Screening of Multiple Potential Control Genes for use in Caste and Body Region Comparisons Using RT-qPCR in Coptotermes formosanus

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 8SrRNA; 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

A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Title: Quantile-quantile (Q-Q) Plot of six fiber traits generated from GWAS analysis following mixed linear model (MLM) using GAPIT software. A) Fiber elongation (ELO), B) Micronaire (MIC), C) Short fiber content (SFC), D) Fiber strength (STR), E) Upper half mean fiber length (UHM), and F) Uniformity index (UI). Description of data: Q-Q plots of six fiber traits generated from GWAS analysis following MLM are included in this figure. The X and Y axis have the expected and observed negative logarithm 10 of p value, respectively generated during GWAS analysis. (DOCX 207 kb

A combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (Gossypium hirsutum L.)

<p>Abstract</p> <p>Background</p> <p>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 (<it>Gossypium hirsutum </it>L.) fiber mutation Ligon lintless-2 is controlled by a single dominant gene (<it>Li₂</it>) that results in significantly shorter fibers than a wild-type. In a near-isogenic state with a wild-type cotton line, <it>Li₂</it>is a model system with which to study fiber elongation.</p> <p>Results</p> <p>Two near-isogenic lines of Ligon lintless-2 (<it>Li₂</it>) cotton, one mutant and one wild-type, were developed through five generations of backcrosses (BC₅). An F₂population was developed from a cross between the two <it>Li₂</it>near-isogenic lines and used to develop a linkage map of the <it>Li₂</it>locus on chromosome 18. Five simple sequence repeat (SSR) markers were closely mapped around the <it>Li₂</it>locus region with two of the markers flanking the <it>Li₂</it>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 <it>Li₂</it>mutant phenotype. Microarray gene expression data led to successful identification of an EST-SSR marker (NAU3991) that displayed complete linkage to the <it>Li₂</it>locus.</p> <p>Conclusions</p> <p>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 <it>Li₂</it>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 <it>Li₂</it>gene.</p

FT-IR Examination of the Development of Secondary Cell Wall in Cotton Fibers

The secondary cell wall development of cotton fibers harvested at 18, 20, 24, 28, 32, 36 and 40 days after flowering was examined using attenuated total reflection Fourier transform-infrared (ATR FT-IR) spectroscopy. Spectra of deuterated cotton fibers did not demonstrate significant changes in their O–H stretching band shapes or positions during development. Only a progressive increase in O–H band intensity was observed. Results indicate that the highly crystalline cellulose component produced during secondary cell wall formation maintains the hydrogen bonding network observed for the primary cell wall. Other general changes were observed for the regular ATR spectra. A progressive intensity increase for bands assigned to cellulose Iβ was observed during fiber development, including a marked intensity increase for vibrations at 1002 and 985 cm−1. In contrast, C–O vibrational bands from dominant conformations observed at 1104, 1052, 1028 cm−1 undergo a modest intensity increase during secondary cell wall development

Multi-omics analysis of pigmentation related to proanthocyanidin biosynthesis in brown cotton (Gossypium hirsutum L.)

Naturally-colored brown cotton (NBC) fiber is an environmentally friendly raw source of fiber for textile applications. The fiber of some NBC cultivars exhibits flame-retardant properties, which can be used in textiles that require flame resistance. Proanthocyanidins or their derivatives are responsible for the brown pigment in NBC; however, how flame retardancy is related to pigmentation in NBC is poorly understood. To gain insight into brown pigment biosynthesis, we conducted comparative transcripts and metabolites profiling analysis of developing cotton fibers between the brown (MC-BL) and white (MC-WL) cotton near-isogenic lines (NILs), genetically different only in the Lc1 locus. In this study, mass spectrometry was used to detect metabolites in BL and WL developing fibers at 8, 12, 16, 20, 24, 36, and 40 days post anthesis (DPA) and mature fibers. Transcripts analysis was performed at two critical fiber developmental points, 8 DPA (fiber elongation) and 20 DPA (secondary cell wall deposition). We found 5836 (ESI MS positive mode) and 4541 (ESI MS negative mode) metabolites significantly different accumulated between BL and WL. Among them, 142 were known non-redundant metabolites, including organic acids, amino acids, and derivatives of the phenylpropanoid pathway. Transcript analysis determined 1691 (8 DPA) and 5073 (20 DPA) differentially expressed genes (DEGs) between BL and WL, with the majority of DEGs down-regulated at 20 DPA. Organic acids of the citric acid cycle were induced, while most of the detected amino acids were reduced in the MC-BL line. Both cis- and trans-stereoisomers of flavan-3-ols were detected in developing MC-WL and MC-BL fibers; however, the gallocatechin and catechin accumulated multiple times higher. Gas chromatography-mass spectrometry (GC-MS) analysis of fatty acids determined that palmitic acid long-chain alcohols were the main constituents of waxes of mature fibers. Energy-dispersive X-ray spectrometry (EDS) analysis of mature fibers revealed that potassium accumulated three times greater in MC-BL than in MC-WL mature fibers. This study provides novel insights into the biosynthesis of pigments and its association with flame retardancy in NBC fibers

Washable Antimicrobial Wipes Fabricated from a Blend of Nanocomposite Raw Cotton Fiber

In this study, a simple and effective way to produce washable antimicrobial wipes was developed based on the unique ability of raw cotton fiber to produce silver nanoparticles. A nanocomposite substructure of silver nanoparticles (25 ± 3 nm) was generated in raw cotton fiber without reducing and stabilizing agents. This nanocomposite raw cotton fiber (2100 ± 58 mg/kg in the concentration of silver) was blended in the fabrication of nonwoven wipes. Blending small amounts in the wipes—0.5% for antimicrobial properties and 1% for wipe efficacy—reduced the viability of S. aureus and P. aeruginosa by 99.9%. The wipes, fabricated from a blend of 2% nanocomposite raw cotton fiber, maintained their antibacterial activities after 30 simulated laundering cycles. The washed wipes exhibited bacterial reductions greater than 98% for both Gram-positive and Gram-negative bacteria

Induction of Low-Level Hydrogen Peroxide Generation by Unbleached Cotton Nonwovens as Potential Wound Dressing Materials

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