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Cotton fibers represent a sustainable and environmentally responsible raw material for the production of nonwoven textiles which are currently dominated by synthetic fibers derived from petrochemicals. Natural variation in quality parameters such as fineness, length, and strength present a challenge for cotton fiber conversion to yarns and in weaving and knitting for conventional textiles. The grading process for cotton fibers addresses this issue by allowing converters to select fibers suitable for specific woven textile applications. However, there has been little attempt to correlate cotton fiber quality traits with nonwoven textiles performance. This study examined the relationship of cotton fiber quality and fluid handling and moisture management performance properties of nonwoven textiles for personal hygiene and disposable applications. This includes potential end-use in diapers and incontinence products as well as disposable textiles for use in clinical settings. Ten recombinant inbred lines of cotton with a broad distribution of fiber quality traits were selected from a multiparent advanced generation intercross population. Fibers were harvested, converted into nonwoven textiles, and subjected to a series of standardized testing protocols. The results indicated that inferior quality coarse cotton fibers subjected to discount market pricing can be selectively utilized for nonwoven applications that benefit from improved moisture management and fluid handling performance.

Arboviral diseases and malaria transmitted by mosquitoes are major health concerns worldwide responsible for millions of deaths annually. Spatial repellents have been used as preventative measures via direct application to the skin or disposable devices worn outside of clothing. Naturally derived, plant-based repellents are safe, effective alternatives to synthetic repellents and may be applied to disposable substrates including adhesive patches. Many disposables are composed of synthetic petrochemical-based polyester and polypropylene nonwoven fabrics, contributing to growing concern surrounding microplastic pollution. Sustainable and biodegradable substrates including those made from cotton are cost effective and environmentally friendly. Therefore, we explored the utilization of cotton-based substrates for the application of natural spatial and synthetic contact insect repellents. Cotton fibers used in the study were commercially available greige cotton, scoured and bleached greige cotton and reginned greige cotton motes, a value-added byproduct of the ginning process. Synthetic polyester and polypropylene were used for comparison. Thermogravimetric/derivative thermogravimetric analysis (TG/DTG) in combination with modulated differential scanning calorimetry (mDSC) were used to discern vaporization properties of repellents from the substrates. Retention times of repellents on the substrates were analyzed using a Fourier-transform infrared spectroscopy–focal plane array detector and compared with the TG/DTG and mDSC data. Mosquito landing assays confirmed the feasibility of using cotton-based substrates treated with plant-based spatial repellents as an effective and environmentally friendly alternative to synthetic materials.

Cotton maturity describes the thickness of the cotton secondary cell wall. There is a need for developing non-destructive methods for measuring maturity that also examine distribution. The current study seeks to expand reported infrared (IR)-based maturity determinations using an IR imaging system with a focal-plane array (FPA) detector. Adapted equations were used to examine the maturity of cotton standards and of a larger set of upland cotton varieties (30 total). Maturity values obtained with a Cottonscope and from IR determinations showed strong linearity, R2 = 0.95, while contour plots provided a visual representation of the maturity distribution in the samples. These results validate the use of IR measurement for examining cotton maturity and establish the use of the FPA IR system for examining and imaging cotton maturity distributions.

A simple method was developed to deposit palladium (Pd) nanoparticles (NPs) within an inexpensive substrate, nonwoven brown cotton fabric, using naturally occurring polyphenols contained within the...

Cotton fibers can be used to produce nonwovens suitable for numerous single use applications including hygiene, wipes, and medical products among others. Cotton comprises a relatively small amount of total raw materials used in nonwovens production compared to the synthetic fibers of polyester and polypropylene, but the use of cotton fibers in nonwovens continues to increase due to demand for disposable products containing natural, sustainable, and biodegradable materials. However, the relationship between cotton fiber classification measurements and nonwoven fabric physical and functional properties are not well characterized. A better understanding of the effects of cotton fiber properties on nonwovens fabric properties will facilitate fiber selection for specific end-use applications. In this study, cotton fibers with broad distributions of fiber quality measurements from 10 recombinant inbred lines of a multi parent advanced generation intercross multiparent advanced generation intercross population were harvested and processed in their greige state into hydroentangled nonwoven fabrics of two distinct basis weights. Tensile testing of lightweight nonwovens indicated fiber length and tensile strength at break were positively correlated with fabric strength, whereas micronaire (air permeability of a fiber bundle) was negatively correlated indicating finer fibers contributed to increased fabric strength. Increased strength of heavyweight fabrics was mainly correlated with higher fiber uniformity index. These results suggest that cotton fibers could be selectively sourced based on fiber quality for specific nonwoven applications and establishes alternative market opportunities for cotton fibers classified as inferior and subject to discount pricing in the woven textile market.

A macro sampling chamber equipped with mid-infrared (IR) focal plane array (FPA) detector was used to examine chemical treatments of cotton fabrics. Conventional IR methods typically examine individual points in a sample, while the FPA detector provides spatially resolved spectra that can corroborate chemical treatment and its distribution on the cotton fabric. Characterizations of three distinct treatments are presented: non-durable treatments of N, N-diethyl-3-methylbenzamide (DEET), an active ingredient in commercially available insect repellents, a phosphazine-based fire retardant, and fabric treated with deuterated water. All chemical treatments examined in this study exhibited distinct vibrational bands that could be used as markers of the fabric treatments. Our results suggest that the mid-IR FPA detector can be used to characterize fabric treatment uniformity and provide qualitative confirmation of fabric chemical treatment.

In this study, hydroentangled cotton nonwovens were identified as effective hosts for mineralization of calcium carbonate (CaCO3) polymorphs to modify and improve their properties. All cotton varieties studied, including raw white cotton, scoured white cotton, and raw brown cotton, readily crystallized CaCO3 via a simple cyclic dipping process. A combination of analyses agreed that the surface chemistry of cotton fibers influenced the formation of different CaCO3 polymorphs. Scoured white cotton that consisted of almost pure cellulose predominantly produced the most stable calcite, whereas raw white and raw brown cottons that contain proteins facilitated the production of partial metastable vaterite. The morphology of calcite was better defined on the scoured cotton. The mineralization altered the hydrophobic surface of raw cottons to be hydrophilic, i.e., two-fold increase in moisture regain and decrease in water contact angle from 130 to 0 degrees. The mineralized cottons also exhibited improved thermal resistance, i.e., slower thermal decomposition with decreased activation energies and reduction in heat release capacity by up to 40%.

Several nonwoven materials were evaluated as candidates for wipe fabrics intended for sensitive applications, namely aviation maintenance. Wipes designed for this purpose must conform to specific guidelines delineated by the appropriate governing bodies. Fabric selections included both synthetic and natural staple fibers such as polyester, Lyocell and raw cotton varieties. A thorough evaluation of extractable material in an array of solvents revealed that cotton-based nonwovens as well as Lyocell have some of the lowest percentages of leachable solids. The resistance of these fabrics to abrasion and the damage incurred by them was also studied. Environmental scanning electron microscopy taken before and after the linting procedure showed that the greige cotton sample demonstrated some of the least damage. Fourier-transform infrared spectroscopy examinations of hexane extracts confirmed the absence of any silicone grease contamination on the wipes materials. Standardized tensile testing indicated that the cotton samples, especially mechanically cleaned greige cotton, have robust tensile properties that are important characteristics for wiping materials. These results indicate that cotton nonwovens, particularly greige cotton, are promising candidates for the development of future aviation and other wipes materials.

The transmission of infectious agents can occur through secondary routes by contact with contaminated inanimate objects in clinical and food service settings. Effective disinfection of exposed surfaces can aid in reducing secondary transmission of infectious agents. Quaternary ammonium compounds (quats) are biocides widely used as active ingredients in disinfecting solutions and are effective against a wide range of microorganisms, including those with antibiotic resistance. Cellulosic fibers such as cotton are desirable as disposable substrates for the application of disinfecting solutions, since they have good absorbency and cleaning properties and are sustainable and biodegradable. However, cotton fibers deplete quats from solution through strong ionic interactions at the solid–liquid interface, thereby reducing the amount of quat deposited onto a surface for effective disinfection. In this study, we used response surface methodology to model the depletion of the quat, alkyldimethylbenzylammonium chloride (ADBAC), onto cotton wipe substrates in the presence of chemical compounds that interfered or competed with the ionic interactions between the quat and the cotton fiber surface. Preliminary efficacy testing successfully demonstrated that an optimized disinfecting ADBAC co-formulation applied with a raw cotton disposable wipe maintained efficacy against representative gram negative ( Pseudomonas aeruginosa) and gram positive ( Staphylococcus aureus) bacteria compared to a control disinfecting solution containing only ADBAC. Our optimized disinfecting ADBAC co-formulation remained efficacious against Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus, and vancomycin-resistant Enterococcus faecalis, demonstrating for the first time that quat adsorption onto cotton substrates can be minimized and efficacy maintained with inexpensive added chemistries.

Tannins, natural phenolic compounds abundant in many plants, exhibit low thermal conductivity and low flammability and have inspired bionic approaches in the development of flame-retardant materials. Still, tannins have been used as a dyeing fixative for cotton, and their potential contribution to developing flame-retardant cotton has not yet been examined. This study shows that tannic acid with the aid of sodium ions can produce intumescent flame-retardant cotton. Treatment with tannic acid alone altered the thermal patterns of the pyrolysis and combustion of cotton and increased the char yield, but the limiting oxygen index (LOI) was not improved significantly. The addition of low concentrations of sodium hydroxide enhanced the adsorption of tannic acid onto cotton and catalyzed the decarboxylation of tannic acid and the dehydration of cotton cellulose at lower temperatures. Such modified thermal reactions as well as the formation of intumescent char led to a reduction in heat release capacity of 82% (from 278 to 51 J/g K) and an increase in the LOI by as much as 30.2% as compared with that for control cotton.

Quaternary ammonium compounds, commonly referred to as quats, are cationic surfactants widely used as the active biocidal ingredient for disposable disinfecting wipes. The cationic nature of quats results in a strong ionic interaction and adsorption onto wipes materials that have an anionic surface charge, such as cellulosic materials, including cotton. The degree of adsorption of quats onto cotton nonwovens is affected by pretreatment of the substrate, more specifically whether it is a greige or a scoured and bleached fabric. This study examined the effect of varying the chemical and physical properties of solutions on the adsorption of the quat alkyl-dimethyl-benzyl-ammonium chloride (ADBAC) onto greige and scoured and bleached cotton nonwoven fabrics produced by hydroentanglement. At a constant surfactant concentration, the liquor ratio, pH, temperature, and concentrations of various electrolytes in the solution were varied and the amount of ADBAC depleted from solution was determined over time. The results suggested that a more alkaline solution increased the amount of ADBAC adsorbed onto both cotton nonwoven fabrics, while a more acidic solution reduced ADBAC adsorption. Likewise, increasing the temperature and concentration of salts in the solution reduced the adsorption of ADBAC onto the cotton fabrics. The presence of nonionic surfactants or low molecular weight quats also reduced ADBAC adsorption onto cotton fabrics in a concentration-dependent manner. The results of this study will provide guidance for optimized chemical formulations compatible with disposable disinfecting cotton-based wipes, cloths, and other cotton-containing implements intended for use in cleaning and disinfecting applications.

Market demands for cotton varieties with improved fiber properties also call for the development of fast, reliable analytical methods for monitoring fiber development and measuring their properties. Currently, cotton breeders rely on instrumentation that can require significant amounts of sample, which complicates fiber development studies. Herein, we explored the use of high-resolution, Fourier-transform infrared (FT-IR) microscopy to examine cotton fiber secondary cell wall development in single fibers. Notably, there was a marked intensity increase for the C-O bending region near 1015 cm–1 and the C-H stretch at 2900 cm–1. These changes agree with those observed with macroscopic FT-IR tests. Chemical distribution maps and principal component analysis plots visually depict these spectral changes. Our results suggest the FT-IR microscopy can potentially be utilized as a tool to monitor and assess important fiber properties, such as cotton maturity, during fiber development.

Brown cotton fibers (SA-1 and MC-BL) studied were inferior to a white cotton fiber (Sure-Grow 747) in fiber quality, i.e., a shorter length, fewer twists, and lower crystallinity, but showed superior thermal resistance in thermogravimetric, differential thermogravimetric, and microscale combustion calorimetric (MCC) analyses. Brown cotton fibers yielded 11–23 % smaller total heat release and 20–40 % greater char. Washing fibers in water and a 1 % NaOH solution showed that rich natural inorganic components and the condensed tannins present in brown cotton are responsible for the unusual thermal property. The loss of inorganics from white cotton during a water wash increased the thermal decomposition temperature of cellulose, resulting in no char yield. However, the stronger binding of metal ions for brown cotton as well as its dominant adsorption of sodium ions after a 1 % NaOH wash facilitated the low-temperature thermal-reaction route; the sodium content showed a significant negative correlation with the heat release capacity of the fiber. Condensed tannins greatly enhanced the adsorption of sodium ions to the fiber and exhibited inherent thermal stability. The limiting oxygen indices (LOI) calculated from the MCC parameters indicated the slower burning characteristic of brown cotton, and its LOI was further increased upon adsorption of sodium ions.

A study was conducted on a commercial grade hydroentanglement system to assess the effects of jet strip configuration in terms of both orifice diameter (0.10 mm, 0.12 mm, and 0.14 mm) as well as the number of orifices per inch (40 and 50) on the properties of resultant nonwoven cotton fabrics at various hydroentanglement pressures (0, 5.0, 7.5, 10.0, 12.5, and 14.0 MPa). It was found that an increase in the energy applied to the fabric web resulted in a nonwoven with increased absorbency. The results of air permeability testing indicate that a combination of variations in the orifice diameter and the number of orifices per inch as well as the energy applied determine the overall air permeability of the fabric. Tensile testing revealed that increasing the energy applied to the fabric resulted in increased strength in both the machine and cross directions and decreased elongations. These results indicate that the mechanical and performance characteristics of nonwoven cotton fabrics produced by hydroentanglement may be manipulated to obtain the desired characteristics for the targeted end-use application.

Wettable nonwoven topsheets are traditionally spunbond polypropylene nonwoven fabrics. The fluid handling performance of hydroentangled greige cotton nonwovens was studied to determine their suitability for topsheet applications based upon analysis of fluid rewet, strikethrough, and acquisition properties; and the relative contributions of nonwoven cotton’s cellulosic and wax components to hydrophobic and hydrophilic fluid transport properties are addressed. It was observed that mechanically cleaned greige cotton nonwovens exhibit certain fluid handling properties that are similar to polypropylene spunbond-meltblown topsheets, partly as a result of the residual wax content. Subsequently, the surface polarity, swelling, and moisture uptake of 100% greige cotton and 50:50 blends of greige cotton and polypropylene hydroentangled nonwovens were studied in comparison with the performance of a commercially available 100% polypropylene spunbond-meltblown topsheets. The surface polarity, swelling, and wettability values obtained from electrokinetic and water contact angle analysis were found to be in agreement with the hydrophobic polypropylene topsheets. Additionally, comfort assessment was undertaken based upon fabric handle profiles using the Leeds University Fabric Handle Evaluation System, which is an objective evaluation based on the quantification of fabric buckling deformations. Of the fabrics studied in this work, 50:50 greige cotton/polypropylene hydroentangled fabrics were the softest as determined by the Leeds University Fabric Handle Evaluation System and exhibited fluid handling properties consistent with the requirements of commercial topsheets.

A comparative study was conducted to identify the effects of processing on physical and combustion properties of needlepunched (NP) and hydroentangled (H-E) nonwoven fabrics produced from fibers of white fiber cotton and a naturally colored brown fiber cotton. A significantly higher degree of flame retardancy (FR) in was observed in fabrics produced from brown cotton fibers compared with white fibers. Calorimetry revealed lower heat release capacity, lower peak heat release rate, and total heat release from brown fibers compared with white fibers. The ash content was also higher in brown fiber samples suggesting higher levels of inorganic elements in the brown fibers. Elemental analyses revealed brown cotton fibers had higher levels of known FR elements including phosphorous and magnesium. The H-E process reduced FR in brown fabrics, which also correlated with a reduction in phosphorous. However, brown H-E fabrics still maintained higher FR than white H-E fabrics. Water content analysis indicated higher water levels in brown fibers, particularly brown greige fibers, which correlated with increased FR. Processing parameters such as energy of H-E did not affect combustion of the two fabric types. Scouring of the brown fiber fabrics reduced, but did not remove coloration, while scouring and bleaching removed the brown color completely. Scouring alone, or scouring and bleaching, completely removed the higher FR properties of the brown fiber fabrics. The results indicate that the mechanism of FR in brown cotton fibers is dependent on multiple compositional factors that may include element content, water content, and compounds related to coloration.

The accurate and precise measurement of cotton maturity and fineness is often difficult, laborious, and/or expensive to perform. The Cottonscope® rapidly, accurately, and precisely measures fiber maturity and fineness with small quantities of sample (approximately 50 mg). Interest has been expressed in the use of different sample weights of fiber, especially lower sample weights by geneticists. A program was implemented to establish the capabilities of the Cottonscope to rapidly and accurately measure maturity (maturity ratio (MR), original polarized light microscopy maturity ratio (MRBF)), fineness, and ribbon width with different sample weights of fiber. The change in sample weight significantly impacted the Cottonscope results for MR, fineness, and ribbon width. Fineness was most impacted by varied sample weight. The impacts of sample weights on the cotton results were removed by re-calibrating the instrument at each sample weight. Decreasing the sample weight below 50 mg increased sample measurement times, especially at 10 mg sample weight. These results demonstrated that the Cottonscope can accurately and precisely measure the fiber’s maturity, fineness, and ribbon width with cotton fiber samples as small as 10 mg.

The pecan nut is a nutrient-rich part of a healthy diet full of beneficial fatty acids and antioxidants, but can also cause allergic reactions in people suffering from food allergy to the nuts. The transcriptome of a developing pecan nut was characterized to identify the gene expression occurring during the process of nut development and to highlight those genes involved in fatty acid metabolism and those that commonly act as food allergens. Pecan samples were collected at several time points during the embryo development process including the water, gel, dough, and mature nut stages. Library preparation and sequencing were performed using Illumina-based mRNA HiSeq with RNA from four time points during the growing season during August and September 2012. Sequence analysis with Trinotate software following the Trinity protocol identified 133,000 unigenes with 52,267 named transcripts and 45,882 annotated genes. A total of 27,312 genes were defined by GO annotation. Gene expression clustering analysis identified 12 different gene expression profiles, each containing a number of genes. Three pecan seed storage proteins that commonly act as allergens, Car i 1, Car i 2, and Car i 4, were significantly up-regulated during the time course. Up-regulated fatty acid metabolism genes that were identified included acyl-[ACP] desaturase and omega-6 desaturase genes involved in oleic and linoleic acid metabolism. Notably, a few of the up-regulated acyl-[ACP] desaturase and omega-6 desaturase genes that were identified have expression patterns similar to the allergen genes based upon gene expression clustering and qPCR analysis. These findings suggest the possibility of coordinated accumulation of lipids and allergens during pecan nut embryogenesis.

Xyloglucan is a matrix polysaccharide found in the cell walls of all land plants. In growing cells, xyloglucan is thought to connect cellulose microfibrils and regulate their separation during wall extension. Ligon lintless-2 (Li2) is a monogenic dominant cotton fiber mutation that causes extreme reduction in lint fiber length with no pleiotropic effects on vegetative growth. Li2 represents an excellent model system to study fiber elongation. To understand the role of xyloglucan in cotton fiber elongation we used the short fiber mutant Li2 and its near isogenic wild type for analysis of xyloglucan content and expression of xyloglucan-related genes in developing fibers. Accumulation of xyloglucan was significantly higher in Li2 developing fibers than in wild type. Genes encoding enzymes for nine family members of xyloglucan biosynthesis were identified in the draft Gossypium hirsutum genome. RNAseq analysis revealed that most differentially expressed xyloglucan-related genes were down-regulated in Li2 fiber cells. RT-qPCR analysis revealed that the peak of expression for the majority of xyloglucan-related genes in wild type developing fibers was 5-16days post anthesis (DPA) compared to 1-3 DPA in Li2 fibers. Thus, our results suggest that early activation of xyloglucan-related genes and down regulation of xyloglucan degradation genes during the elongation phase lead to elevated accumulation of xyloglucan that restricts elongation of fiber cells in Li2.

Background Cotton supplies a great majority of natural fiber for the global textile industry. The negative correlation between yield and fiber quality has hindered breeders’ ability to improve these traits simultaneously. A multi-parent advanced generation inter-cross (MAGIC) population developed through random-mating of multiple diverse parents has the ability to break this negative correlation. Genotyping-by-sequencing (GBS) is a method that can rapidly identify and genotype a large number of single nucleotide polymorphisms (SNP). Genotyping a MAGIC population using GBS technologies will enable us to identify marker-trait associations with high resolution. Results An Upland cotton MAGIC population was developed through random-mating of 11 diverse cultivars for five generations. In this study, fiber quality data obtained from four environments and 6071 SNP markers generated via GBS and 223 microsatellite markers of 547 recombinant inbred lines (RILs) of the MAGIC population were used to conduct a genome wide association study (GWAS). By employing a mixed linear model, GWAS enabled us to identify markers significantly associated with fiber quantitative trait loci (QTL). We identified and validated one QTL cluster associated with four fiber quality traits [short fiber content (SFC), strength (STR), length (UHM) and uniformity (UI)] on chromosome A07. We further identified candidate genes related to fiber quality attributes in this region. Gene expression and amino acid substitution analysis suggested that a regeneration of bulb biogenesis 1 (GhRBB1_A07) gene is a candidate for superior fiber quality in Upland cotton. The DNA marker CFBid0004 designed from an 18 bp deletion in the coding sequence of GhRBB1_A07 in Acala Ultima is associated with the improved fiber quality in the MAGIC RILs and 105 additional commercial Upland cotton cultivars. Conclusion Using GBS and a MAGIC population enabled more precise fiber QTL mapping in Upland cotton. The fiber QTL and associated markers identified in this study can be used to improve fiber quality through marker assisted selection or genomic selection in a cotton breeding program. Target manipulation of the GhRBB1_A07 gene through biotechnology or gene editing may potentially improve cotton fiber quality. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3249-2) contains supplementary material, which is available to authorized users.

Hard surface cleaning and disinfection is critically important in environments where microbial contamination can result in the spread of food-borne illnesses and infectious diseases. Successful disinfection of a hard surface can be impeded by the presence of a soil load in the form of protein, fat or other material. Fibrous materials used as applicators for surface disinfecting solutions require careful consideration to ensure the active ingredient remains efficacious. Of equal importance are the mechanical and surface properties of the applicator including tensile strength, cleaning efficiency, and absorbency. Therefore, the successful disinfection of a hard surface can be greatly enhanced by an applicator that also effectively removes organic contaminants, is strong enough to resist structural failure, and reduces water waste when a disinfecting solution is applied. The cleaning and physical properties of nonwoven applicators in the form of disposable wipes composed of cotton, rayon, polyester, and blends thereof were evaluated with several assays. Dynamic wiping assays, surface roughness, and tensile testing were conducted to compare the physical and surface properties of the wipes. The removal of organic contaminants was found to correlate with higher wipe surface roughness that increased with cellulosic fiber content. Tensile testing demonstrated the greige cotton, which has not been subjected to processing such as scouring or bleaching, had increased wet strength while rayon wipes lost significant strength when wet. Greige cotton wipes were also produced as a sustainable product with reduced absorbency that would minimize water usage and waste. The results indicated that inclusion of greige cotton fibers in wipes offers improvements over currently available wipes without sacrificing strength or cleaning efficiency.

A total of seven source fiber types were selected for use in the manufacturing of nonwoven roll goods: polyester; polypropylene; rayon; greige cotton from two sources; mechanically cleaned greige cotton; and scoured and bleached cotton. The microbial burden of each source fiber was measured as a preliminary assessment of microbial contamination using heterotrophic spread plate counts. Greige cotton fibers exhibited the highest levels of total microbial contamination, which were reduced by both storage time and trash removal in the form of mechanical cleaning. Changes in microbial burden levels were measured at each step in the nonwoven manufacturing process. The hydroentanglement process resulted in the greatest overall reduction in microbial burden with no detectable levels of aerobic microbial contamination present on any of the final hydroentangled roll goods regardless of the source fiber. No detectable levels of aerobic microbial regrowth were observed on any fabrics despite storage time or ambient storage conditions. Analysis of suspended solids present in hydroentanglement effluents collected during fabric production revealed significantly less suspended solids from synthetic fibers compared to all cotton fiber types. The study provided insight and potential guidelines that could be incorporated into a nonwoven processing line to ensure specific sterility requirements are met for various converters in end-uses such as hygiene and medical applications.

The length of cotton fiber is an important agronomic trait that directly affects the quality of yarn and fabric. Understanding the molecular basis of fiber elongation would provide a means for improvement of fiber length. Ligon-lintless-1 (Li 1 ) and −2 (Li 2 ) are monogenic and dominant mutations that result in an extreme reduction in the length of lint fiber on mature seeds. In a near-isogenic state with wild type cotton these two short fiber mutants provide an effective model system to study the mechanisms of fiber elongation. Plant miRNAs regulate many aspects of growth and development. However, the mechanism underlying the miRNA-mediated regulation of fiber development is largely unknown. Small RNA libraries constructed from developing fiber cells of the short fiber mutants Li 1 and Li 2 and their near-isogenic wild type lines were sequenced. We identified 24 conservative and 147 novel miRNA families with targets that were detected through degradome sequencing. The distribution of the target genes into functional categories revealed the largest set of genes were transcription factors. Expression profiles of 20 miRNAs were examined across a fiber developmental time course in wild type and short fiber mutations. We conducted correlation analysis between miRNA transcript abundance and the length of fiber for 11 diverse Upland cotton lines. The expression patterns of 4 miRNAs revealed significant negative correlation with fiber lengths of 11 cotton lines. Our results suggested that the mutations have changed the regulation of miRNAs expression during fiber development. Further investigations of differentially expressed miRNAs in the Li 1 and Li 2 mutants will contribute to better understanding of the regulatory mechanisms of cotton fiber development. Four miRNAs negatively correlated with fiber length are good candidates for further investigations of miRNA regulation of important genotype dependent fiber traits. Thus, our results will contribute to further studies on the role of miRNAs in cotton fiber development and will provide a tool for fiber improvement through molecular breeding.

Background The length of cotton fiber is an important agronomic trait that directly affects the quality of yarn and fabric. Understanding the molecular basis of fiber elongation would provide a means for improvement of fiber length. Ligon-lintless-1 (Li1) and −2 (Li2) are monogenic and dominant mutations that result in an extreme reduction in the length of lint fiber on mature seeds. In a near-isogenic state with wild type cotton these two short fiber mutants provide an effective model system to study the mechanisms of fiber elongation. Plant miRNAs regulate many aspects of growth and development. However, the mechanism underlying the miRNA-mediated regulation of fiber development is largely unknown. Results Small RNA libraries constructed from developing fiber cells of the short fiber mutants Li1 and Li2 and their near-isogenic wild type lines were sequenced. We identified 24 conservative and 147 novel miRNA families with targets that were detected through degradome sequencing. The distribution of the target genes into functional categories revealed the largest set of genes were transcription factors. Expression profiles of 20 miRNAs were examined across a fiber developmental time course in wild type and short fiber mutations. We conducted correlation analysis between miRNA transcript abundance and the length of fiber for 11 diverse Upland cotton lines. The expression patterns of 4 miRNAs revealed significant negative correlation with fiber lengths of 11 cotton lines. Conclusions Our results suggested that the mutations have changed the regulation of miRNAs expression during fiber development. Further investigations of differentially expressed miRNAs in the Li1 and Li2 mutants will contribute to better understanding of the regulatory mechanisms of cotton fiber development. Four miRNAs negatively correlated with fiber length are good candidates for further investigations of miRNA regulation of important genotype dependent fiber traits. Thus, our results will contribute to further studies on the role of miRNAs in cotton fiber development and will provide a tool for fiber improvement through molecular breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2715-1) contains supplementary material, which is available to authorized users.

Cellulose synthase catalytic subunits (CesAs) are the catalytic sites within a multisubunit complex for cellulose biosynthesis in plants. CesAs have been extensively studied in diploid plants, but are not well characterized in polyploid plants. Gossypium hirsutum is an allotetraploid cotton species producing over 90% of the world's cotton fibers. Although G. hirsutum CesAs (GhCesAs) are responsible for cellulose production in cotton fiber, very limited numbers of GhCesA genes have been identified. Here, we report isolating and characterizing a pair of homeologous CesA2 genes and their full-length cDNAs from allotetraploid cotton. The GhCesA2-A(T) gene from the A-subgenome and GhCesA2-D(T) gene from the D-subgenome were screened from a G. hirsutum BAC library. These genes shared 92% sequence similarity throughout the entire sequence. The coding sequences were nearly identical, and the deduced amino acid sequences from GhCesA2-A(T) (1,039 amino acids) and GhCesA2-D(T) (1,040 amino acids) were identical except four amino acids, whereas the noncoding sequences showed divergence. Sequence analyses showed that all exons of GhCesA2-A(T) contained consensus splice donor dinucleotides, but one exon in GhCesA2-D(T) contained nonconsensus splice donor dinucleotides. Although the nonconsensus splice donor dinucleotides were previously suggested to be involved in alternative splice or pseudogenization, our results showed that a majority of GhCesA2-A(T) and GhCesA2-D(T) transcripts consisted of functional and full-length transcripts with little evidence for alternative mRNA isoforms in developing cotton fibers. Expression analyses showed that GhCesA2-A(T) and GhCesA2-D(T) shared common temporal and spatial expression patterns, and they were highly and preferentially expressed during the cellulose biosynthesis stage in developing cotton fibers. The observations of higher expression levels of both GhCesA2-A(T) and GhCesA2-D(T) in developing fibers of one near-isogenic line (NIL) with higher fiber bundle strength over the other NIL with lower fiber bundle strength suggested that the differential expression of genes associated with secondary cell wall cellulose biosynthesis in developing fiber might affect cotton fiber properties.

Growing degree days required for cotton (Gossypium hirsutum L.) growth and development were recorded for four growing seasons and compared with fi ber-quality measurements and gene expression data indicative of different stages of fi ber development. Fiber-bundle strength differences between the Upland cotton near-isogenic lines MD 52ne and MD 90ne were observed using immature and mature fi bers collected at different time points of development stages. Previously characterized fi ber-bundle-strength differences between the near-isogenic lines, known as a result of early entrance into the transition stage of fi ber development, were present as early as 20 d postanthesis and persisted to boll opening and fi ber maturity. The onset of transition stage was correlated with the accumulated degree day heat units from the day of anthesis in both cotton lines in all seasons. Fiber-quality measurements obtained over multiple growing seasons indicated that an earlier entrance into the transition stage of fi ber development resulted in increased fi ber-bundle strength. These data suggest that the identifi cation of genes associated with early entrance into the transition stage can be used to temporally manipulate fi ber development and improve fi ber quality.

Cotton breeding for resistance to root-knot nematode (RKN) [Meloidogyne incognita (Kofoid and White) Chitwood] is hindered by the lack of convenient and reliable screening methods for resistant plants. The identifi cation of molecular markers closely linked to RKN resistance will facilitate the development of RKN resistant cultivars through marker-assisted selection (MAS). Our objective was to identify and develop new DNA markers that are associated with RKN resistance in cotton. Using three pairs of nearisogenic (NIL) resistant (R) and susceptible (S) lines, two AFLP markers, two RAPD markers, and three RGA markers were identifi ed to be polymorphic between the NIL-R and NIL-S lines. One RAPD marker was converted into a sequence-tagged site (STS) marker. In an F 2 population of ‘ST 474’ × ‘Auburn 634 RNR’, the two RAPD markers and the STS marker were mapped to the same linkage group containing several markers that were previously reported to be linked with the RKN resistance gene rkn1 on chromosome 11 in ‘Acala NemX’. All these markers were found to be associated with a major RKN resistance gene, presumably Mi 2 in the resistant line Auburn 634 RNR, suggesting that rkn1 and Mi 2 are either allelic or closely linked. In addition, no susceptible recombinants were found in a resistance screen of 200 F 2 plants from the cross Acala NemX × Auburn 634 RNR. The utility of the two RAPD markers and the converted STS marker were evaluated using 23 R and 8 S germplasm lines. The RAPD and STS markers, along with other previously reported markers associated with RKN resistance will be useful in germplasm screening, MAS for RKN resistance, and map-based clon

Disease resistance (R) genes have been isolated from many plant species and R genes with domains of nucleotide binding sites (NBS) and leucine-rich repeats (LRR) represent the largest R gene family. The objective of this investigation was to test a resistance gene analog (RGA) anchored marker system, called amplified fragment length polymorphism (AFLP)-RGA in cotton (Gossypium spp.). The AFLP-RGA analysis uses one degenerate RGA primer designed from various NBS and LRR domains of R genes in combination with one selective AFLP primer in a PCR reaction. Out of a total of 446 AFLP-RGA bands amplified by 22 AFLP-RGA primer combinations, 76 (17.0%) and 37 (8.3%) were polymorphic within four G. hirsutum L. genotypes and four G. barbadense L. cotton genotypes, respectively. The number of polymorphic AFLP-RGA bands (256) between G. hirsutum and G. barbadense was much higher (57.4%). This level of polymorphism mirrors that of AFLP. The genetic similarity among the eight genotypes based on AFLP-RGA or AFLP lead to similar results in genotype grouping at the species and intraspecies level. However, RGA markers amplified by only degenerate RGA primers could not discriminate several genotypes. AFLP-RGA offers a great flexibility for numerous primer combinations in a genome-wide search for RGAs. Due to the distribution of RGAs or RGA clusters in the plant genome, genome-wide AFLP-RGA analysis provides a useful resource for candidate gene mapping of R genes for disease resistance in cotton.

The 18-kDa δ-class zein protein is characterized by having the highest mol% methionine content of any of the known zeins. Sequencing of the 18-kDa zein cDNA revealed an error in the published nucleotide sequence, which changes the 18-kDa amino acid sequence from residues 25 to 38. These changes result in a higher degree of homology between the 10- and 18-kDa zeins than previously reported. Expression of the 18-kDa zein gene under the control of the CaMV 35S promoter results in stable transcript and protein accumulation in leaf tissues of transgenic tobacco. Co-expression of the 15- and 18-kDa zein genes followed by immunolocalization revealed that both proteins accumulate in the same protein bodies. Furthermore, there is a 16-fold increase in accumulation of the 18-kDa zein protein in co-expressing tobacco plants. Transgenic tobacco leaves co-expressing the 15- and 18-kDa zein genes, or expressing only the 18-kDa zein gene, accumulate the 18-kDa zein transcript to equal levels. This suggests that the 15-kDa zein protein stabilizes the 18-kDa zein protein when sequestered in protein bodies. The possibility of 18-kDa zein protein stabilization by the 15-kDa zein protein is further evidenced by L-[35S] methionine pulse-chase experiments. A dramatic decrease in the rate of 18-kDa protein degradation in transgenic tobacco leaves co-expressing the 15- and 18-kDa zein genes was observed when compared with 18-kDa protein degradation in transgenic tobacco leaves expressing only the 18-kDa zein gene.

Greige cotton is an intact plant fiber. The cuticle and primary cell wall near the outer surface of the cotton fiber contains pectin, peroxidases, superoxide dismutase (SOD), and trace metals, which are associated with hydrogen peroxide (H₂O₂) generation during cotton fiber development. Traditionally, the processing of cotton into gauze involves scouring and bleaching processes that remove the components in the cuticle and primary cell wall. The use of unbleached, greige cotton fibers in dressings, has been relatively unexplored. We have recently determined that greige cotton can generate low levels of H₂O₂ (5-50 micromolar). Because this may provide advantages for the use of greige cotton-based wound dressings, we have begun to examine this in more detail. Both brown and white cotton varieties were examined in this study. Brown cotton was found to have a relatively higher hydrogen peroxide generation and demonstrated different capacities for H₂O₂ generation, varying from 1 to 35 micromolar. The H₂O₂ generation capacities of white and brown nonwoven greige cottons were also examined at different process stages with varying chronology and source parameters, from field to nonwoven fiber. The primary cell wall of nonwoven brown cotton appeared very intact, as observed by transmission electron microscopy, and possessed higher pectin levels. The levels of pectin, SOD, and polyphenolics, correlated with H₂O₂ generation.

Formosan subterranean termites, Coptotermes formosanus , are a significant worldwide pest. Molecular gene expression is an important tool for understanding the physiology of organisms. The recent advancement of molecular tools for Coptotermes formosanus is leading to the advancement of the understanding of termite physiology. One of the first steps in analyzing gene expression is the normalization to constant reference genes. Stable reference genes that have constant expression across multiple treatments are important for accurately comparing target genes' expression. The objective of this investigation was to analyze and validate a set of potential reference genes including 8S rRNA; Glyceraldehyde 3-phosphate dehydrogenase ( Gadphd ); ribosomal protein L7 ( RPL ); β -actin (BA1) ; α -tubulin ( Atube ); α -actin ( Aactin ); and elongation factor ( Elong ) as standards for analysis of transcriptional changes in the termite Coptotermes formosanus , across two phenotypic castes, body regions, and colonies. We also compared the expression of hexamerin -1 and 2 using stable and unstable reference genes to demonstrate the importance of consistent control genes. Our results demonstrate that 18S and RPL can serve as reliable expression standards when comparing these different castes and body regions, and we show that C. formosanus Hex-1 and Hex-2 have expression patterns similar to that previously described in R. flavipes .

Next generation sequencing (RNA-seq) technology was used to evaluate the effects of the Ligon lintless-2 (Li2) short fiber mutation on transcriptomes of both subgenomes of allotetraploid cotton (Gossypium hirsutum L.) as compared to its near-isogenic wild type. Sequencing was performed on 4 libraries from developing fibers of Li2 mutant and wild type near-isogenic lines at the peak of elongation followed by mapping and PolyCat categorization of RNA-seq data to the reference D5 genome (G. raimondii) for homeologous gene expression analysis. The majority of homeologous genes, 83.6% according to the reference genome, were expressed during fiber elongation. Our results revealed: 1) approximately two times more genes were induced in the AT subgenome comparing to the DT subgenome in wild type and mutant fiber; 2) the subgenome expression bias was significantly reduced in the Li2 fiber transcriptome; 3) Li2 had a significantly greater effect on the DT than on the AT subgenome. Transcriptional regulators and cell wall homeologous genes significantly affected by the Li2 mutation were reviewed in detail. This is the first report to explore the effects of a single mutation on homeologous gene expression in allotetraploid cotton. These results provide deeper insights into the evolution of allotetraploid cotton gene expression and cotton fiber development.

Ligon lintless-2, a monogenic dominant cotton (Gossypium hirsutum L.) fiber mutation, causing extreme reduction in lint fiber length with no pleiotropic effects on vegetative growth, represents an excellent model system to study fiber elongation. A UDP-glycosyltransferase that was highly expressed in developing fibers of the mutant Ligon lintless-2 was isolated. The predicted amino acid sequence showed ~53% similarity with Arabidopsis UGT73C sub-family members and the UDP-glycosyltransferase was designated as UGT73C14. When expressed in Escherichia coli as a recombinant protein with a maltose binding protein tag, UGT73C14 displayed enzymatic activity toward ABA and utilized UDP-glucose and UDP-galactose as the sugar donors. The recombinant UGT73C14 converted natural occurring isoform (+)-cis, trans-ABA better than (+)-trans, trans-ABA and (-)-cis, trans-ABA. Transgenic Arabidopsis plants constitutively overexpressing UGT73C14 did not show phenotypic changes under standard growth conditions. However, the increased glycosylation of ABA resulted in phenotypic changes in post-germinative growth and seedling establishment, confirming in vivo activity of UGT73C14 for ABA. This suggests that the expression level of UGT73C14 is regulated by the observed elevated levels of ABA in developing fibers of the Li 2 mutant line and may be involved in the regulation of ABA homeostasis.

Background Cotton fiber length is an important quality attribute to the textile industry and longer fibers can be more efficiently spun into yarns to produce superior fabrics. There is typically a negative correlation between yield and fiber quality traits such as length. An understanding of the regulatory mechanisms controlling fiber length can potentially provide a valuable tool for cotton breeders to improve fiber length while maintaining high yields. The cotton (Gossypium hirsutum L.) fiber mutation Ligon lintless-2 is controlled by a single dominant gene (Li 2 ) that results in significantly shorter fibers than a wild-type. In a near-isogenic state with a wild-type cotton line, Li 2 is a model system with which to study fiber elongation. Results Two near-isogenic lines of Ligon lintless-2 (Li 2 ) cotton, one mutant and one wild-type, were developed through five generations of backcrosses (BC5). An F2 population was developed from a cross between the two Li 2 near-isogenic lines and used to develop a linkage map of the Li 2 locus on chromosome 18. Five simple sequence repeat (SSR) markers were closely mapped around the Li 2 locus region with two of the markers flanking the Li 2 locus at 0.87 and 0.52 centimorgan. No apparent differences in fiber initiation and early fiber elongation were observed between the mutant ovules and the wild-type ones. Gene expression profiling using microarrays suggested roles of reactive oxygen species (ROS) homeostasis and cytokinin regulation in the Li 2 mutant phenotype. Microarray gene expression data led to successful identification of an EST-SSR marker (NAU3991) that displayed complete linkage to the Li 2 locus. Conclusions In the field of cotton genomics, we report the first successful conversion of gene expression data into an SSR marker that is associated with a genomic region harboring a gene responsible for a fiber trait. The EST-derived SSR marker NAU3991 displayed complete linkage to the Li 2 locus on chromosome 18 and resided in a gene with similarity to a putative plectin-related protein. The complete linkage suggests that this expressed sequence may be the Li 2 gene.

Gene expression profiles of developing cotton (Gossypium hirsutum L.) fibers from two near-isogenic lines (NILs) that differ in fiber-bundle strength, short-fiber content, and in fewer than two genetic loci were compared using an oligonucleotide microarray. Fiber gene expression was compared at five time points spanning fiber elongation and secondary cell wall (SCW) biosynthesis. Fiber samples were collected from field plots in a randomized, complete block design, with three spatially distinct biological replications for each NIL at each time point. Microarray hybridizations were performed in a loop experimental design that allowed comparisons of fiber gene expression profiles as a function of time between the two NILs. Overall, developmental expression patterns revealed by the microarray experiment agreed with previously reported cotton fiber gene expression patterns for specific genes. Additionally, genes expressed coordinately with the onset of SCW biosynthesis in cotton fiber correlated with gene expression patterns of other SCW-producing plant tissues. Functional classification and enrichment analysis of differentially expressed genes between the two NILs revealed that genes associated with SCW biosynthesis were significantly up-regulated in fibers of the high-fiber quality line at the transition stage of cotton fiber development. For independent corroboration of the microarray results, 15 genes were selected for quantitative reverse transcription PCR analysis of fiber gene expression. These analyses, conducted over multiple field years, confirmed the temporal difference in fiber gene expression between the two NILs. We hypothesize that the loci conferring temporal differences in fiber gene expression between the NILs are important regulatory sequences that offer the potential for more targeted manipulation of cotton fiber quality.

Cotton fibers (cottonseed trichomes) are a well-established model system for investigating cellulose biosynthesis. Cotton ovules, excised from ovaries prior to fertilization, will continue to develop and produce trichomes in vitro under defined conditions when auxin and gibberellic acid are present. Our team is also using cotton fiber development in vitro as a model to investigate plant cell differentiation at the single-cell level and to identify the regulatory components of the transition from cell elongation to secondary wall biogenesis. These two developmental phases determine key properties of fiber quality and yield. Fiber cells elongate to 1-1.5 cm in culture and then produce a thick, cellulosic secondary cell wall. During the transition from cell expansion to secondary wall thickening, the rate of cellulose biosynthesis rises nearly 100-fold. A similar increase in cellulose biosynthetic capacity occurs in fibers produced in vitro by ovule cultures. Although the genes for the cellulose synthase catalytic subunit, CesA, were first described from cotton fiber, little is known about

The number of cotton (Gossypium sp.) ovule epidermal cells differentiating into fiber initials is an important factor affecting cotton yield and fiber quality. Despite extensive efforts in determining the molecular mechanisms regulating fiber initial differentiation, only a few genes responsible for fiber initial differentiation have been discovered. To identify putative genes directly involved in the fiber initiation process, we used a cotton ovule culture technique that controls the timing of fiber initial differentiation by exogenous phytohormone application in combination with comparative expression analyses between wild type and three fiberless mutants. The addition of exogenous auxin and gibberellins to pre-anthesis wild type ovules that did not have visible fiber initials increased the expression of genes affecting auxin, ethylene, ABA and jasmonic acid signaling pathways within 1 h after treatment. Most transcripts expressed differentially by the phytohormone treatment in vitro were also differentially expressed in the ovules of wild type and fiberless mutants that were grown in planta. In addition to MYB25-like, a gene that was previously shown to be associated with the differentiation of fiber initials, several other differentially expressed genes, including auxin/indole-3-acetic acid (AUX/IAA) involved in auxin signaling, ACC oxidase involved in ethylene biosynthesis, and abscisic acid (ABA) 8'-hydroxylase an enzyme that controls the rate of ABA catabolism, were co-regulated in the pre-anthesis ovules of both wild type and fiberless mutants. These results support the hypothesis that phytohormonal signaling networks regulate the temporal expression of genes responsible for differentiation of cotton fiber initials in vitro and in planta.

Degenerate primers designed from conserved motifs of known plant resistance gene products were used to amplify genomic DNA sequences from the root-knot nematode (Meloidogyne incognita) resistance genetic source, Upland cotton (Gossypium hirsutum) cultivar Auburn 634 RNR. A total of 165 clones were isolated, and sequence analysis revealed 57 of the clones to be novel nucleotide sequences, many containing the resistance (R)-protein nucleotide-binding site motif. A cluster analysis was performed with resistance gene analogue (RGA) nucleotide sequences isolated in this study, in addition to 99 cotton RGA nucleotide sequences already deposited in GenBank, to generate a phylogenetic tree of cotton R genes. The cotton RGA nucleotide sequences were arranged into 11 groups and 56 sub-groups, based on genetic distances. Multiple sequence alignments were performed on the RGA sequences of each sub-group, and either the consensus sequences or individual RGA sequences were used to design 61 RGA-sequence-tagged site primers. A recombinant inbred line (RIL) population of cultivated tetraploid cotton was genotyped using RGA-specific primers that amplified polymorphic fragments between the two RIL parents. Nine RGA markers were mapped to homeologous chromosomes 12 and 26, based on linkage to existing markers that are located on these chromosomes.