Phylogenetically distinct cellulose synthase genes support secondary wall thickening in arabidopsis shoot trichomes and cotton fiber

GhGRF4/GhARF2-GhGASA24 module regulates fiber cell wall thickness by modulating cellulose biosynthesis in upland cotton (Gossypium hirsutum)

Fiber elongation rate is an essential characteristic of cotton fiber in the textile industry, yet it has been largely overlooked in genetic studies. Gibberellins (GAs) and auxin (IAA) are recognized for their role in directing numerous developmental processes in plants by influencing cell differentiation and elongation. However, the degree to which GA-IAA interaction governs cellular elongation in cotton fiber cells remains to be fully understood. In this study, we identified a causal gene, Gibberellic Acid-Stimulated in Arabidopsis 24 (GhGASA24), that appears to be responsible for fiber elongation rate via regulating fiber cell wall thickness. Subsequent experiments revealed that GhGASA24 influences cell wall formation by promoting the expression of GhCesA8 and GhCesA10. Our findings suggest that Auxin Response Factor 2 (GhARF2) regulates fiber elongation rate by directly binding to the AuxRE elements in GhGASA24 promoter. In addition, we identified Growth Regulation Factor 4 (GhGRF4) as a transcription factor that interacts with GhARF2 to form a heterodimer complex, which also transcriptionally activates GhGASA24. Intriguingly, GhGRF4 regulates GhARF2 expression by directly binding to its promoter, thereby acting as a cascade regulator to enhance the transcriptional levels of GhGASA24. We propose that the GhGRF4/GhARF2-GhGASA24-GhCesAs module may contribute to fiber cell wall thickness by modulating cellulose biosynthesis, and provide a theoretical basis for improvement of fiber quality.

Identification of quantitative trait loci for lodging and related agronomic traits in soybean (Glycine max [L.] Merr.)

BACKGROUND

Lodging, a crucial agronomic trait linked to soybean yield, poses a significant challenge in soybean production. Nevertheless, there has been less research on soybean lodging compared to other important agronomic traits, hindering progress in breeding high-yield soybeans. Our goals were to investigate lodging, pinpoint quantitative trait loci (QTL) linked to lodging, and forecast potential candidate genes linked to this trait. To achieve this, we employed a recombinant inbred line (RIL) population derived from a cross between Guizao 1 and B13 (GB) across various environments.

RESULTS

The lodging score of the RIL population was found to be significantly positively correlated with flowering time, maturity time, plant height, number of main stem nodes, stem diameter, and internode length, with correlation coefficients ranging from 0.457 to 0.783. A total of 84 QTLs associated with soybean lodging and related traits were identified using the GB population. The contribution of phenotypic variance ranged from 1.26 to 66.87%, with LOD scores ranging from 2.52 to 69.22. Additionally, within these QTLs, a stable major QTL associated with lodging was newly discovered in the GB population. Out of the ten major QTLs associated with other related traits, nine of them were situated within the qLD-4-1 interval of the major lodging score locus, displaying phenotypic variations ranging from 12.10 to 66.87%. Specific alterations in gene expression were revealed through the analysis of resequencing data from the two parental lines, potentially indicating their significant roles in lodging. Subsequently, it was determined through qRT-PCR that four genes are likely to be the major genes controlling soybean lodging.

CONCLUSIONS

This study's findings offer valuable insights into the genetic underpinnings of soybean lodging resistance traits. By comprehending the potential genetic factors associated with lodging, this research lays the groundwork for breeding high-yield soybeans with improved lodging resistance.

Unraveling the lncRNA-miRNA-mRNA Regulatory Network Involved in Poplar Coma Development through High-Throughput Sequencing

Poplar coma, the fluff-like appendages of seeds originating from the differentiated surface cells of the placenta and funicle, aids in the long-distance dispersal of seeds in the spring. However, it also poses hazards to human safety and causes pollution in the surrounding environment. Unraveling the regulatory mechanisms governing the initiation and development of coma is essential for addressing this issue comprehensively. In this study, strand-specific RNA-seq was conducted at three distinct stages of coma development, revealing 1888 lncRNAs and 52,810 mRNAs. The expression profiles of lncRNAs and mRNAs during coma development were analyzed. Subsequently, potential target genes of lncRNAs were predicted through co-localization and co-expression analyses. Integrating various types of sequencing data, lncRNA-miRNA-TF regulatory networks related to the initiation of coma were constructed. Utilizing identified differentially expressed genes encoding kinesin and actin, lncRNA-miRNA-mRNA regulatory networks associated with the construction and arrangement of the coma cytoskeleton were established. Additionally, relying on differentially expressed genes encoding cellulose synthase, sucrose synthase, and expansin, lncRNA-miRNA-mRNA regulatory networks related to coma cell wall synthesis and remodeling were developed. This study not only enhances the comprehension of lncRNA but also provides novel insights into the molecular mechanisms governing the initiation and development of poplar coma.

An aldehyde dehydrogenase gene, GhALDH7B4_A06, positively regulates fiber strength in upland cotton (Gossypium hirsutum L.)

High fiber strength (FS) premium cotton has significant market demand. Consequently, enhancing FS is a major objective in breeding quality cotton. However, there is a notable lack of known functionally applicable genes that can be targeted for breeding. To address this issue, our study used specific length-amplified fragment sequencing combined with bulk segregant analysis to study FS trait in an F2 population. Subsequently, we integrated these results with previous quantitative trait locus mapping results regarding fiber quality, which used simple sequence repeat markers in F2, F2:3, and recombinant inbred line populations. We identified a stable quantitative trait locus qFSA06 associated with FS located on chromosome A06 (90.74-90.83 Mb). Within this interval, we cloned a gene, GhALDH7B4_A06, which harbored a critical mutation site in coding sequences that is distinct in the two parents of the tested cotton line. In the paternal parent Ji228, the gene is normal and referred to as GhALDH7B4_A06O; however, there is a nonsense mutation in the maternal parent Ji567 that results in premature termination of protein translation, and this gene is designated as truncated GhALDH7B4_A06S. Validation using recombinant inbred lines and gene expression analysis revealed that this mutation site is correlated with cotton FS. Virus-induced gene silencing of GhALDH7B4 in cotton caused significant decreases in FS and fiber micronaire. Conversely, GhALDH7B4_A06O overexpression in Arabidopsis boosted cell wall component contents in the stem. The findings of our study provide a candidate gene for improving cotton fiber quality through molecular breeding.

Genome-wide association studies for earliness, MYMIV resistance, and other associated traits in mungbean (Vigna radiata L. Wilczek) using genotyping by sequencing approach

Yellow mosaic disease (YMD) remains a major constraint in mungbean (Vigna radiata (L.)) production; while short-duration genotypes offer multiple crop cycles per year and help in escaping terminal heat stress, especially during summer cultivation. A comprehensive genotyping by sequencing (GBS)-based genome-wide association studies (GWAS) analysis was conducted using 132 diverse mungbean genotypes for traits like flowering time, YMD resistance, soil plant analysis development (SPAD) value, trichome density, and leaf area. The frequency distribution revealed a wide range of values for all the traits. GBS studies identified 31,953 high-quality single nucleotide polymorphism (SNPs) across all 11 mungbean chromosomes and were used for GWAS. Structure analysis revealed the presence of two genetically distinct populations based on ΔK. The linkage disequilibrium (LD) varied throughout the chromosomes and at r2 = 0.2, the mean LD decay was estimated as 39.59 kb. Two statistical models, mixed linear model (MLM) and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) identified 44 shared SNPs linked with various candidate genes. Notable candidate genes identified include FPA for flowering time (VRADI10G01470; chr. 10), TIR-NBS-LRR for mungbean yellow mosaic India virus (MYMIV) resistance (VRADI09G06940; chr. 9), E3 ubiquitin-protein ligase RIE1 for SPAD value (VRADI07G28100; chr. 11), WRKY family transcription factor for leaf area (VRADI03G06560; chr. 3), and LOB domain-containing protein 21 for trichomes (VRADI06G04290; chr. 6). In-silico validation of candidate genes was done through digital gene expression analysis using Arabidopsis orthologous (compared with Vigna radiata genome). The findings provided valuable insight for marker-assisted breeding aiming for the development of YMD-resistant and early-maturing mungbean varieties.

Cotton fiber as a model for understanding shifts in cell development under domestication

Cotton fiber provides the predominant plant textile in the world, and it is also a model for plant cell wall biosynthesis. The development of the single-celled cotton fiber takes place across several overlapping but discrete stages, including fiber initiation, elongation, the transition from elongation to secondary cell wall formation, cell wall thickening, and maturation and cell death. During each stage, the developing fiber undergoes a complex restructuring of genome-wide gene expression change and physiological/biosynthetic processes, which ultimately generate a strikingly elongated and nearly pure cellulose product that forms the basis of the global cotton industry. Here, we provide an overview of this developmental process focusing both on its temporal as well as evolutionary dimensions. We suggest potential avenues for further improvement of cotton as a crop plant.

Estimating the combining ability and genetic parameters for growth habit, yield, and fiber quality traits in some Egyptian cotton crosses

It is crucial to understand how targeted traits in a hybrid breeding program are influenced by gene activity and combining ability. During the three growing seasons of 2015, 2016, and 2017, a field study was conducted with twelve cotton genotypes, comprised of four testers and eight lines. Thirty-two F1 crosses were produced in the 2015 breeding season using the line x tester mating design. The twelve genotypes and their thirty-two F1 crosses were then evaluated in 2016 and 2017. The results demonstrated highly significant differences among cotton genotypes for all the studied traits, showing a wide range of genetic diversity in the parent genotypes. Additionally, the line-x-tester interaction was highly significant for all traits, suggesting the impact of both additive and non-additive variations in gene expression. Furthermore, the thirty-two cotton crosses showed high seed cotton output, lint cotton yield, and fiber quality, such as fiber length values exceeding 31 mm and a fiber strength above 10 g/tex. Accordingly, selecting lines and testers with high GCA effects and crosses with high SCA effects would be an effective approach to improve the desired traits in cotton and develop new varieties with excellent yield and fiber quality.

Comparative transcriptome analysis reveals key pathways and genes involved in trichome development in tea plant (Camellia sinensis)

Trichomes, which develop from epidermal cells, are considered one of the important characteristics of the tea plant [Camellia sinensis (L.) O. Kuntze]. Many nutritional and metabolomic studies have indicated the important contributions of trichomes to tea products quality. However, understanding the regulation of trichome formation at the molecular level remains elusive in tea plants. Herein, we present a genome-wide comparative transcriptome analysis between the hairless Chuyeqi (CYQ) with fewer trichomes and the hairy Budiaomao (BDM) with more trichomes tea plant genotypes, toward the identification of biological processes and functional gene activities that occur during trichome development. In the present study, trichomes in both cultivars CYQ and BDM were unicellular, unbranched, straight, and soft-structured. The density of trichomes was the highest in the bud and tender leaf periods. Further, using the high-throughput sequencing method, we identified 48,856 unigenes, of which 31,574 were differentially expressed. In an analysis of 208 differentially expressed genes (DEGs) encoding transcription factors (TFs), five may involve in trichome development. In addition, on the basis of the Gene Ontology (GO) annotation and the weighted gene co-expression network analysis (WGCNA) results, we screened several DEGs that may contribute to trichome growth, including 66 DEGs related to plant resistance genes (PRGs), 172 DEGs related to cell wall biosynthesis pathway, 29 DEGs related to cell cycle pathway, and 45 DEGs related to cytoskeleton biosynthesis. Collectively, this study provided high-quality RNA-seq information to improve our understanding of the molecular regulatory mechanism of trichome development and lay a foundation for additional trichome studies in tea plants.

Secondary cell wall patterning-connecting the dots, pits and helices

All plant cells are encased in primary cell walls that determine plant morphology, but also protect the cells against the environment. Certain cells also produce a secondary wall that supports mechanically demanding processes, such as maintaining plant body stature and water transport inside plants. Both these walls are primarily composed of polysaccharides that are arranged in certain patterns to support cell functions. A key requisite for patterned cell walls is the arrangement of cortical microtubules that may direct the delivery of wall polymers and/or cell wall producing enzymes to certain plasma membrane locations. Microtubules also steer the synthesis of cellulose-the load-bearing structure in cell walls-at the plasma membrane. The organization and behaviour of the microtubule array are thus of fundamental importance to cell wall patterns. These aspects are controlled by the coordinated effort of small GTPases that probably coordinate a Turing's reaction-diffusion mechanism to drive microtubule patterns. Here, we give an overview on how wall patterns form in the water-transporting xylem vessels of plants. We discuss systems that have been used to dissect mechanisms that underpin the xylem wall patterns, emphasizing the VND6 and VND7 inducible systems, and outline challenges that lay ahead in this field.

The Pivotal Role of Major Chromosomes of Sub-Genomes A and D in Fiber Quality Traits of Cotton

Lack of precise information about the candidate genes involved in a complex quantitative trait is a major obstacle in the cotton fiber quality improvement, and thus, overall genetic gain in conventional phenotypic selection is low. Recent molecular interventions and advancements in genome sequencing have led to the development of high-throughput molecular markers, quantitative trait locus (QTL) fine mapping, and single nucleotide polymorphisms (SNPs). These advanced tools have resolved the existing bottlenecks in trait-specific breeding. This review demonstrates the significance of chromosomes 3, 7, 9, 11, and 12 of sub-genomes A and D carrying candidate genes for fiber quality. However, chromosome 7 carrying SNPs for stable and potent QTLs related to fiber quality provides great insights for fiber quality-targeted research. This information can be validated by marker-assisted selection (MAS) and transgene in Arabidopsis and subsequently in cotton.

GhMYB7 promotes secondary wall cellulose deposition in cotton fibres by regulating GhCesA gene expression through three distinct cis-elements

Cotton fibre is the most important source for natural textiles. The secondary cell walls (SCWs) of mature cotton fibres contain the highest proportion of cellulose content (> 90%) in any plant. The onset and progression of SCW cellulose synthesis need to be tightly controlled to balance fibre elongation and cell wall deposition. However, regulatory mechanisms that control cellulose synthesis during cotton fibre growth remain elusive. Here, we conducted genetic and functional analyses demonstrating that the R2R3-MYB GhMYB7 controls cotton fibre cellulose synthesis. Overexpression of GhMYB7 in cotton sped up SCW cellulose biosynthesis in fibre cells, and led to shorter fibres with thicker walls. By contrast, RNA interference (RNAi) silencing of GhMYB7 delayed fibre SCW cellulose synthesis and resulted in elongated fibres with thinner walls. Furthermore, we demonstrated that GhMYB7 regulated cotton fibre SCW cellulose synthases by directly binding to three distinct cis-elements in the respective GhCesA4, GhCesA7 and GhCesA8 promoters. We found that this regulatory mechanism of cellulose synthesis was 'hi-jacked' also by other GhMYBs. Together, our findings uncover a hitherto-unknown mechanism that cotton fibre employs to regulate SCW cellulose synthesis. Our results also provide a strategy for genetic improvement of SCW thickness of cotton fibre.

GhGASA10-1 promotes the cell elongation in fiber development through the phytohormones IAA-induced

BACKGROUND

Cotton is an important cash crop. The fiber length has always been a hot spot, but multi-factor control of fiber quality makes it complex to understand its genetic basis. Previous reports suggested that OsGASR9 promotes germination, width, and thickness by GAs in rice, while the overexpression of AtGASA10 leads to reduced silique length, which is likely to reduce cell wall expansion. Therefore, this study aimed to explore the function of GhGASA10 in cotton fibers development.

RESULTS

To explore the molecular mechanisms underlying fiber elongation regulation concerning GhGASA10-1, we revealed an evolutionary basis, gene structure, and expression. Our results emphasized the conservative nature of GASA family with its origin in lower fern plants S. moellendorffii. GhGASA10-1 was localized in the cell membrane, which may synthesize and transport secreted proteins to the cell wall. Besides, GhGASA10-1 promoted seedling germination and root extension in transgenic Arabidopsis, indicating that GhGASA10-1 promotes cell elongation. Interestingly, GhGASA10-1 was upregulated by IAA at fiber elongation stages.

CONCLUSION

We propose that GhGASA10-1 may promote fiber elongation by regulating the synthesis of cellulose induced by IAA, to lay the foundation for future research on the regulation networks of GASA10-1 in cotton fiber development.

Transcriptomic Analysis of Seasonal Gene Expression and Regulation during Xylem Development in “Shanxin” Hybrid Poplar (Populus davidiana × Populus bolleana)

Xylem development is a key process for wood formation in woody plants. To study the molecular regulatory mechanisms related to xylem development in hybrid poplar P. davidiana × P. bolleana, transcriptome analyses were conducted on developing xylem at six different growth stages within a single growing season. Xylem development and differentially expressed genes in the six time points were selected for a regulatory analysis. Xylem development was observed in stem sections at different growth stages, which showed that xylem development extended from the middle of April to early August and included cell expansion and secondary cell wall biosynthesis. An RNA-seq analysis of six samples with three replicates was performed. After transcriptome assembly and annotation, the differentially expressed genes (DEGs) were identified, and a Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and expression analysis of the DEGs were performed on each sample. On average, we obtained >20 million clean reads per sample, which were assembled into 84,733 nonredundant transcripts, of which there were 17,603 unigenes with lengths >1 kb. There were 14,890 genes that were differentially expressed among the six stages. The upregulated DEGs were enriched in GO terms related to cell wall biosynthesis between S1 vs. S2 or S3 vs. S4 and, in GO terms, related to phytohormones in the S1 vs. S2 or S4 vs. S5 comparisons. The downregulated DEGs were enriched in GO terms related to cell wall biosynthesis between S4 vs. S5 or S5 vs. S6 and, in GO terms, related to hormones between S1 vs. S2 or S2 vs. S3. The KEGG pathways in the DEGs related to “phenylpropanoid biosynthesis”, “plant hormone signal transduction” and “starch and sucrose metabolism” were significantly enriched among the different stages. The DEGs related to cell expansion, polysaccharide metabolism and synthesis, lignin synthesis, transcription factors and hormones were identified. The identification of genes involved in the regulation of xylem development will increase our understanding of the molecular regulation of wood formation in trees and, also, offers potential targets for genetic manipulation to improve the properties of wood.

Genetic Analysis of the Transition from Wild to Domesticated Cotton (Gossypium hirsutum L.)

The evolution and domestication of cotton is of great interest from both economic and evolutionary standpoints. Although many genetic and genomic resources have been generated for cotton, the genetic underpinnings of the transition from wild to domesticated cotton remain poorly known. Here we generated an intraspecific QTL mapping population specifically targeting domesticated cotton phenotypes. We used 466 F₂ individuals derived from an intraspecific cross between the wild Gossypium hirsutum var. yucatanense (TX2094) and the elite cultivar G. hirsutum cv. Acala Maxxa, in two environments, to identify 120 QTL associated with phenotypic changes under domestication. While the number of QTL recovered in each subpopulation was similar, only 22 QTL were considered coincident (i.e., shared) between the two locations, eight of which shared peak markers. Although approximately half of QTL were located in the A-subgenome, many key fiber QTL were detected in the D-subgenome, which was derived from a species with unspinnable fiber. We found that many QTL are environment-specific, with few shared between the two environments, indicating that QTL associated with G. hirsutum domestication are genomically clustered but environmentally labile. Possible candidate genes were recovered and are discussed in the context of the phenotype. We conclude that the evolutionary forces that shape intraspecific divergence and domestication in cotton are complex, and that phenotypic transformations likely involved multiple interacting and environmentally responsive factors.

A cotton NAC domain transcription factor, GhFSN5, negatively regulates secondary cell wall biosynthesis and anther development in transgenic Arabidopsis

NAC domain transcription factors (TFs) are plant-specific transcriptional regulators, some of which play crucial roles in secondary cell wall (SCW) biosynthesis in plants. Cotton is one of the most important natural fiber producing crops, whose mature fiber SCW contains more than 90% cellulose with very small amounts of xylan and lignin, but little is known about the molecular mechanism underlying fiber SCW formation. We previously identified seven fiber preferentially expressed NAC members, GhFSN1-7. One, GhFSN1, was demonstrated to positively regulate fiber SCW thickening, but the functions of other GhFSN members remain unknown. In this study, roles of GhFSN5 were dissected. qRT-PCR analysis showed that GhFSN5 was predominantly transcribed during the fiber SCW thickening stage. In addition, a large number of fiber SCW biosynthetic genes and SCW-related TFs were co-expressed with GhFSN5. Heterologous expression of GhFSN5 in Arabidopsis resulted in plants with smaller siliques and severe sterility. Anther dehiscence in transgenic lines was not substantially affected, but most pollen was collapsed and nonviable. Furthermore, cellulose and lignin contents in inflorescence stems as well as roots were reduced in transgenic lines, compared with the wild type. Moreover, a set of SCW biosynthetic genes for cellulose, xylan and lignin and several transcription factors involved in regulation of SCW formation were down-regulated in transgenic plants. Our findings indicate that GhFSN5 acts as a negative regulator of SCW formation and anther development and expands our understanding of transcriptional regulation of SCW biosynthesis.

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

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.

Convergent evolution of hetero-oligomeric cellulose synthesis complexes in mosses and seed plants

In seed plants, cellulose is synthesized by rosette-shaped cellulose synthesis complexes (CSCs) that are obligate hetero-oligomeric, comprising three non-interchangeable cellulose synthase (CESA) isoforms. The moss Physcomitrella patens has rosette CSCs and seven CESAs, but its common ancestor with seed plants had rosette CSCs and a single CESA gene. Therefore, if P. patens CSCs are hetero-oligomeric, then CSCs of this type evolved convergently in mosses and seed plants. Previous gene knockout and promoter swap experiments showed that PpCESAs from class A (PpCESA3 and PpCESA8) and class B (PpCESA6 and PpCESA7) have non-redundant functions in secondary cell wall cellulose deposition in leaf midribs, whereas the two members of each class are redundant. Based on these observations, we proposed the hypothesis that the secondary class A and class B PpCESAs associate to form hetero-oligomeric CSCs. Here we show that transcription of secondary class A PpCESAs is reduced when secondary class B PpCESAs are knocked out and vice versa, as expected for genes encoding isoforms that occupy distinct positions within the same CSC. The class A and class B isoforms co-accumulate in developing gametophores and co-immunoprecipitate, suggesting that they interact to form a complex in planta. Finally, secondary PpCESAs interact with each other, whereas three of four fail to self-interact when expressed in two different heterologous systems. These results are consistent with the hypothesis that obligate hetero-oligomeric CSCs evolved independently in mosses and seed plants and we propose the constructive neutral evolution hypothesis as a plausible explanation for convergent evolution of hetero-oligomeric CSCs.

Genome-Wide Identification of R2R3-MYB Transcription Factors Regulating Secondary Cell Wall Thickening in Cotton Fiber Development

MYB proteins represent one of the largest transcription factor (TF) families in plants, some of which act as key transcriptional regulators of secondary cell wall (SCW) biosynthesis. Cotton (Gossypium hirsutum) fiber is thought to be an ideal single-cell model to study cell elongation and SCW biosynthesis. However, little knowledge regarding the TFs controlling fiber SCW biosynthesis, particularly for R2R3-MYBs is known. By far, no comprehensive genome-wide analysis of the secondary wall-associated R2R3-MYBs has been reported in cultivated tetraploid upland cotton. In this study, we identified 419 R2R3-MYB genes by systematically examining the cotton genome. A combination of phylogenetic, RNA-seq and co-expression analyses indicated that 36 R2R3-MYBs were either preferentially or highly expressed in 20 day post anthesis (dpa) fibers and are putative SCW regulators. Among these MYB genes, 22 MYBs are homologs of known SCW MYB proteins and the other 14 MYBs are novel proteins without prior reported SCW biosynthesis-related functions. Finally, we highlighted on the roles of two MYBs named GhMYB46_D13 and GhMYB46_D9, both of which displayed the highest expression in 20 dpa fibers. Expression of GhMYB46_D13 or GhMYB46_D9 individually in Arabidopsis resulted in ectopic SCW deposition in transgenic plants. Furthermore, both GhMYB46_D13 and GhMYB46_D9 were able to activate the cotton fiber SCW cellulose synthase gene promoters. Thus, we have identified 36 R2R3-MYBs as potential SCW regulators in cotton fibers that represent strong candidates for further functional studies during fiber development and SCW thickening.

De Novo Transcriptome Assembly of Agave H11648 by Illumina Sequencing and Identification of Cellulose Synthase Genes in Agave Species

Agave plants are important crassulacean acid metabolism (CAM) plants with multiple agricultural uses, such as being used in tequila and fiber production. Agave hybrid H11648 ((A. amaniensis Trel. and Nowell × A. angustifolia Haw.) × A. amaniensis) is the main cultivated Agave species for fiber production in large tropical areas around the world. In this study, we conducted a transcriptome analysis of A. H11648. About 49.25 million clean reads were obtained by Illumina paired-end sequencing. De novo assembly produced 148,046 unigenes with more than 40% annotated in public databases, or matched homologs in model plants. More homologous gene pairs were found in Asparagus genome than in Arabidopsis or rice, which indicated a close evolutionary relationship between Asparagus and A. H11648. CAM-related gene families were also characterized as previously reported in A. americana. We further identified 12 cellulose synthase genes (CesA) in Asparagus genome and 38 CesA sequences from A. H11648, A. americana, A. deserti and A. tequilana. The full-length CesA genes were used as references for the cloning and assembly of their homologs in other Agave species. As a result, we obtained CesA1/3/4/5/7 genes with full-length coding region in the four Agave species. Phylogenetic and expression analysis revealed a conserved evolutionary pattern, which could not explain the distinct fiber traits in different Agave species. We inferred that transcriptional regulation might be responsible for Agave fiber development. This study represents the transcriptome of A. H11648, which would expand the number of Agave genes and benefit relevant studies of Agave fiber development.

Fiber Quality Improvement in Upland Cotton (Gossypium hirsutum L.): Quantitative Trait Loci Mapping and Marker Assisted Selection Application

Genetic improvement in fiber quality is one of the main challenges for cotton breeders. Fiber quality traits are controlled by multiple genes and are classified as complex quantitative traits, with a negative relationship with yield potential, so the genetic gain is low in traditional genetic improvement by phenotypic selection. The availability of Gossypium genomic sequences facilitates the development of high-throughput molecular markers, quantitative trait loci (QTL) fine mapping and gene identification, which helps us to validate candidate genes and to use marker assisted selection (MAS) on fiber quality in breeding programs. Based on developments of high density linkage maps, QTLs fine mapping, marker selection and omics, we have performed trait dissection on fiber quality traits in diverse populations of upland cotton. QTL mapping combined with multi-omics approaches such as, RNA sequencing datasets to identify differentially expressed genes have benefited the improvement of fiber quality. In this review, we discuss the application of molecular markers, QTL mapping and MAS for fiber quality improvement in upland cotton.

Ectopic Expression of PtoMYB74 in Poplar and Arabidopsis Promotes Secondary Cell Wall Formation

In vascular plants, R2R3-MYB transcription factors are important regulators of secondary cell wall formation. Although 192 annotated R2R3 MYB genes were identified in the poplar genome, only a few members were characterized to participate in the regulation of the secondary cell wall biosynthesis. In this paper, we identify an R2R3-MYB transcription factor, PtoMYB74, which is predicted to be an ortholog of Arabidopsis AtMYB61, a transcription activator that regulates the secondary cell wall formation, lignin biosynthesis, stomatal aperture, and the mucilage of seed coat. PtoMYB74 is mainly expressed in the stems, especially in the xylem tissues and organs. PtoMYB74 as a transcriptional activator is localized to the nucleus. The overexpression of PtoMYB74 increased the secondary cell wall thickness of vessels in transgenic poplar and changed the secondary cell wall compositions. The expression levels of lignin and cellulose biosynthetic genes were elevated in the transgenic poplar overexpressing PtoMYB74 compared to the wild type, while there was no change in the xylan biosynthetic genes. Transcriptional activation assays demonstrated that PtoMYB74 could activate the promoters of structural genes in the lignin and cellulose biosynthetic pathways. Taken together, our data show that PtoMYB74 positively regulates the secondary cell wall biosynthesis in poplar.

Comparative transcriptome study of hairy and hairless tea plant (Camellia sinensis) shoots

Trichome (also referred to as 'háo' in tea) is a key feature in both tea products and tea plant (Camellia sinensis) selection breeding. Although trichomes are used as a model for studying cell differentiation and have been well studied in many plant species, the regulation of trichome formation at the molecular level is poorly understood in tea plants. In the present study, the hairy and hairless tea plant cultivars Fudingdabaicha (FDDB) and Rongchunzao (RCZ), respectively, were used to study this mechanism. We characterised tea plant trichomes as unicellular and unbranched structures. High-throughput Illumina sequencing yielded approximately 277.0 million high-quality clean reads from the FDDB and RCZ cultivars. After de novo assembly, 161,444 unigenes were generated, with an average length of 937 bp. Among these unigenes, 81,425 were annotated using public databases, and 55,201 coding sequences and 4004 transcription factors (TFs) were identified. In total, 21,599 differentially expressed genes (DEGs) were identified between RCZ and FDDB, of which 10,785 DEGs were up-regulated and 10,814 DEGs were down-regulated. Genes involved in the DNA replication pathway were significantly enriched. Furthermore, between FDDB and RCZ, DEGs related to TFs, phytohormone signals, and cellulose synthesis were identified, suggesting that certain genes involved in these pathways are crucial for trichome initiation in tea plants. Together, the results of this study provide novel data to improve our understanding of the potential molecular mechanisms of trichome formation and lay a foundation for additional trichome studies in tea plants.

Emerging Functions for Cell Wall Polysaccharides Accumulated during Eudicot Seed Development

The formation of seeds is a reproductive strategy in higher plants that enables the dispersal of offspring through time and space. Eudicot seeds comprise three main components, the embryo, the endosperm and the seed coat, where the coordinated development of each is important for the correct formation of the mature seed. In addition, the seed coat protects the quiescent progeny and can provide transport mechanisms. A key underlying process in the production of seed tissues is the formation of an extracellular matrix termed the cell wall, which is well known for its essential function in cytokinesis, directional growth and morphogenesis. The cell wall is composed of a macromolecular network of polymers where the major component is polysaccharides. The attributes of polysaccharides differ with their composition and charge, which enables dynamic remodeling of the mechanical and physical properties of the matrix by adjusting their production, modification or turnover. Accordingly, the importance of specific polysaccharides or modifications is increasingly being associated with specialized functions within seed tissues, often through the spatio-temporal accumulation or remodeling of particular polymers. Here, we review the evolution and accumulation of polysaccharides during eudicot seed development, what is known of their impact on wall architecture and the diverse roles associated with these in different seed tissues.

Seed coats as an alternative molecular factory: thinking outside the box

Seed coats as commodities. Seed coats play important roles in the protection of the embryo from biological attack and physical damage by the environment as well as dispersion strategies. A significant part of the energy devoted by the mother plant to seed production is channeled into the production of the cell layers and metabolites that surround the embryo. Nevertheless, in crop species these are often discarded post-harvest and are a wasted resource that could be processed to yield co-products. The production of novel compounds from existing metabolites is also a possibility. A number of macromolecules are already accumulated in these maternal layers that could be exploited in industrial applications either directly or via green chemistry, notably flavonoids, lignin, lignan, polysaccharides, lipid polyesters and waxes. Here, we summarize our knowledge of the in planta biosynthesis pathways of these macromolecules and their molecular regulation as well as potential applications. We also outline recent work aimed at providing further tools for increasing yields of existing molecules or the development of novel biotech approaches, as well as trial studies aimed at exploiting this underused resource.

Single-Cell Genomic Analysis in Plants

Individual cells in an organism are variable, which strongly impacts cellular processes. Advances in sequencing technologies have enabled single-cell genomic analysis to become widespread, addressing shortcomings of analyses conducted on populations of bulk cells. While the field of single-cell plant genomics is in its infancy, there is great potential to gain insights into cell lineage and functional cell types to help understand complex cellular interactions in plants. In this review, we discuss current approaches for single-cell plant genomic analysis, with a focus on single-cell isolation, DNA amplification, next-generation sequencing, and bioinformatics analysis. We outline the technical challenges of analysing material from a single plant cell, and then examine applications of single-cell genomics and the integration of this approach with genome editing. Finally, we indicate future directions we expect in the rapidly developing field of plant single-cell genomic analysis.

Papillae formation on trichome cell walls requires the function of the mediator complex subunit Med25

Glassy Hair 1 (GLH1) gene that promotes papillae formation on trichome cell walls was identified as a subunit of the transcriptional mediator complex MED25. The MED25 gene is shown to be expressed in trichomes. The expression of the trichome development marker genes GLABRA2 (GL2) and Ethylene Receptor2 (ETR2) is not affected in the glh1 mutant. Presented data suggest that Arabidopsis MED25 mediator component is likely involved in the transcription of genes promoting papillae deposition in trichomes. The plant cell wall plays an important role in communication, defense, organization and support. The importance of each of these functions varies by cell type. Specialized cells, such as Arabidopsis trichomes, exhibit distinct cell wall characteristics including papillae. To better understand the molecular processes important for papillae deposition on the cell wall surface, we identified the GLASSY HAIR 1 (GLH1) gene, which is necessary for papillae formation. We found that a splice-site mutation in the component of the transcriptional mediator complex MED25 gene is responsible for the near papillae-less phenotype of the glh1 mutant. The MED25 gene is expressed in trichomes. Reporters for trichome developmental marker genes GLABRA2 (GL2) and Ethylene Receptor2 (ETR2) were not affected in the glh1 mutant. Collectively, the presented results show that MED25 is necessary for papillae formation on the cell wall surface of leaf trichomes and suggest that the Arabidopsis MED25 mediator component is likely involved in the transcription of a subset of genes that promote papillae deposition in trichomes.

Proteomic Analysis of Differences in Fiber Development between Wild and Cultivated Gossypium hirsutum L

Upland cotton (Gossypium hirsutum L.) is one of the world's most important fiber crops, accounting for more than 90% of all cotton production. While their wild progenitors have relatively short and coarse, often tan-colored fibers, modern cotton cultivars possess longer, finer, stronger, and whiter fiber. In this study, the wild and cultivated cottons (YU-3 and TM-1) selected show significant differences on fibers at 10 days postanthesis (DPA), 20 DPA, and mature stages at the morphological level. To explore the effects of domestication, reveal molecular mechanisms underlying these phenotypic differences, and better inform our efforts to further enhance cotton fiber quality, isobaric tags for relative and absolute protein quantification-facilitated proteomic methods were performed on developing fibers. There were 6990 proteins identified; among them, 336 were defined as differentially expressed proteins between fibers of wild versus domesticated cotton. The down- or up-regulated proteins in wild cotton were involved in phenylpropanoid biosynthesis, zeatin biosynthesis, fatty acid elongation, and other processes. Association analysis between transcriptome and proteome showed positive correlations between transcripts and proteins at both 10 DPA and 20 DPA. Differences in proteomics have been verified at the mRNA level by quantitative real-time polymerase chain reaction and have been validated at the physiological and biochemical levels by POD (peroxidase) activity assays and ZA (zeatin) content estimates. This work corroborates the major pathways involved in cotton fiber development and demonstrates that POD activity and zeatin content have a great potential related to fiber elongation and thickening.

Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls

BACKGROUND

Knowledge of plant secondary cell wall (SCW) regulation and deposition is mainly based on the Arabidopsis model of a 'typical' lignocellulosic SCW. However, SCWs in other plants can vary from this. The SCW of mature cotton seed fibres is highly cellulosic and lacks lignification whereas xylem SCWs are lignocellulosic. We used cotton as a model to study different SCWs and the expression of the genes involved in their formation via RNA deep sequencing and chemical analysis of stem and seed fibre.

RESULTS

Transcriptome comparisons from cotton xylem and pith as well as from a developmental series of seed fibres revealed tissue-specific and developmentally regulated expression of several NAC transcription factors some of which are likely to be important as top tier regulators of SCW formation in xylem and/or seed fibre. A so far undescribed hierarchy was identified between the top tier NAC transcription factors SND1-like and NST1/2 in cotton. Key SCW MYB transcription factors, homologs of Arabidopsis MYB46/83, were practically absent in cotton stem xylem. Lack of expression of other lignin-specific MYBs in seed fibre relative to xylem could account for the lack of lignin deposition in seed fibre. Expression of a MYB103 homolog correlated with temporal expression of SCW CesAs and cellulose synthesis in seed fibres. FLAs were highly expressed and may be important structural components of seed fibre SCWs. Finally, we made the unexpected observation that cell walls in the pith of cotton stems contained lignin and had a higher S:G ratio than in xylem, despite that tissue's lacking many of the gene transcripts normally associated with lignin biosynthesis.

CONCLUSIONS

Our study in cotton confirmed some features of the currently accepted gene regulatory cascade for 'typical' plant SCWs, but also revealed substantial differences, especially with key downstream NACs and MYBs. The lignocellulosic SCW of cotton xylem appears to be achieved differently from that in Arabidopsis. Pith cell walls in cotton stems are compositionally very different from that reported for other plant species, including Arabidopsis. The current definition of a 'typical' primary or secondary cell wall might not be applicable to all cell types in all plant species.

Cellulosic fibres of flax recruit both primary and secondary cell wall cellulose synthases during deposition of thick tertiary cell walls and in the course of graviresponse

Cellulose synthesising complex consists of cellulose synthase (CESA) subunits encoded by a multigene family; different sets of CESA genes are known to be expressed during primary and secondary cell wall formation. We examined the expression of LusCESAs in flax (Linum usitatissimum L.) cellulosic fibres at various stages of development and in the course of graviresponse by means of RNA-Seq and quantitative PCR. Transcripts for both primary and secondary cell wall-related CESAs were abundant in fibres depositing highly cellulosic tertiary cell walls. Gravistimulation of flax plants temporally increased the abundance of CESA transcripts, specifically in phloem fibres located at the pulling stem side. Construction of coexpression networks for LusCESAs revealed that both primary and secondary cell wall-related CESAs were involved in the joint coexpression group in fibres depositing tertiary cell walls, as distinct from other tissues, where these genes were within separate groups. The obtained data suggest that fibres depositing tertiary cell walls have a specific mechanism of cellulose biosynthesis and a specific way of its regulation.

Formation of wood secondary cell wall may involve two type cellulose synthase complexes in Populus

Cellulose biosynthesis is mediated by cellulose synthases (CesAs), which constitute into rosette-like cellulose synthase complexe (CSC) on the plasma membrane. Two types of CSCs in Arabidopsis are believed to be involved in cellulose synthesis in the primary cell wall and secondary cell walls, respectively. In this work, we found that the two type CSCs participated cellulose biosynthesis in differentiating xylem cells undergoing secondary cell wall thickening in Populus. During the cell wall thickening process, expression of one type CSC genes increased while expression of the other type CSC genes decreased. Suppression of different type CSC genes both affected the wall-thickening and disrupted the multilaminar structure of the secondary cell walls. When CesA7A was suppressed, crystalline cellulose content was reduced, which, however, showed an increase when CesA3D was suppressed. The CesA suppression also affected cellulose digestibility of the wood cell walls. The results suggest that two type CSCs are involved in coordinating the cellulose biosynthesis in formation of the multilaminar structure in Populus wood secondary cell walls.

Genome-wide identification of multifunctional laccase gene family in cotton (Gossypium spp.); expression and biochemical analysis during fiber development

The single-celled cotton fibers, produced from seed coat epidermal cells are the largest natural source of textile fibers. The economic value of cotton fiber lies in its length and quality. The multifunctional laccase enzymes play important roles in cell elongation, lignification and pigmentation in plants and could play crucial role in cotton fiber quality. Genome-wide analysis of cultivated allotetraploid (G. hirsutum) and its progenitor diploid (G. arboreum and G. raimondii) cotton species identified 84, 44 and 46 laccase genes, respectively. Analysis of chromosomal location, phylogeny, conserved domain and physical properties showed highly conserved nature of laccases across three cotton species. Gene expression, enzymatic activity and biochemical analysis of developing cotton fibers was performed using G. arboreum species. Of the total 44, 40 laccases showed expression during different stages of fiber development. The higher enzymatic activity of laccases correlated with higher lignin content at 25 DPA (Days Post Anthesis). Further, analysis of cotton fiber phenolic compounds showed an overall decrease at 25 DPA indicating possible incorporation of these substrates into lignin polymer during secondary cell wall biosynthesis. Overall data indicate significant roles of laccases in cotton fiber development, and presents an excellent opportunity for manipulation of fiber development and quality.

GhMCS1, the Cotton Orthologue of Human GRIM-19, Is a Subunit of Mitochondrial Complex I and Associated with Cotton Fibre Growth

GRIM-19 (Gene associated with Retinoid-Interferon-induced Mortality 19) is a subunit of mitochondrial respiratory complex I in mammalian systems, and it has been demonstrated to be a multifunctional protein involved in the cell cycle, cell motility and innate immunity. However, little is known about the molecular functions of its homologues in plants. Here, we characterised GhMCS1, an orthologue of human GRIM-19 from cotton (Gossypium hirsutum L.), and found that it was essential for maintaining complex integrity and mitochondrial function in cotton. GhMCS1 was detected in various cotton tissues, with high levels expressed in developing fibres and flowers and lower levels in leaves, roots and ovules. In fibres at different developmental stages, GhMCS1 expression peaked at 5-15 days post anthesis (dpa) and then decreased at 20 dpa and diminished at 25 dpa. By Western blot analysis, GhMCS1 was observed to be localised to the mitochondria of cotton leaves and to colocalise with complex I. In Arabidopsis, GhMCS1 overexpression enhanced the assembly of complex I and thus respiratory activity, whereas the GhMCS1 homologue (At1g04630) knockdown mutants showed significantly decreased respiratory activities. Furthermore, the mutants presented with some phenotypic changes, such as smaller whole-plant architecture, poorly developed seeds and fewer trichomes. More importantly, in the cotton fibres, both the GhMCS1 transcript and protein levels were correlated with respiratory activity and fibre developmental phase. Our results suggest that GhMCS1, a functional ortholog of the human GRIM-19, is an essential subunit of mitochondrial complex I and is involved in cotton fibre development. The present data may deepen our knowledge on the potential roles of mitochondria in fibre morphogenesis.

Cotton fiber tips have diverse morphologies and show evidence of apical cell wall synthesis

Cotton fibers arise through highly anisotropic expansion of a single seed epidermal cell. We obtained evidence that apical cell wall synthesis occurs through examining the tips of young elongating Gossypium hirsutum (Gh) and G. barbadense (Gb) fibers. We characterized two tip types in Gh fiber (hemisphere and tapered), each with distinct apical diameter, central vacuole location, and distribution of cell wall components. The apex of Gh hemisphere tips was enriched in homogalacturonan epitopes, including a relatively high methyl-esterified form associated with cell wall pliability. Other wall components increased behind the apex including cellulose and the α-Fuc-(1,2)-β-Gal epitope predominantly found in xyloglucan. Gb fibers had only one narrow tip type featuring characters found in each Gh tip type. Pulse-labeling of cell wall glucans indicated wall synthesis at the apex of both Gh tip types and in distal zones. Living Gh hemisphere and Gb tips ruptured preferentially at the apex upon treatment with wall degrading enzymes, consistent with newly synthesized wall at the apex. Gh tapered tips ruptured either at the apex or distantly. Overall, the results reveal diverse cotton fiber tip morphologies and support primary wall synthesis occurring at the apex and discrete distal regions of the tip.

Transcriptomic analysis supports the role of CATION EXCHANGER 1 in cellular homeostasis and oxidative stress limitation during cadmium stress

Investigation of genetic determinants of Cd tolerance in the Zn/Cd hyperaccumulator Arabidopsis halleri allowed the identification of the vacuolar Ca(2+)/H(+) exchanger encoding CAX1 gene. CAX1 was proposed to interfere with the positive feedback loop between Reactive Oxygen Species (ROS) production and Cd-induced cytosolic Ca(2+) spikes, especially at low external Ca(2+) supply. In this study expression of genes involved in ROS homeostasis, cell wall composition, apoplastic pH regulation and Ca(2+) homeostasis were monitored in Arabidopsis thaliana wild-type and cax1-1 knock-out mutant and in Arabidopsis halleri wild-type exposed to cadmium or in control conditions. Clustering the outputs of the expression analysis in a gene co-expression network revealed that CAX1 and genes involved in Ca(2+) cellular homeostasis, apoplastic pH and oxidative stress response were highly correlated in A. thaliana, but not in A. halleri. Many of the studied genes were already highly expressed in A. halleri and/or their expression was not modified by exposure to Cd. The results further supported the role of CAX1 in the regulation of cytosolic ROS accumulation as well as the existence of different cell wall modifications strategies in response to Cd in Arabidopsis thaliana and halleri.

Insights into the Ecology and Evolution of Polyploid Plants through Network Analysis

Polyploidy is a widespread phenomenon throughout eukaryotes, with important ecological and evolutionary consequences. Although genes operate as components of complex pathways and networks, polyploid changes in genes and gene expression have typically been evaluated as either individual genes or as a part of broad-scale analyses. Network analysis has been fruitful in associating genomic and other 'omic'-based changes with phenotype for many systems. In polyploid species, network analysis has the potential not only to facilitate a better understanding of the complex 'omic' underpinnings of phenotypic and ecological traits common to polyploidy, but also to provide novel insight into the interaction among duplicated genes and genomes. This adds perspective to the global patterns of expression (and other 'omic') change that accompany polyploidy and to the patterns of recruitment and/or loss of genes following polyploidization. While network analysis in polyploid species faces challenges common to other analyses of duplicated genomes, present technologies combined with thoughtful experimental design provide a powerful system to explore polyploid evolution. Here, we demonstrate the utility and potential of network analysis to questions pertaining to polyploidy with an example involving evolution of the transgressively superior cotton fibres found in polyploid Gossypium hirsutum. By combining network analysis with prior knowledge, we provide further insights into the role of profilins in fibre domestication and exemplify the potential for network analysis in polyploid species.

Comprehensive Analysis of the COBRA-Like (COBL) Gene Family in Gossypium Identifies Two COBLs Potentially Associated with Fiber Quality

COBRA-Like (COBL) genes, which encode a plant-specific glycosylphosphatidylinositol (GPI) anchored protein, have been proven to be key regulators in the orientation of cell expansion and cellulose crystallinity status. Genome-wide analysis has been performed in A. thaliana, O. sativa, Z. mays and S. lycopersicum, but little in Gossypium. Here we identified 19, 18 and 33 candidate COBL genes from three sequenced cotton species, diploid cotton G. raimondii, G. arboreum and tetraploid cotton G. hirsutum acc. TM-1, respectively. These COBL members were anchored onto 10 chromosomes in G. raimondii and could be divided into two subgroups. Expression patterns of COBL genes showed highly developmental and spatial regulation in G. hirsutum acc. TM-1. Of them, GhCOBL9 and GhCOBL13 were preferentially expressed at the secondary cell wall stage of fiber development and had significantly co-upregulated expression with cellulose synthase genes GhCESA4, GhCESA7 and GhCESA8. Besides, GhCOBL9 Dt and GhCOBL13 Dt were co-localized with previously reported cotton fiber quality quantitative trait loci (QTLs) and the favorable allele types of GhCOBL9 Dt had significantly positive correlations with fiber quality traits, indicating that these two genes might play an important role in fiber development.

A R2R3-MYB transcription factor that is specifically expressed in cotton (Gossypium hirsutum) fibers affects secondary cell wall biosynthesis and deposition in transgenic Arabidopsis

Secondary cell wall (SCW) is an important industrial raw material for pulping, papermaking, construction, lumbering, textiles and potentially for biofuel production. The process of SCW thickening of cotton fibers lays down the cellulose that will constitute the bulk (up to 96%) of the fiber at maturity. In this study, a gene encoding a MYB-domain protein was identified in cotton (Gossypium hirsutum) and designated as GhMYBL1. Quantitative real-time polymerase chain reaction (RT-PCR) analysis revealed that GhMYBL1 was specifically expressed in cotton fibers at the stage of secondary wall deposition. Further analysis indicated that this protein is a R2R3-MYB transcription factor, and is targeted to the cell nucleus. Overexpression of GhMYBL1 in Arabidopsis affected the formation of SCW in the stem xylem of the transgenic plants. The enhanced SCW thickening also occurred in the interfascicular fibers, xylary fibers and vessels of the GhMYBL1-overexpression transgenic plants. The expression of secondary wall-associated genes, such as CesA4, CesA7, CesA8, PAL1, F5H and 4CL1, were upregulated, and consequently, cellulose and lignin biosynthesis were enhanced in the GhMYBL1 transgenic plants. These data suggested that GhMYBL1 may participate in modulating the process of secondary wall biosynthesis and deposition of cotton fibers.

Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation

Background

The morphogenesis of single-celled cotton fiber includes extreme elongation and staged cell wall differentiation. Designing strategies for improving cotton fiber for textiles and other uses relies on uncovering the related regulatory mechanisms. In this research we compared the transcriptomes and metabolomes of two Gossypium genotypes, Gossypium barbadense cv Phytogen 800 and G. hirsutum cv Deltapine 90. When grown in parallel, the two types of fiber developed similarly except for prolonged fiber elongation in the G. barbadense cultivar. The data were collected from isolated fibers between 10 to 28 days post anthesis (DPA) representing: primary wall synthesis to support elongation; transitional cell wall remodeling; and secondary wall cellulose synthesis, which was accompanied by continuing elongation only in G. barbadense fiber.

Results

Of 206 identified fiber metabolites, 205 were held in common between the two genotypes. Approximately 38,000 transcripts were expressed in the fiber of each genotype, and these were mapped to the reference set and interpreted by homology to known genes. The developmental changes in the transcriptomes and the metabolomes were compared within and across genotypes with several novel implications. Transitional cell wall remodeling is a distinct stable developmental stage lasting at least four days (18 to 21 DPA). Expression of selected cell wall related transcripts was similar between genotypes, but cellulose synthase gene expression patterns were more complex than expected. Lignification was transcriptionally repressed in both genotypes. Oxidative stress was lower in the fiber of G. barbadense cv Phytogen 800 as compared to G. hirsutum cv Deltapine 90. Correspondingly, the G. barbadense cultivar had enhanced capacity for management of reactive oxygen species during its prolonged elongation period, as indicated by a 138-fold increase in ascorbate concentration at 28 DPA.

Conclusions

The parallel data on deep-sequencing transcriptomics and non-targeted metabolomics for two genotypes of single-celled cotton fiber showed that a discrete developmental stage of transitional cell wall remodeling occurs before secondary wall cellulose synthesis begins. The data showed how lignification can be transcriptionally repressed during secondary cell wall synthesis, and they implicated enhanced capacity to manage reactive oxygen species through the ascorbate-glutathione cycle as a positive contributor to fiber length.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1708-9) contains supplementary material, which is available to authorized users.

Plant cellulose synthesis: CESA proteins crossing kingdoms

Cellulose is a biopolymer of considerable economic importance. It is synthesised by the cellulose synthase complex (CSC) in species ranging from bacteria to higher plants. Enormous progress in our understanding of bacterial cellulose synthesis has come with the recent publication of both the crystal structure and biochemical characterisation of a purified complex able to synthesis cellulose in vitro. A model structure of a plant CESA protein suggests considerable similarity between the bacterial and plant cellulose synthesis. In this review article we will cover current knowledge of how plant CESA proteins synthesise cellulose. In particular the focus will be on the lessons learned from the recent work on the catalytic mechanism and the implications that new data on cellulose structure has for the assembly of CESA proteins into the large complex that synthesis plant cellulose microfibrils.

Expression divergence of cellulose synthase (CesA) genes after a recent whole genome duplication event in Populus

Secondary cell wall-associated CesA genes in Populus have undergone a functional differentiation in expression pattern that may be attributable to evolutionary alteration of regulatory modules. Gene duplication is an important mechanism for functional divergence of genes. Secondary cell wall-associated cellulose synthase genes (CesA4, CesA7 and CesA8) are duplicated in Populus plants due to a recent whole genome duplication event. Here, we demonstrate that duplicate CesA genes show tissue-dependent expression divergence in Populus plants. Real-time PCR analysis of Populus CesA genes suggested that Pt × tCesA8-B was more highly expressed than Pt × tCesA8-A in phloem and secondary xylem tissue of mature stem. Histochemical and histological analyses of transformants expressing a GFP-GUS fusion gene driven by Populus CesA promoters revealed that the duplicate CesA genes showed different expression patterns in phloem fibers, secondary xylem, root cap and leaf trichomes. We predicted putative cis-regulatory motifs that regulate expression of secondary cell wall-associated CesA genes, and identified 19 motifs that are highly conserved in the CesA gene family of eudicotyledonous plants. Furthermore, a transient transactivation assay identified candidate transcription factors that affect levels and patterns of expression of Populus CesA genes. The present study reveals that secondary cell wall-associated CesA genes in Populus have undergone a functional differentiation in expression pattern that may be attributable to evolutionary alteration of regulatory modules.

Two cotton fiber-associated glycosyltransferases, GhGT43A1 and GhGT43C1, function in hemicellulose glucuronoxylan biosynthesis during plant development

Xylan is the major hemicellulosic constituent in dicot secondary cell walls. Cell wall composition of cotton fiber changes dynamically throughout development. Not only the amounts but also the molecular sizes of the hemicellulosic polysaccharides show substantial changes during cotton fiber development. However, none of the genes encoding glycosyltransferases (GTs) responsible for synthesizing xylan have been isolated and characterized in cotton fiber. In this study, we applied a bioinformatics approach and identified two putative GTs from cotton, designated GhGT43A1 and GhGT43C1, which belong to the CAZy GT43 family and are closely related to Arabidopsis IRX9 and IRX14, respectively. We show that GhGT43A1 is highly and preferentially expressed in 15 and 20 days post-anthesis (dpa) cotton fiber, whereas GhGT43C1 is ubiquitously expressed in most organs, with especially high expression in 15 dpa fiber and hypocotyl. Complementation analysis demonstrates that GhG43A1 and GhGT43C1 are orthologs of Arabidopsis IRX9 and IRX14, respectively. Furthermore, we show that overexpression of GhGT43A1 or GhGT43C1 in Arabidopsis results in increased xylan content. We also show that overexpression of GhGT43A1 or GhGT43C1 leads to more cellulose deposition. These findings suggest that GhGT43A1 and GhGT43C1 likely participate in xylan synthesis during fiber development.

Alfalfa Cellulose synthase gene expression under abiotic stress: a Hitchhiker's guide to RT-qPCR normalization

Abiotic stress represents a serious threat affecting both plant fitness and productivity. One of the promptest responses that plants trigger following abiotic stress is the differential expression of key genes, which enable to face the adverse conditions. It is accepted and shown that the cell wall senses and broadcasts the stress signal to the interior of the cell, by triggering a cascade of reactions leading to resistance. Therefore the study of wall-related genes is particularly relevant to understand the metabolic remodeling triggered by plants in response to exogenous stresses. Despite the agricultural and economical relevance of alfalfa (Medicago sativa L.), no study, to our knowledge, has addressed specifically the wall-related gene expression changes in response to exogenous stresses in this important crop, by monitoring the dynamics of wall biosynthetic gene expression. We here identify and analyze the expression profiles of nine cellulose synthases, together with other wall-related genes, in stems of alfalfa plants subjected to different abiotic stresses (cold, heat, salt stress) at various time points (e.g. 0, 24, 72 and 96 h). We identify 2 main responses for specific groups of genes, i.e. a salt/heat-induced and a cold/heat-repressed group of genes. Prior to this analysis we identified appropriate reference genes for expression analyses in alfalfa, by evaluating the stability of 10 candidates across different tissues (namely leaves, stems, roots), under the different abiotic stresses and time points chosen. The results obtained confirm an active role played by the cell wall in response to exogenous stimuli and constitute a step forward in delineating the complex pathways regulating the response of plants to abiotic stresses.

Cotton KNL1, encoding a class II KNOX transcription factor, is involved in regulation of fibre development

In this study, the GhKNL1 (KNOTTED1-LIKE) gene, encoding a classical class II KNOX protein was identified in cotton (Gossypium hirsutum). GhKNL1 was preferentially expressed in developing fibres at the stage of secondary cell wall (SCW) biosynthesis. GhKNL1 was localized in the cell nucleus, and could interact with GhOFP4, as well as AtOFP1, AtOFP4, and AtMYB75. However, GhKNL1 lacked transcriptional activation activity. Dominant repression of GhKNL1 affected fibre development of cotton. The expression levels of genes related to fibre elongation and SCW biosynthesis were altered in transgenic fibres of cotton. As a result, transgenic cotton plants produced aberrant, shrunken, and collapsed fibre cells. Length and cell-wall thickness of fibres of transgenic cotton plants were significantly reduced compared with the wild type. Furthermore, overexpression and dominant repression of GhKNL1 in Arabidopsis resulted in a reduction in interfascicular fibre cell-wall thickening of basal stems of transgenic plants. Complementation revealed that GhKNL1 rescued the defective phenotype of Arabidopsis knat7 mutant in some extent. These data suggest that GhKNL1, as a transcription factor, participates in regulating fibre development of cotton.

Aberrant phenotype and transcriptome expression during fiber cell wall thickening caused by the mutation of the Im gene in immature fiber (im) mutant in Gossypium hirsutum L

BACKGROUND

The immature fiber (im) mutant of Gossypium hirsutum L. is a special cotton fiber mutant with non-fluffy fibers. It has low dry weight and fineness of fibers due to developmental defects in fiber secondary cell wall (SCW).

RESULTS

We compared the cellulose content in fibers, thickness of fiber cell wall and fiber transcriptional profiling during SCW development in im mutant and its near-isogenic wild-type line (NIL) TM-1. The im mutant had lower cellulose content and thinner cell walls than TM-1 at same fiber developmental stage. During 25 ~ 35 day post-anthesis (DPA), sucrose content, an important carbon source for cellulose synthesis, was also significantly lower in im mutant than in TM-1. Comparative analysis of fiber transcriptional profiling from 13 ~ 25 DPA indicated that the largest transcriptional variations between the two lines occurred at the onset of SCW development. TM-1 began SCW biosynthesis approximately at 16 DPA, whereas the same fiber developmental program in im mutant was delayed until 19 DPA, suggesting an asynchronous fiber developmental program between TM-1 and im mutant. Functional classification and enrichment analysis of differentially expressed genes (DEGs) between the two NILs indicated that genes associated with biological processes related to cellulose synthesis, secondary cell wall biogenesis, cell wall thickening and sucrose metabolism, respectively, were significantly up-regulated in TM-1. Twelve genes related to carbohydrate metabolism were validated by quantitative reverse transcription PCR (qRT-PCR) and confirmed a temporal difference at the earlier transition and SCW biosynthesis stages of fiber development between TM-1 and im mutant.

CONCLUSIONS

We propose that Im is an important regulatory gene influencing temporal differences in expression of genes related to fiber SCW biosynthesis. This study lays a foundation for cloning the Im gene, elucidating molecular mechanism of fiber SCW development and further genetic manipulation for the improvement of fiber fineness and maturity.

Polyploidy and the petal transcriptome of Gossypium

Background

Genes duplicated by polyploidy (homoeologs) may be differentially expressed in plant tissues. Recent research using DNA microarrays and RNAseq data have described a cacophony of complex expression patterns during development of cotton fibers, petals, and leaves. Because of its highly canalized development, petal tissue has been used as a model tissue for gene expression in cotton. Recent advances in cotton genome annotation and assembly now permit an enhanced analysis of duplicate gene deployment in petals from allopolyploid cotton.

Results

Homoeologous gene expression levels were quantified in diploid and tetraploid flower petals of Gossypium using the Gossypium raimondii genome sequence as a reference. In the polyploid, most homoeologous genes were expressed at equal levels, though a subset had an expression bias of A_T and D_T copies. The direction of gene expression bias was conserved in natural and recent polyploids of cotton. Conservation of direction of bias and additional comparisons between the diploids and tetraploids suggested different regulation mechanisms of gene expression. We described three phases in the evolution of cotton genomes that contribute to gene expression in the polyploid nucleus.

Conclusions

Compared to previous studies, a surprising level of expression homeostasis was observed in the expression patterns of polyploid genomes. Conserved expression bias in polyploid petals may have resulted from cis-acting modifications that occurred prior to polyploidization. Some duplicated genes were intriguing exceptions to general trends. Mechanisms of gene regulation for these and other genes in the cotton genome warrants further investigation.

Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome

The single-celled cotton (Gossypium hirsutum) fiber provides an excellent model to investigate how human selection affects phenotypic evolution. To gain insight into the evolutionary genomics of cotton domestication, we conducted comparative transcriptome profiling of developing cotton fibers using RNA-Seq. Analysis of single-celled fiber transcriptomes from four wild and five domesticated accessions from two developmental time points revealed that at least one-third and likely one-half of the genes in the genome are expressed at any one stage during cotton fiber development. Among these, ∼5,000 genes are differentially expressed during primary and secondary cell wall synthesis between wild and domesticated cottons, with a biased distribution among chromosomes. Transcriptome data implicate a number of biological processes affected by human selection, and suggest that the domestication process has prolonged the duration of fiber elongation in modern cultivated forms. Functional analysis suggested that wild cottons allocate greater resources to stress response pathways, while domestication led to reprogrammed resource allocation toward increased fiber growth, possibly through modulating stress-response networks. This first global transcriptomic analysis using multiple accessions of wild and domesticated cottons is an important step toward a more comprehensive systems perspective on cotton fiber evolution. The understanding that human selection over the past 5,000+ years has dramatically re-wired the cotton fiber transcriptome sets the stage for a deeper understanding of the genetic architecture underlying cotton fiber synthesis and phenotypic evolution.

Ever since Darwin biologists have recognized that comparative study of crop plants and their wild relatives offers a powerful framework for generating insights into the mechanisms that underlie evolutionary change. Here, we study the domestication process in cotton, Gossypium hirsutum, an allopolyploid species (containing two different genomes) which initially was domesticated approximately 5000 years ago, and which primarily is grown for its single-celled seed fibers. Strong directional selection over the millennia was accompanied by transformation of the short, coarse, and brown fibers of wild plants into the long, strong, and fine white fibers of the modern cotton crop plant. To explore the evolutionary genetics of cotton domestication, we conducted transcriptome profiling of developing cotton fibers from multiple accessions of wild and domesticated cottons. Comparative analysis revealed that the domestication process dramatically rewired the transcriptome, affecting more than 5,000 genes, and with a more evenly balanced usage of the duplicated copies arising from genome doubling. We identify many different biological processes that were involved in this transformation, including those leading to a prolongation of fiber elongation and a reallocation of resources toward increased fiber growth in modern forms. The data provide a rich resource for future functional analyses targeting crop improvement and evolutionary objectives.

Arabidopsis GLASSY HAIR genes promote trichome papillae development

Specialized plant cells form cell walls with distinct composition and properties pertinent to their function. Leaf trichomes in Arabidopsis form thick cell walls that support the upright growth of these large cells and, curiously, have strong light-reflective properties. To understand the process of trichome cell-wall maturation and the molecular origins of this optical property, mutants affected in trichome light reflection were isolated and characterized. It was found that GLASSY HAIR (GLH) genes are required for the formation of surface papillae structures at late stages of trichome development. Trichomes in these mutants appeared transparent due to unobstructed light transmission. Genetic analysis of the isolated mutants revealed seven different gene loci. Two--TRICHOME BIREFRINGENCE (TBR) and NOK (Noeck)--have been reported previously to have the glassy trichome mutant phenotype. The other five glh mutants were analysed for cell-wall-related phenotypes. A significant reduction was found in cellulose content in glh2 and glh4 mutant trichomes. In addition to the glassy trichome phenotype, the glh6 mutants showed defects in leaf cuticular wax, and glh6 was found to represent a new allele of the eceriferum 10 (cer10) mutation. Trichomes of the glh1 and glh3 mutants did not show any other phenotypes beside reduced papillae formation. These data suggest that the GLH1 and GLH3 genes may have specific functions in trichome papillae formation, whereas GLH2, GLH4, and GLH6 genes are also involved in deposition of other cell-wall components.