9.1 Introduction

As the world’s leading natural fiber and the second largest oilseed crop, cotton (Gossypium) is a mainstay of global economies. In the later years of the twentieth century, biotechnology has advanced with unprecedented speed and ever-widening range of involvement of different disciplines and technologies. Transgenic insect-resistant Bt cotton was the first biotechnology crop grown in China, by which China has become the second country in the world in developing Bt cotton after USA (ISAAA report, 2007, from internet data). The rapid increase in transgenic cotton acreage in such a short period of time attests to the overall success of agricultural biotechnology.

Cotton fiber plays an irreplaceable role in the textile industry owing to its excellent natural properties. With people’s increasing living standards and pursuit of returning to nature, good quality cotton textile is in great demand. Therefore, fiber modification has become one of the main objectives for cotton breeding. In the past decade, traditional and hybridization breeding has played a critical role in the improvement of cotton fiber quality. However, further progress can be difficult largely due to the long breeding cycle, insufficient germplasm resources, and negative correlation between fiber productivity and quality. In recent years, rapid development of functional genomics, genetic and analytic tools, especially comprehensive profiling of gene expression of cotton fiber cells, and application of model systems (such as Arabidopsis, tobacco, and yeast) has provided a new opportunity to improve the cotton fiber traits by genetic modification. As new generations of sequencing technologies such as Solexa (known as Illumina) and 454 pyrosequencing (Roche) have drastically lowered the cost of DNA sequencing, international collaborations on cotton genome sequencing have become possible. Without doubt, genome sequence information will greatly deepen our understanding of the cotton crop, genome evolution, fiber cell development, cellulose and cell wall biosynthesis, and accelerate molecular breeding of new cotton cultivars (Chen et al. 2007).

9.2 Transcriptome of Cotton Fiber

Lint fibers of cotton are extensively elongated single epidermal cells that develop on the outer surface of ovules (outer integument). Cotton fiber initiates from 1 day preanthesis to 1 day postanthesis (DPA) and undergoes rapid elongation immediately after fertilization (Wu et al. 2006). The development of cotton fiber can be divided into four distinct but overlapping stages including fiber initiation, elongation, secondary cell wall deposition, and maturation (Basra and Malik 1984; Kim and Triplett 2001). Cotton fiber initiation and elongation are two important stages during cotton fiber development, as the initiation program determines the number of ovule epidermal cells that will differentiate into fiber cells and thus affects fiber yield, and the elongation stage is crucial for the final fiber length, a key trait of fiber quality. Cotton functional genomics studies related to fiber development focus on these two stages (Xu et al. 2007).

Transcriptome analysis, a powerful and high throughput tool to detect differentially expressed genes, has been extensively applied not only to reveal physiological states of cells, but also to identify gene functions. This approach is of great importance for cotton plants, as the complexity of cotton genome makes its investigation difficult and costly (Wilkins and Arpat 2005). An early attempt compared gene expression of 5–10-DPA ovules of a fuzzless-lintless (fl) mutant with those of ovules from the wild-type cotton (Gossypium hirsutum cv. Xu-142) using cDNA array containing 1,536 cDNA clones (Li et al. 2002a), which identified several genes whose transcripts were enriched in fiber cells, including GhWBC1 (Zhu et al. 2003), GhRDL1 (Wang et al. 2004), and GhSAHH (Li et al. 2008). Arpat et al. (2004) took a genomics approach to cotton fiber research by examining a large number of expressed sequence tags (ESTs) from elongating cotton fiber cells. They identified approximately 14,000 unique genes from 46,630 ESTs present in developing cotton fiber. The fiber transcriptome was estimated to represent 35%–40% of the genes in the cotton genome. Almost two-third of these annotated genes fell into three major categories: cell wall structure and biogenesis, cytoskeleton-related, and energy/carbohydrate metabolism (Arpat et al. 2004). Oligonucleotide microarrays revealed dynamic changes in gene expression between primary and secondary cell wall biogenesis, with more than 2,500 genes down-regulated at the end of the active elongation period and 81 genes preferentially upregulated during secondary cell wall synthesis. This study sheds new insight into how transcriptional activity defines different physiological and biochemical states in fiber cells at different developmental stages and also provided numerous potentially interesting target genes for functional characterization (Arpat et al. 2004). In a later large-scale transcriptome analysis, a cDNA library from wild-type cotton ovules at fast elongation stage, which the cotton fiber elongate rapidly after initiation of elongation, was used, and a total of 12,233 unique sequences from 29,992 high-quality ESTs were obtained. Among them, 2,522 genes were significantly upregulated during elongation stage. In comparison with transcriptomes of the 3- and 10-DPA wild-type ovules and those of the fl mutant, 778 genes were fiber specific (Shi et al. 2006). More recently, gene expression in relation to metabolite changes of cotton fiber during cell elongation and secondary cell wall synthesis stages were analyzed, which showed that the genes involved in auxin signaling, cell wall-loosening, and lipid metabolism were highly expressed during fiber elongation stage. At secondary cell wall synthesis stage, genes related to cellulose biosynthesis were predominantly transcribed, whereas many other metabolic pathways were inactive. Transcriptional and metabolite profiling and enzyme activities were consistent with a specialization process of cotton fiber development toward cellulose synthesis (Gou et al. 2007).

Compared to the fiber cell elongation stage, the molecular feature of cotton fiber initiation stage remains largely mysterious. Fiber cell initiation is a complex process involving many pathways, including various signaling and transcriptional regulation components. Yang et al. (2006) generated an EST library, named GH_TMO ESTs library, using the ovules of earlier stages (−3 to 3DPA). In comparison with approximately 178,000 existing ESTs derived from elongating fibers and nonfiber tissues, GH_TMO ESTs show a significant enrichment of the genes encoding putative transcription factors, such as MYB and WRKY proteins and the genes encoding predicted proteins involved in auxin, brassinosteroid (BR), gibberellic acid (GA), abscisic acid (ABA) and ethylene signaling pathways. These data are consistent not only with the known roles of MYB and WRKY transcription factors in leaf trichome initiation in Arabidopsis, but also with the effects of phytohormones on fiber cell development documented by using in vitro cotton ovule culture system. Interestingly, most of the phytohormonal pathway-related genes were induced prior to the activation of MYB-like genes, implying an important role of phytohormones in cell fate determination (Yang et al. 2006). In another investigation, gene expression profiles of the 0-DPA ovules of six fiber development mutants were compared with those of the wild-type cotton, using cDNA microarray, which showed that 13 different genes were downregulated in some or all of the six mutants. Among them GhMYB25, which shows a high sequence identity to Antirrhinum MYB gene MIXTA, was upregulated in fiber initials relative to adjacent nonfiber ovule epidermal cells on the day of anthesis, suggesting a possible involvement of GhMYB25 in cotton fiber initiation (Wu et al. 2006) (Table 9.1).

Table 9.1 Transcription factor genes related to cotton fiber development and their Arabidopsis homologs
Full size table

A comprehensive global cotton EST database was set up in 2006 with a total of 185,000 ESTs collected from more than 30 different cDNA libraries from various cotton tissues and organs. By sequence comparisons, 51,107 unique genes were identified and 33,665 of them represent partial or full-length nonrepeated coding regions (Udall et al. 2006). About 375,392 ESTs are now available for the Gossypium species in the Genbank database. A rich source of ESTs and cDNA sequences is invaluable not only for understanding the mechanisms regulating cotton fiber development, but also for cotton genomics studies and for generating new molecular markers for breeding. For example, from 489 primer pairs derived from EST-SSR, 123 polymorphisms were found. These markers were distributed over 20 chromosomes and six linkage groups in the cotton genetic map (Han et al. 2006).

9.3 Functional Identification of Genes Related to Cotton Fiber Development

9.3.1 Transcription Factors

Cotton fibers are seed epidermal hairs, which share many features with leaf trichomes, although the cotton fiber is unbranched. The models established for Arabidopsis leaf trichomes may provide a framework for understanding fiber cell initiation and elongation (Table 9.1). MYB transcription factors are key regulators controlling Arabidopsis trichomes development. GLABRA (GL1) is a well-documented R2R3 MYB transcription factor regulating trichome fate determination, and gl1 loss-of function mutants show a glabrous phenotype with only few trichomes on the edge of rosette leaves (Oppenheimer et al. 1991). AtMYB23 is also an R2R3 MYB transcriptional regulator and has partially overlapping functions with GL1 (Kirik et al. 2005). Genetic and molecular evidence shows that GL1 forms a multimeric complex with TRANSPARENT TESTA GLABRA1 (TTG1), a WD40 protein (Walker et al. 1999), and GLABRA3 (GL3) or EGL3, a basic helix-loop-helix protein (Payne et al. 2000; Esch et al. 2003; Zhang et al. 2003). GL1-TTG-GL3 complex triggers trichome cell initiation probably by controlling the expression of GLABRA2 (GL2), which encodes a homeodomain-leucine zipper protein (Ramsay and Glover 2005; Serna and Martin 2006). A small family of single-repeat MYB proteins, including CAPRICE (CPC), TRIPTYCHON (TRY), TRICHOMELESS1 (TCL1), ENHANCER OF TRY AND CPC1 (ETC1) and ETC2, negatively regulates trichome initiation and spacing by competing with GL1 for binding to GL3 (Kirik et al. 2004a, b; Wang et al. 2007).

Recent progress on isolation of transcription factors potentially involved in cotton fiber development has provided clues to understanding the early event of cotton fiber development. MYB genes were among the first group under investigation, with emphasis on their expression patterns and evolution in diploid and polyploidy cotton (Loguerico et al. 1999; Cedroni et al. 2003). GaMYB2/FIF1, a GL1-like gene of G. arboreum, is expressed early in developing fiber cells. When properly expressed in Arabidopsis, GaMYB2 was able to restore trichome development to the glabrous gl1 mutant, and its overexpression produced ectopic trichomes on the seed coat, strongly suggesting that GaMYB2 participates in regulating cotton fiber development (Wang et al. 2004). Suo et al. (2003) reported the identification of 55 MYB genes which were expressed in ovules during fiber initiation. Among them GhMYB109, another homolog of GL1, was specifically expressed in cotton fiber initials and elongating fibers. GhMYB25, a homolog of AmMIXTA/AmMYBML1 that controls conical cell and trichome differentiation in Antirrhinum majus petals (Martin et al. 2002; Perez-Rodriguez et al. 2005), was predominately expressed in ovules and fiber cell initials. Overexpression of GhMYB25 in tobacco plants increased branches of leaf trichomes (Wu et al. 2006); whether it is involved in cotton fiber development is an interesting question to be answered. Two cotton single MYB repeat genes, GhCPC1 and GhCPC2, were expressed in fiber cells at 1DPA, and one of them was downregulated in the fiber cells compared to ovule (Taliercio and Boykin 2007). Whether these putative CPC homologs of cotton play a critical role in fiber cell spacing awaits investigation.

Four putative AtTTG1 homologs have been isolated from the ancestral D diploid genomes of tetraploid cotton G. hirsutum. All of them are widely expressed in various organs, including ovules and fibers. When expressed in Arabidopsis, GhTTG1 and GhTTG3 were able to restore trichome formation, seed coat pigmentation, mucilage production, and root hair positioning in the ttg1 mutant (Humphries et al. 2005).

Three homeobox (HOX) genes, GhHOX1, GhHOX2, and GhHOX3, have been identified from cotton as well (Table 9.1). At the predicted amino acid sequence level, they show 66%, 34%, and 37% identities to Arabidopsis GL2, respectively. At least one of them, GhHOX1 that is closest to Arabidopsis GL2, may function in fiber development, as GhHOX1 was able to revert the glabrous phenotype of gl2 mutant, indicating that this homeodomain-leucine zipper protein shares similar function with GL2 in controlling trichome development (Guan et al. 2008).

In the Arabidopsis trichome model, both the positive and the negative MYB regulators interact with the bHLH protein GL3. Both GaMYB2 and GhMYB109 contain the conserved amino acid signature for interaction with bHLH proteins (Serna and Martin 2006). Two GL3-like bHLH cDNAs from cotton ovule, GhDEL65 (AF336280) and GhDEL61 (AF336279), have been deposited in the Genbank (Mandaokar et al. 2003; Shangguan et al. 2008). It will be interesting to examine if they behave like GL3 during cotton fiber development.

Taken together, nearly all the molecular components involved in controlling Arabidopsis trichome development characterized so far have their counterparts in cotton ovule and fiber cells. The ability of cotton transcription factors like GaMYB2, GhMYB109, GhTTG1, GhTTG3, and GhHOX1 to complement the respective trichome mutants of Arabidopsis suggests a similar molecular event triggering cotton fiber and Arabidopsis trichome formation.

9.3.2 Phytohormones

Plant hormones control almost all aspects of plant growth and development. Both the earlier in vitro studies and the recent functional genomics analyses have suggested phytohormones as critical regulators of cotton fiber development and boll retention. In the ESTs library of −3–3DPA (GH_TMO ESTs library), about 230 putative Abscisic acid (ABA)-, Brassinosteroid (BR)-, Gibberellic Acid (GA)-, ethylene- and auxin-related sequences were identified, indicating a role of phytohormones in early stages of fiber development (Yang et al. 2006).

9.3.2.1 Auxin and GA

For several decades, combinations of auxin and GA have been known to promote fiber cell development of in vitro cultured ovules. Exogenous application of indoacetic acid (IAA) and GA3 to flower buds in planta or unfertilized ovules in vitro resulted in an increase of fiber cell number (Beasley and Ting 1974; Gialvails and Seagull 2001). The GH_TMO ESTs library revealed several genes involved in GA biosynthesis, such as GA20ox, GA2ox, POTH1, and KO, and signaling transduction components including GA1, RGL2, RGL1, DPF1, PHOR1, RSG, and GAMYB. Moreover, the library contained putative auxin-related genes, including those of auxin biosynthesis (YUCCAs, CYP83B1s, and NIT2), signaling (ARFs, AUX1, TIR1, and PINs) and transport (AUX1 and PIN1) (Yang et al. 2006), further supporting the importance of auxin and GA in cotton fiber development.

In a cDNA array analysis, five putative auxin response genes were found to be highly expressed in fibers during fast elongation stage (6–12DPA), while their transcript levels were low both before and after the fast elongation stage (Gou et al. 2007). By contrast, expression of a putative auxin-repressed gene (homologous to AF336307) did not increase until the start of secondary cell wall synthesis. These data suggest a high level of auxin response present in rapidly elongating fiber cells and further support the classical assumption that auxin plays a role in promoting cotton fiber elongation (Gou et al. 2007).

9.3.2.2 BR and Ethylene

BR is required for normal plant growth and development. In general, BR has a similar effect as auxin in positively influencing fiber cell development. Application of low concentrations of brassinolide (BL) promoted fiber elongation whereas brassinazole (Brz), a brassinosteroid biosynthesis inhibitor, inhibited fiber development (Sun et al. 2004, 2005; Shi et al. 2006). Treatment of cotton floral buds with Brz resulted in complete absence of fiber differentiation (Sun et al. 2005), and this inhibitory effect could be reversed by simultaneous BL application, confirming that BR is required for fiber initiation and elongation.

The GH_TMO library is enriched with the ESTs corresponding to genes involved in BR biosynthetic and signaling pathways (Yang et al. 2006). BRI1 EMS SUPPRESSOR1 (BES1) is a downstream positive regulator in BR signaling pathway. Overexpression of BES1 was able to promote stem elongation in Arabidopsis. Two putative cotton BES1 homologs were present in the GH_TMO library, but not in the cDNA libraries derived from elongating fibers, suggesting an enhanced role of BR in fiber cell differentiation. BR-INSENSITIVE 2 (BIN2) is presumed to be a negative regulator of BL signaling, and overexpression of BIN2 delayed the development of Arabidopsis. The mRNAs of putative cotton BIN2 homologs were highly accumulated during fiber cell elongation stage (Sun and Allen 2005). At the same time, the cotton homolog of Arabidopsis BRASSINOSTEROID INSENSITIVE1 (BRI1), which encodes a transmembrane BL receptor, was also expressed. Overexpression of cotton BRI1 rescued the phenotype of bri1 mutant of Arabidopsis (Sun et al. 2004). Expression of the fiber genes associated with cell elongation, including XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE (XTH) and EXPANSIN (EXP), ACYL CARRIER PROTEIN (ACP) and ARABINOGALACTAN PROTEIN (AGP) and GhTUB1 (microtubule protein), was increased in ovules treated with BL and suppressed by Brz application, demonstrating that BR promotes fiber elongation by upregulating the expression of genes involved in cell expansion and cell wall reconstruction (Sun et al. 2005). DE-ETIOLATION 2 (DET2), a steroid 5α-reductase, catalyzes a major rate-limiting step of BR biosynthesis in Arabidopsis. A high level of GhDET2 transcripts was detected during the fiber initiation and rapid elongation stages. Antisense-mediated suppression of GhDET2 inhibited both fiber initiation and fiber elongation (Luo et al. 2007). Therefore, the level BRs play a crucial role in the initiation and elongation of cotton fiber cells, suggesting that modulation of BR biosynthesis may improve fiber quality and yield.

Interestingly, physiology and gene expression studies by Zhu and his colleagues revealed an apparent role of ethylene in promoting fiber development (Shi et al. 2006). Addition of ethylene promoted fiber growth in the in vitro cultured ovules, whereas application of aminoethoxyvinylglycine (AVG), an ethylene inhibitor, inhibited fiber cell elongation. In addition, mRNA levels of three cotton 1-aminocyclopropane-1-carboxylate (ACC)-oxidase (ACO) genes peaked during fiber elongation. They further demonstrated that saturated very-long-chain fatty acids (VLCFAs; C20:0–C30:0) may act upstream of ethylene to maximize the extensibility of cotton fibers. The lignoceric acid (C24:0) stimulated ACO gene expression rapidly that resulted in substantial elevation of ethylene production (Qin et al. 2007). In fact, molecular investigation of rice (Oryza sativa) and the marsh dock (Rumex palustris) also illustrated that ethylene was a major factor to promote underwater elongation of stems or leaves along with interactions with other hormones (Jackson 2007).

9.3.2.3 ABA and Cytokinin

ABA was proposed to play a negative role in cotton fiber growth, as application of ABA to the culture of unfertilized ovules caused retardation of fiber development (Beasley and Ting 1974). The inhibitory effect of ABA was partially compensated for by an addition of cytokinin, although cytokinin alone also showed an inhibitory effect on fiber growth (Lee et al. 2007). A notable feature of cotton fiber development is the overlap of elongation and second cell wall biosynthesis stages. It was shown that the high level of endogenous ABA occurred at 16DPA, when the content of cellulose was increasing dramatically, implicating a rise of ABA content as a signal of secondary cell wall biosynthesis, and that the ratio of ABA to auxin levels might be relevant to the regulation of secondary cell wall thickening (Yang et al. 2001).

9.3.3 Cytoskeleton Genes

Expansins are cell wall proteins that facilitate cell wall extension by disruption of noncovalent bonds between wall components. Six genes encoding expansins were isolated. Among them transcripts of GhEXP1 were abundant in fiber cells (Harmer et al. 2002). In developing cotton fiber cells, four genes that belong to the α-expansin family were highly expressed during the fiber outgrowth and fast elongation stages, and were generally downregulated when cells entered the secondary cell wall synthesis stage (Gou et al. 2007).

Microtubules are considered dynamic structures that play a central role in many important processes, such as cell division, cell motility, intracellular transport, and cell shaping. In plants, microtubules with α- and β-tubulins as the major structural components are especially important for cell morphogenesis. Cotton fiber cells contain abundant amounts of tubulins. He et al. (2008) identified 795 cotton tubulin ESTs and cloned 19 β-tubulin (GhTUB) genes at cDNA level; of them nine GhTUBs were expressed at higher levels in the elongating fiber cells than in ovules of the fl mutants. The expression of Gh-β-TubL was correlated with the elongation pattern of fiber cells, and its mRNAs were barely detected in fl ovules. Overexpression of Gh-β-TubL in fission yeast promoted longitudinal growth by 1.74 fold (Ji et al. 2002). Another β-tubulin gene, GhTUB1, was also highly expressed in cotton fiber cells. Histochemical assay of the GhTUB1 promoter fused to the β-Glucuronidase (GUS) reporter gene in transgenic cotton plants showed that high levels of GUS activities were located in young fiber cells, with weak or no GUS expression in other tissues (Li et al. 2002b).

Actin cytoskeleton plays an important role in cell morphogenesis and is essential for cell elongation and tip growth. Actins are encoded by a multigene family that comprises dozens or even hundreds of ACTIN (ACT) genes. In cotton, 15 GhACT genes have been identified, among them GhACT1 was highly transcribed in elongating fiber cells from 8 to 14DPA; importantly, its transcript was barely detectable in other tissues. RNA interference (RNAi) of GhACT1 substantially reduced the accumulation of its mRNA and protein, and disrupted the actin cytoskeleton network in fibers, resulting in a dramatic reduction of fiber length, but without significant inhibition on fiber initiation, suggesting that GhACT1 has a critical function in fiber elongation (Li et al. 2005).

Profilin is an important actin-binding protein involved in regulating the organization of actin filaments. Expression of a cotton profilin gene (GhPFN1) is tightly associated with fast elongation of fiber cells. Overexpression of GhPFN1 in transgenic tobacco cells was correlated with the formation of elongated cells that contained thicker and longer microfilament cables (Wang et al. 2005), suggesting that GhPFN1 may play a role in cotton fiber elongation by promoting actin polymerization.

9.3.4 Other Genes

From a physiological view, the process of fiber cell elongation is associated with strong cell turgor pressure and plasmodesmatal dynamics. During fiber cell development, plasmodesmata are opened from 0 to 9DPA, closed at 10DPA, and opened again at 16DPA. Rapid cell elongation is also associated with transporter activities, with a high expression level of sugar transporter gene during elongating stage (Ruan et al. 2001). SuSy, an encoding sucrose synthase, is highly expressed in initiating and elongating fiber cells, but not in adjacent normal epidermal cells. SuSy expression was dramatically reduced in the epidermis of fl mutant ovule, in correlation with the lack of fiber initials (Ruan and Chourey 1998). Suppression of SuSy expression in transgenic plants resulted in reduced hexose levels in the ovules with a reduction of SuSy activity by 70% or more in ovule epidermis, leading to a fiberless phenotype (Ruan et al. 2003).

In the secondary cell wall synthesis stage, cellulose synthesis is a major event in cotton fiber. Cotton ceLA1 and ceLA2 were the first plant cellulose synthase (CesA) genes identified (Pear et al. 1996). At least five CesA genes showed increased expression levels during secondary cell wall synthesis (Gou et al. 2007). Expression of the gene encoding endo-1,4-/D-glucanase, a cell wall related enzyme, was decreased when cell elongation ceased (Shimizu et al. 1997), suggesting that it plays a specific role during fast elongation stage.

9.3.5 Fiber-Specific Promoters

Compared to the constitutive promoters, such as the CaMV 35S promoter, a tissue-specific promoter can direct target gene expression in a specified tissue without altering pathways in other tissues, thus avoiding negative effects on plant growth. Promoters from a number of fiber-specific genes have been isolated and their activities were assayed using transgenic plants. Most of the fiber gene promoters examined show trichome- or fiber-specific (or preferential) activities and are of value in genetic engineering of cotton fiber traits. Promoter of E6, the first isolated fiber-specific gene, was the first one used for engineering cotton fiber quality (John and Keller 1996). GhRDL1, a gene highly expressed in cotton fiber cells at the rapid elongation stages, encodes a BURP-domain containing protein (Li et al. 2002a). GaRDL1 promoter exhibited a trichome-specific expression pattern in transgenic Arabidopsis plants (Wang et al. 2004). GhTUB1 transcripts accumulated preferentially in fiber cells and pGhTUB1::GUS fusion reporter was expressed at a high level in fibers, with only a much lower level in other tissues (Li et al. 2002b). Some other promoters are less tissue specific. For example, promoters of three cotton lipid transfer protein genes, LTP3, LTP6, and FSltp4, and other genes such as GhGlcAT1 and GhRGP1 were able to direct GUS gene expression in leaves and stems in transgenic tobacco plants (Hsu et al. 1999; Delaney et al. 2007; Wu and Liu 2006; Wu et al. 2007). A recent report (Shangguan et al. 2008) showed that the promoter of GaMYB2 is active in various trichome cells. In cotton, GaMYB2 promoter exhibited activities in developing fiber cells and trichomes of other aerial organs, including leaf, stem, and bract. In Arabidopsis, GaMYB2 promoter was specific to trichomes. It is interesting that in tobacco plants, GaMYB2 promoter directed GUS expression exclusively in glandular cells of the glandular-secreting trichomes. In addition to their application in genetic engineering, these promoters provide a valuable tool to dissecting the molecular mechanisms that regulate gene expression in leaf trichomes and cotton fiber cells.

9.4 Experimental Systems Used for Investigation of Cotton Fiber Genes

Cotton transformation is awfully tedious and the long process of tissue culture often induces phenotypic changes, particularly in T0 generation plants. Till now, only a few genes have been functionally characterized using transgenic cotton plants, including SuSy (Ruan et al. 2003), GhACT1 (Li et al. 2005), GhDET2 (Luo et al. 2007), and GhMYB109 (Pu et al. 2008). To accelerate research, several exogenous systems including Arabidopsis, tobacco, and yeast have been employed for functional analyses of cotton genes. However, given the fact that Arabidopsis and Gossypium belong to different plant families (Brassicaceae and Malvaceae, respectively), and that Arabidopsis does not produce trichomes on seed, none of these “models” mentioned can replace cotton. Therefore, a more efficient and stable transformation procedure is required for cotton functional genomics. Very recently, application of virus induced gene silencing (VIGS) system on cotton has been reported (Tuttle et al. 2008). If the silencing effect can spread into ovules, VIGS can be greatly helpful for the molecular dissection of cotton fiber development.

9.5 Summary and Perspectives

In recent years, comprehensive analyses of gene expression profiles have provided a large number of candidate genes that are potentially involved in cotton fiber development and growth. However, how these genes are coordinately expressed and how their products can perform in concert remains largely unknown. There is no doubt that cotton genome research will provide enormous genomic data that the entire community of cotton scientists and breeders are waiting for. Improvement of technologies such as genetic transformation will further enable validation of function of many of these candidate genes. VIGS technology is also urgently needed for large scale functional genomics research of cotton.