Background: Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species.
Results: Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from >50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to target the diversity of the transcriptome and previously studied cotton genes, transcription factors, and genes with homology to Arabidopsis. A small portion of the oligonucleotides target unidentified protein coding sequences, thereby providing an element of gene discovery. Because many oligonucleotides were based on ESTs from fiber-specific cDNA libraries, the microarray has direct application for analysis of the fiber transcriptome. To illustrate the utility of the microarray, we hybridized labeled bud and leaf cDNAs from G. hirsutum and demonstrate technical consistency of results.
Conclusion: The cotton oligonucleotide microarray provides a reproducible platform for transcription profiling in cotton, and is made publicly available through http://cottonevolution.info.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225879 | PMC |
http://dx.doi.org/10.1186/1471-2164-8-81 | DOI Listing |
Talanta
December 2024
School of Food Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, China; Xinjiang Tianrun Dairy Co.,Ltd., Wuchang Road No. 2702, Urumqi, China. Electronic address:
In recent years, nanozymes have been widely used in the field of biosensing and food safety testing due to their advantages of low cost, high stability, easy modification and adjustable catalytic activity. However, how to reduce the signal interference generated by reducing substances, macromolecules and colored substances in the food matrix in nanozymes-based colorimetric sensing is still a major challenge. In this paper, using Listeria monocytogenes as a model analyte, sodium sulfonyl methacrylate (SBMA) polymers were modified onto cotton swabs by photothermal polymerization and combined with Listeria monocytogenes-specific aptamer (Apt1) to prepare swabs that can specifically capture and isolate Listeria monocytogenes from complex matrices (SBMA/Apt1 cotton swab).
View Article and Find Full Text PDFJ Basic Microbiol
November 2024
Department of Plant Pathology, CCS Haryana Agricultural University, Hisar, Haryana, India.
Cotton root rot caused by Macrophomina phaseolina pose a significant threat to cotton production, leading to substantial yield and quality losses. Early and accurate diagnosis of this pathogen in soil is crucial for effective disease management. This study presents a pioneering investigation into the utilization of the nit gene encoding nitrilase for the development of a molecular diagnostic assay aimed at the rapid detection of M.
View Article and Find Full Text PDFBMC Plant Biol
July 2024
School of Agriculture, Center of Wheat Research, Henan Key Laboratory of Hybrid Wheat, Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China.
Background: Powdery mildew (caused by Blumeria graminis f. sp. tritici (Bgt)) and leaf rust (caused by Puccinia triticina (Pt)) are prevalent diseases in wheat (Triticum aestivum L.
View Article and Find Full Text PDFTalanta
March 2024
Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, 450018, China. Electronic address:
Numerous aptamers against various targets have been identified through the technology of systematic evolution of ligands by exponential enrichment (SELEX), but the affinity of these aptamers are often insufficient due to the limitations of SELEX. Therefore, a more rational in silico screening strategy (ISS) was developed for efficient screening of high affinity aptamers, which took shape complementarity and thermodynamic stability into consideration. Neuron specific enolase (NSE), a tumor marker, was selected as the target molecule.
View Article and Find Full Text PDFGenome
March 2024
State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China.
Discrimination of chromosome is essential for chromosome manipulation or visual chromosome characterization. Oligonucleotide probes can be employed to simplify the procedures of chromosome identification in molecular cytogenetics due to its simplicity, fastness, cost-effectiveness, and high efficiency. So far, however, visual identification of cotton chromosomes remains unsolved.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!