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Full-Text Articles in Life Sciences
Improving Cotton Agronomics With Diverse Genomic Technologies, Aaron Robert Sharp
Improving Cotton Agronomics With Diverse Genomic Technologies, Aaron Robert Sharp
Theses and Dissertations
Agronomic outcomes are the product of a plant's genotype and its environment. Genomic technologies allow farmers and researchers new avenues to explore the genetic component of agriculture. These technologies can also enhance understanding of environmental effects. With a growing world population, a wide variety of tools will be necessary to increase the agronomic productivity. Here I use massively parallel, deep sequencing of RNA (RNA-Seq) to measure changes in cotton gene expression levels in response to a change in the plant's surroundings caused by conservation tillage. Conservation tillage is an environmentally friendly, agricultural practice characterized by little or no inversion of …
Transcriptome And Methylation Analysis Of Gossypium Petal Tissue, Aditi Rambani
Transcriptome And Methylation Analysis Of Gossypium Petal Tissue, Aditi Rambani
Theses and Dissertations
Polyploidization instantly doubles all genome content by combining two genomes that have markedly different methylation and gene expression levels. This process may be accompanied by genetic and epigenetic changes in each genome. Sequencing of the transcriptome (RNA-seq) and the methylome (bisulfite treated libraries whole genome libraries) were used to measure gene expression and methylation levels of genic regions of allopolyploid cotton petals and petals of their diploid relatives. Many differentially expressed genes detected by RNA-seq were consistent with expression levels previously detected by microarrays. RNA-seq results also reconfirmed the presence of general polyploid gene expression trends like expression level dominance …
Marker Discovery In Allotetraploid Cotton Using 454 Pyrosequencing, Robert L. Byers
Marker Discovery In Allotetraploid Cotton Using 454 Pyrosequencing, Robert L. Byers
Theses and Dissertations
A narrow germplasm base and a complex allotetraploid genome have historically made the discovery of single nucleotide polymorphism (SNP) markers difficult in cotton (Gossypium hirsutum). We conducted a genome reduction experiment to identify SNPs from two accessions of G. hirsutum and two accessions of G. barbadense. Approximately 2 million sequence reads were assembled into contigs with an N50 of 508 bp and analyzed for SNPs. A total of 11,834 and 1,679 SNPs between the accessions G. hirsutum and G. barbadense, respectively, were identified with highly conservative parameters (a minimum read depth of 8x at each SNP …
Duplicate Gene Expression In Allopolyploid Gossypium Reveals Two Temporally Distinct Phases Of Expression Evolution, Joshua Udall, Lex E. Flagel, Dan Nettleton, Jonathan F. Wendel
Duplicate Gene Expression In Allopolyploid Gossypium Reveals Two Temporally Distinct Phases Of Expression Evolution, Joshua Udall, Lex E. Flagel, Dan Nettleton, Jonathan F. Wendel
Faculty Publications
Polyploidy has played a prominent role in shaping the genomic architecture of the angiosperms. Through allopolyploidization, several modern Gossypium (cotton) species contain two divergent, although largely redundant genomes. Owing to this redundancy, these genomes can play host to an array of evolutionary processes that act on duplicate genes. Results- We compared homoeolog (genes duplicated by polyploidy) contributions to the transcriptome of a natural allopolyploid and a synthetic interspecific F1 hybrid, both derived from a merger between diploid species from the Gossypium A-genome and D-genome groups. Relative levels of A- and D-genome contributions to the petal transcriptome were determined for 1,383 …
Spotted Cotton Oligonucleotide Microarrays For Gene Expression Analysis, Joshua Udall, Lex E. Flagel, Foo Chung, Andrew W. Woodward, Ran Hovav, Ryan A. Rapp, Jordan M. Swanson, Jinsuk J. Lee, Alan R. Gingle, Dan Nettleton, Christopher D. Town, Z. Jeffrey Chen, Jonathan F. Wendel
Spotted Cotton Oligonucleotide Microarrays For Gene Expression Analysis, Joshua Udall, Lex E. Flagel, Foo Chung, Andrew W. Woodward, Ran Hovav, Ryan A. Rapp, Jordan M. Swanson, Jinsuk J. Lee, Alan R. Gingle, Dan Nettleton, Christopher D. Town, Z. Jeffrey Chen, Jonathan F. Wendel
Faculty Publications
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.