Christopher D. Delhom

Transcript profiling by microarray and marker analysis of the short cotton (Gossypium hirsutum L.) fiber mutant Ligon lintless-1 (Li1)

BackgroundCotton fiber length is very important to the quality of textiles. Understanding the genetics and physiology of cotton fiber elongation can provide valuable tools to the cotton industry by targeting genes or other molecules responsible for fiber elongation. Ligon Lintless-1 (Li1) is a monogenic mutant in Upland cotton (Gossypium hirsutum) which exhibits an early cessation of fiber elongation resulting in very short fibers (< 6 mm) at maturity. This presents an excellent model system for studying the underlying molecular and cellular processes involved with cotton fiber elongation. Previous reports have characterized Li1 at early cell wall elongation and during later secondary cell wall synthesis, however there has been very limited analysis of the transition period between these developmental time points.ResultsPhysical and morphological measurements of the Li1 mutant fibers were conducted, including measurement of the cellulose content during development. Affymetrix microarrays were used to analyze transcript profiles at the critical developmental time points of 3 days post anthesis (DPA), the late elongation stage of 12 DPA and the early secondary cell wall synthesis stage of 16 DPA. The results indicated severe disruption to key hormonal and other pathways related to fiber development, especially pertaining to the transition stage from elongation to secondary cell wall synthesis. Gene Ontology enrichment analysis identified several key pathways at the transition stage that exhibited altered regulation. Genes involved in ethylene biosynthesis and primary cell wall rearrangement were affected, and a primary cell wall-related cellulose synthase was transcriptionally repressed. Linkage mapping using a population of 2,553 F2 individuals identified SSR markers associated with the Li1 genetic locus on chromosome 22. Linkage mapping in combination with utilizing the diploid G. raimondii genome sequences permitted additional analysis of the region containing the Li1 gene.ConclusionsThe early termination of fiber elongation in the Li1 mutant is likely controlled by an early upstream regulatory factor resulting in the altered regulation of hundreds of downstream genes. Several elongation-related genes that exhibited altered expression profiles in the Li1 mutant were identified. Molecular markers closely associated with the Li1 locus were developed. Results presented here will lay the foundation for further investigation of the genetic and molecular mechanisms of fiber elongation.

Functional analyses of cotton (Gossypium hirsutum L.) immature fiber (im) mutant infer that fiber cell wall development is associated with stress responses.

BackgroundCotton fiber maturity is an important factor for determining the commercial value of cotton. How fiber cell wall development affects fiber maturity is not well understood. A comparison of fiber cross-sections showed that an immature fiber (im) mutant had lower fiber maturity than its near isogenic wild type, Texas marker-1 (TM-1). The availability of the im mutant and TM-1 provides a unique way to determine molecular mechanisms regulating cotton fiber maturity.ResultsTranscriptome analysis showed that the differentially expressed genes (DEGs) in the im mutant fibers grown under normal stress conditions were similar to those in wild type cotton fibers grown under severe stress conditions. The majority of these DEGs in the im mutant were related to stress responses and cellular respiration. Stress is known to reduce the activity of a classical respiration pathway responsible for energy production and reactive oxygen species (ROS) accumulation. Both energy productions and ROS levels in the im mutant fibers are expected to be reduced if the im mutant is associated with stress responses. In accord with the prediction, the transcriptome profiles of the im mutant showed the same alteration of transcriptional regulation that happened in energy deprived plants in which expressions of genes associated with cell growth processes were reduced whereas expressions of genes associated with recycling and transporting processes were elevated. We confirmed that ROS production in developing fibers from the im mutant was lower than that from the wild type. The lower production of ROS in the im mutant fibers might result from the elevated levels of alternative respiration induced by stress.ConclusionThe low degree of fiber cell wall thickness of the im mutant fibers is associated with deregulation of the genes involved in stress responses and cellular respiration. The reduction of ROS levels and up-regulation of the genes involved in alternative respirations suggest that energy deprivation may occur in the im mutant fibers.

Rapid measurement of cotton fiber maturity and fineness by image analysis microscopy using the Cottonscope

Two of the important cotton fiber quality and processing parameters are fiber maturity and fineness. Fiber maturity is the degree of development of the fiber’s secondary wall, and fiber fineness is a measure of the fiber’s linear density and can be expressed as mass per unit length. A well-known method for fiber maturity and fineness is a cross-section image analysis and microscopy measurement. In general, typical cross-section image analysis and microscopy methods for fiber maturity and fineness can be slow and tedious to perform. Much interest has been shown in improved and rapid routine measurements of fiber maturity and fineness in the laboratory. The Cottonscope® is a new small footprint instrument for measuring fiber maturity and fineness, consisting of a longitudinal measurement of weighted fiber snippets in water using polarized light microscopy and image analysis. A program was implemented to assess the potential and capabilities of the Cottonscope to measure cotton lint maturity and fineness and to determine the major operational impacts on the Cottonscope results. The measurement was fast and easy to perform. The major operational impact on the Cottonscope results was environmental conditions (room temperature and relative humidity), and its impact was a concern for fineness only. Very good method agreement was observed between the Cottonscope and image analysis and microscopy method for maturity and fineness, with moderate coefficients of determination, R2s, and low residuals. Recommended operational protocols for routine Cottonscope measurements were developed.

Molecular markers associated with the immature fiber ( im ) gene affecting the degree of fiber cell wall thickening in cotton ( Gossypium hirsutum L.)

Cotton fiber fineness and maturity measured indirectly as micronaire (MIC) are important properties of determining fiber grades in the textile market. To understand the genetic control and molecular mechanisms of fiber fineness and maturity, we studied two near isogenic lines, Gossypiumhirsutum, Texas Marker-1 wild type (TM-1) and immature fiber (im) mutant showing a significant difference in MIC values. The fibers from im mutant plants were finer and less mature with lower MIC values than those from the recurrent parent, TM-1. A comprehensive fiber property analysis of TM-1 and im mutant showed that the lower MIC of fibers in im mutant was due to the lower degree of fiber cell wall thickening as compared to the TM-1 fibers. Using an F2 population comprising 366 progenies derived from a cross between TM-1 and im mutant, we confirmed that the immature fiber phenotype present in a mutant plant was controlled by one single recessive gene im. Furthermore, we identified 13 simple sequence repeat markers that were closely linked to the im gene located on chromosome 3. Molecular markers associated with the im gene will lay the foundation to further investigate genetic information required for improving cotton fiber fineness and maturity.

Understanding the influence of fiber length on the High Volume Instrument™ measurement of cotton fiber strength

An earlier study confirmed the influence of cotton fiber length characteristics on the High Volume Instrument™ (HVI) strength measurement and devised a quantitative correction factor to compensate for the effect. The current paper investigated the validity of two important assumptions utilized in the previous study. Firstly, single fiber testing confirmed that the particular sample preparation method used to generate samples of different fiber length characteristics from a common cotton sliver did not introduce any inherent damage to the fibers (and so this could not be the explanation for the observed trend in measured fiber strength as a function of fiber length). Secondly, the positioning of the jaws relative to the beard in the HVI strength measurement was explored. This positioning was found to be quite variable for replicate measurements on the same cotton being a function of the size of each individual beard. The average positioning between the different samples was found to be similar and this validated the assumption and approach used previously for deriving the correction factor for that particular sample set. Characterizing the position of the jaws was extended using a wider range of cotton samples. The HVI positioning algorithm appears to not simply be a function of the size of the beard (i.e. the ‘amount’ parameter), but is also dependent on fiber length characteristics. It was also observed that the reported HVI elongation values displayed both a significant bias due to fiber length and also a dependence on the size of individual beards tested.

The GhTT2_A07 gene is linked to the brown colour and natural flame retardancy phenotypes of Lc1 cotton ( Gossypium hirsutum L.) fibres

Highlight The brown fibre cotton Lc1 locus is linked to a 1.4Mb genomic inversion that activates GhTT2_A07. This mutation upregulates flavonoid biosynthesis and confers natural flame retardancy.

The Immature Fiber Mutant Phenotype of Cotton (Gossypium hirsutum) Is Linked to a 22-bp Frame-Shift Deletion in a Mitochondria Targeted Pentatricopeptide Repeat Gene

Cotton seed trichomes are the most important source of natural fibers globally. The major fiber thickness properties influence the price of the raw material, and the quality of the finished product. The recessive immature fiber (im) gene reduces the degree of fiber cell wall thickening by a process that was previously shown to involve mitochondrial function in allotetraploid Gossypium hirsutum. Here, we present the fine genetic mapping of the im locus, gene expression analysis of annotated proteins near the locus, and association analysis of the linked markers. Mapping-by-sequencing identified a 22-bp deletion in a pentatricopeptide repeat (PPR) gene that is completely linked to the immature fiber phenotype in 2837 F2 plants, and is absent from all 163 cultivated varieties tested, although other closely linked marker polymorphisms are prevalent in the diversity panel. This frame-shift mutation results in a transcript with two long open reading frames: one containing the N-terminal transit peptide that targets mitochondria, the other containing only the RNA-binding PPR domains, suggesting that a functional PPR protein cannot be targeted to mitochondria in the im mutant. Taken together, these results suggest that PPR gene Gh_A03G0489 is involved in the cotton fiber wall thickening process, and is a promising candidate gene at the im locus. Our findings expand our understanding of the molecular mechanisms that modulate cotton fiber fineness and maturity, and may facilitate the development of cotton varieties with superior fiber attributes.

An assessment of alternative cotton fibre quality attributes and their relationship with yarn strength

Abstract. Knowing the yarn-strength performance potential of cotton fibre is advantageous to spinners during mill preparation, and to researchers developing new genotypes and management strategies to produce better fibre. Standard High Volume Instrument (HVI) fibre quality attributes include micronaire (a combined measure of fibre linear density and maturity) and bundle tensile properties. While these attributes relate well to yarn strength, alternative fibre quality attributes may better explain the variation in yarn strength. Two field experiments over two seasons were conducted to assess the fibre and yarn performance of some Australian cotton genotypes. The aim was to assess and compare alternative measures for micronaire, and to compare bundle and single-fibre tensile measurements, and assess the relative yarn-strength predictive performance of these attributes. Specific fibre measurement comparisons were for linear density (double-compression Fineness Maturity Tester (FMT) and gravimetric), maturity ratio (FMT, polarised light, calculated, and cross-sectional), and tensile properties (HVI bundle and Favimat Robot single fibre). Multiple linear regression models for yarn strength that included yarn manufacturing variables and standard HVI fibre quality parameters performed well (standard error of prediction (SEP) 2.40 cN tex–1). Multiple linear regression models performed better when alternatives to micronaire were used, e.g. using gravimetric linear density (SEP, 2.15 cN tex–1) or laser photometric determined ribbon width (SEP 1.71 cN tex–1). Yarn strength models were also better when single fibre tensile properties were substituted for bundle tensile properties (SEP 1.07 cN tex–1). The substitution of alternative fineness variables for micronaire or single-fibre strength for bundle strength in a simple fibre quality index also improved the prediction of yarn strength.

Silver-cotton nanocomposites: Nano-design of microfibrillar structure causes morphological changes and increased tenacity

The interactions of nanoparticles with polymer hosts have important implications for directing the macroscopic properties of composite fibers, yet little is known about such interactions with hierarchically ordered natural polymers due to the difficulty of achieving uniform dispersion of nanoparticles within semi-crystalline natural fiber. In this study we have homogeneously dispersed silver nanoparticles throughout an entire volume of cotton fiber. The resulting electrostatic interaction and distinct supramolecular structure of the cotton fiber provided a favorable environment for the controlled formation of nanoparticles (12 ± 3 nm in diameter). With a high surface-to-volume ratio, the extensive interfacial contacts of the nanoparticles efficiently “glued” the structural elements of microfibrils together, producing a unique inorganic-organic hybrid substructure that reinforced the multilayered architecture of the cotton fiber.

Comparative physical and chemical analyses of cotton fibers from two near isogenic upland lines differing in fiber wall thickness

The thickness of cotton fiber cell walls is an important property that partially determines the economic value of cotton. To better understand the physical and chemical manifestations of the genetic variations that regulate the degree of fiber wall thickness, we used a comprehensive set of methods to compare fiber properties of the immature fiber (im) mutant, called immature because it produces thin-walled fibers, and its isogenic wild type Texas Marker-1 (TM-1) that is a standard upland cotton variety producing normal fibers with thick walls. Comprehensive structural analyses showed that im and TM-1 fibers shared a common developmental process of cell wall thickening, contrary to the previous report that the phase in the im fiber development might be retarded. No significant differences were found in cellulose content, crystallinity index, crystal size, matrix polymer composition, or in ribbon width between the isogenic fibers. In contrast, significant differences were detected in their linear density, cross-section micrographs of fibers from opened bolls, and in the lateral order between their cellulose microfibrils (CMFs). The cellulose mass in a given fiber length was lower and the CMFs were less organized in the im fibers compared with the TM-1 fibers. The presented results imply that the disruption of CMF organization or assembly in the cell walls may be associated with the immature phenotype of the im fibers.