns ◽  
Wood Property ◽  
Moso Bamboo ◽  
Functional Studies ◽  
Bamboo Shoots ◽  
Potential Association ◽  
Nac Gene Family

NAC (NAM, ATAF, and CUC) transcription factors (TFs) are implicated in the transcriptional regulation of diverse processes and have been characterized in a number of plant species. However, NAC TFs are still not well understood in bamboo, especially their potential association with the secondary cell wall (SCW). Here, 94 PeNACs were identified and characterized in moso bamboo (Phyllostachys edulis). Based on their gene structures and conserved motifs, the PeNACs were divided into 11 groups according to their homologs in Arabidopsis. PeNACs were expressed variously in different tissues of moso bamboo, suggesting their functional diversity. Fifteen PeNACs associated with the SCW were selected for co-expression analysis and validation. It was predicted that 396 genes were co-expressed with the 15 PeNACs, in which 16 and 55 genes were involved in the lignin catabolic process and cellulose biosynthetic process respectively. As the degree of lignification in the growing bamboo shoots increased, all 15 PeNACs were upregulated with a trend of rising first and then decreasing except PeNAC37, which increased continuously. These results indicated that these PeNACs might play important roles in SCW biosynthesis and lignification in bamboo shoots. Seven of 15 PeNACs had been found positively co-expressed with seven PeMYBs, and they had similar expression patterns with those of the PeMYBs in bamboo shoots. The targeted sites of miR164 were found in 16 PeNACs, of which three PeNACs associated with SCW were validated to have an opposite expression trend to that of miR164 in growing bamboo shoots. In addition, three PeNACs were selected and verified to have self-activation activities. These results provide comprehensive information of the NAC gene family in moso bamboo, which will be helpful for further functional studies of PeNACs to reveal the molecular regulatory mechanisms of bamboo wood property.

Comparative Investigation of Secondary Cell Wall Development in Cotton Fiber Near Isogenic Lines Using Attenuated Total Reflection Fourier Transform Infrared Spectroscopy (ATR FT-IR)

2019 ◽  
Vol 73 (3) ◽  
pp. 329-336 ◽  
Author(s):  
Yongliang Liu ◽  
Hee-Jin Kim
Keyword(s):  
Cell Wall ◽  
Fourier Transform ◽  
Secondary Cell Wall ◽  
Fiber Strength ◽  
Total Reflection ◽  
Attenuated Total Reflection ◽  
Near Isogenic Lines ◽  
Significant Difference ◽  
Ft Ir ◽  
Fiber Maturity

In this investigation, we applied previously proposed simple algorithms to analyze the attenuated total reflection Fourier transform infrared (ATR FT-IR) spectra of cotton fibers during secondary cell wall (SCW) biosynthesis. The infrared crystallinity ( CIIR) and maturity ( MIR) indices were compared from developmental fibers representing two pairs of upland cotton near isogenic lines (NILs). One pair of NILs consisted of Texas Marker-1 (TM-1) and an immature fiber ( im) mutant that differ in fiber maturity. The other pair of NILs included MD52ne and MD90ne that show variations in fiber strength. The observations revealed significant difference in the MIR values between developmental TM-1 and im NILs grown at a field in crop year 2015, and also a significant difference in the CIIR values between these NILs grown at the same field in crop year 2011. These different patterns of CIIR and MIR values during fiber development for the two different crop years indicated the impact of genetics and crop year on the development of fiber maturity and crystallinity of the TM-1 and im fibers. Furthermore, the tendency of linking CIIR with MIR values suggested that the im fibers have more CIIR development than the TM-1 fibers when the fibers have the similar MIR values. In contrast, the NIL pair having variations in fiber strength showed insignificant differences in the patterns of CIIR and MIR as well as the relationship between CIIR and MIR values. The results suggested that CIIR and MIR indices from ATR FT-IR measurement could be used to facilitate the understanding of how fiber genetics and crop year affect fiber maturity and crystallinity during SCW biosynthesis.

scholarly journals Identification of Candidate Genes Controlling Fiber Quality Traits in Upland Cotton Through Integration of Meta-QTL, Significant SNP and Transcriptomic Data

2020 ◽  
Author(s):  
XU Shudi ◽  
Zhenyuan Pan ◽  
Feifan Yin ◽  
Qingyong Yang ◽  
Zhongxu Lin ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Cotton Fiber ◽  
Molecular Mechanisms ◽  
Fiber Strength ◽  
Fiber Quality ◽  
Significant Snps ◽  
Fiber Development ◽  
Computational Technique ◽  
Quality Traits ◽  
Fiber Quality Traits

Abstract Background Meta-analysis of quantitative trait locus (QTL) is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies. The combination of meta-QTL intervals, significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants. Results In our study, 884 QTL associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1, as a result, 74 meta-QTL were identified, including 19 meta-QTL for fiber length (FL), 18 meta-QTL for fiber strength (FS), 11 meta-QTL for fiber uniformity (FU), 11 meta-QTL for fiber elongation (FE), and 15 meta-QTL for micronaire (MIC). Combined with 8589 significant SNPs associated with fiber quality traits collected from 15 studies, 297 candidate genes were identified in the meta-QTL intervals, 20 of which showed high expression specifically in the developing fibers. According to the function annotations, some of the 20 key candidate genes are associated with the fiber development. Conclusions This study provides not only stable QTLs used for marker-assisted selection (MAS), but also candidate genes to uncover the molecular mechanisms for cotton fiber development.

scholarly journals Genome-Wide Identification, Evolution, and Transcriptional Profiling ofPP2CGene Family inBrassica rapa

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
Nadeem Khan ◽  
Han Ke ◽  
Chun-mei Hu ◽  
Emal Naseri ◽  
Muhammad Salman Haider ◽  
...  
Keyword(s):  
Sequence Data ◽  
Transcriptional Profiling ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Vital Role ◽  
Future Research ◽  
Evolutionary Analysis ◽  
Paralogous Gene ◽  
Gene Pairs ◽  
Genome Wide

The type 2C protein which belongs to the major group of protein phosphatases (PP2C) plays a vital role in abscisic acid (ABA) signaling and signal transductions processes. In the present study, 131PP2Cgenes were identified in total inBrassica rapaand categorized into thirteen subgroups based on their phylogenetic relationships. TheseB. rapaPP2C are structurally conserved based on amino acid sequence alignment, phylogenetic analysis, and conserved domains. Moreover, we utilized previously reported RNA-sequence data on various tissues (root, stem, leaf, flower, and silique), which suggests overlapping expression pattern in 29 paralogous gene pairs. The qRT-PCR validation of 15 paralogous gene pairs depicts distinct expression patterns in response to various abiotic stresses, such as heat, cold, ABA, and drought. Interestingly, stress-responsiveBraPP2Ccandidate genes were also identified, suggesting their significance in stress-tolerance mechanism inB. rapa. The evolutionary analysis for 15 paralogous gene pairs suggested that only three pairs have the positive selection and remaining were purifying in nature. The presented results of this study hasten our understanding of the molecular evolution of thePP2Cgene family inB. rapa. Thus, it will be ultimately helping in future research for facilitating the functional characterization ofBraPP2Cgenes in developing the abiotic stress tolerant plants.

Molecular weight and organization of cellulose at different stages of cotton fiber development

2018 ◽  
Vol 89 (5) ◽  
pp. 726-738 ◽  
Author(s):  
Sumedha Liyanage ◽  
Noureddine Abidi
Keyword(s):  
Molecular Weight ◽  
Cell Wall ◽  
Cotton Fiber ◽  
Fiber Strength ◽  
Gel Permeation Chromatography ◽  
Solvent System ◽  
Fiber Development ◽  
Cotton Fibers ◽  
Continuous Change ◽  
Cotton Fiber Development

There is a continuous change in cell wall composition and organization during cotton fiber development. Cotton fiber strength correlates to the molecular weight (MW) and molecular weight distribution (MWD), and organization of cellulose chains in the secondary cell wall. These parameters change drastically during fiber development. This study reports on the MW, MWD, and organization of cellulose in cotton fibers harvested from two cotton cultivars of Gossypium hirsutum L., (Texas Marker-1 and TX55) at different levels of maturity. Fiber dissolution is necessary to estimate the molecular properties of cellulose. Cellulose in mature cotton fibers is larger in MW and highly crystalline and, therefore, poorly dissolves in common solvent systems. To facilitate the dissolution, fibers were first pretreated with 23% sodium hydroxide and then dissolved in a dimethylacetamide/lithium chloride solvent system. Gel permeation chromatography of dissolved fibers indicated that cellulose in both cultivars reaches its maximum MW around 30 days post anthesis. Fourier transform infrared microspectroscopy imaging in the transmission mode indicates changes in cellulose distribution in cotton fibers with fiber development. The distributions of infrared vibrations of cellulose at 897 (β-linkage of cellulose), 1161 (anti-symmetrical C-O-C stretching of cellulose), and 1429 cm−1 (CH2 scissoring of cellulose) provided information on cellulose deposition in intact cotton fibers.

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