Cotton Genome Initiative (ICGI) #2131
Date: Sunday, January 12
4:00 pm - 6:10 pm
Location: Pacific Salon 2
Description:
Moderators/Organizers: David Stelly Texas A&M University, Tianzhen Zhang Nanjing Agricultural University
Advances in cotton genomics will be the main theme, e.g., the development, practice and uses of cotton genomics and genomics resources. A committee-chosen speaker line-up In 2014 will include five speakers, each addressing very different aspects of cotton genomics. The speakers hail from diverse institutions and world locations. In 2014, we will also try something new. We will devote one 20-minute time slot to a rapid-fire set of 15 ~1-minute oral introductions of posters about cotton genomics posters. Each 1-minute oral description will be made by the poster presenter, so will also introduce him/her to the audience.
4:00 PM - 4:20 PM
Presenters: Xiao-Ya Chen Shanghai Institute of Plant Physiology and Ecology, Ju-Xin Ruan Shanghai Institute of Plant Physiology and Ecology, Lei Yang Shanghai Institute of Plant Physiology and Ecology, Chang-Qing Yang Shanghai Institute of Plant Physiology and Ecology
W221 - Elucidation of Gossypol Biosynthesis Pathway
Cotton plants accumulate gossypol and related sesquiterpene aldehydes, which function as phytoalexins against pathogens and herbivores. Till now progress has been made in characterization of gossypol biosynthetic pathway, and several enzymes catalyzing early steps of the pathway have been cloned, including farnesyl pyrophosphate synthase (FPS), (+)-σ-cadinene synthase (CDN) and the P450 monooxygenase CYP706B1.
To elucidate the downstream steps, we performed comparative transcriptome analysis of glanded and glandless cotton plants, which resulted in isolation of genes that are preferentially or specifically expressed in the glanded cultivar. Of these, one encodes a P450 monooxygenase (CQ1) and another encodes a short chain alcohol dehydrogenase (CQ2), and both were strongly induced by fungal elicitor. In vitro assays with recombinant proteins showed that CQ2 was able to convert the 8-hydroxy-σ-cadinene into a new compound (A), which was further hydroxylated by CQ1. Moreover, CQ1 also showed the hydroxylation activity towards (+)-σ-cadinene, leading to 8-hydroxy-σ-cadinene. When either CQ1 or CQ2expression was down-regulated by virus induced gene silencing (VIGS), content of gossypol was decreased significantly, and increased accumulation of intermediates was detected. These data indicate that CQ1 and CQ2 are gossypol biosynthesis pathway enzymes that function downstream of CDN and CYP706B1.
With recent and continuous release of cotton genome data, we performed analysis of gene families of the enzymes involved in gossypol biosynthesis, and some of the results will be discussed during presentation.
4:20 PM - 4:40 PM
Presenters: Gregory Thyssen Cotton Fiber Biosciences Unit, USDA-ARS-SRRC, Xianliang Song Cotton Fiber Biosciences Unit, USDA-ARS-SRRC, Marina Naoumkina Cotton Fiber Biosciences Unit, USDA-ARS-SRRC, Hee Jin Kim Cotton Fiber Biosciences Unit, USDA-ARS-SRRC, David D. Fang Cotton Fiber Biosciences Unit, USDA-ARS-SRRC
W222 - Dynamic Replication and Transcription of Organellar Genomes in Developing Fiber Cells of Upland Cotton (Gossypium hirsutum L.)
The DNA of plant cells is located in three compartments, the nucleus, chloroplasts and mitochondria.
The genomes of the organelles, chloroplasts and mitochondria, are present in many copies in the
cells of most tissues, with multiple organelles per cell and often multiple genomes per organelle.
Even in non-green tissues, the chloroplasts and mitochondria are the sites of metabolism critical to
energy production. Here we report that the copy number of organellar genomes changes during cotton
fiber development. We also describe the transcriptional program of each organelle during fiber cell
development and identify differences between the wild-type program and those of cotton fiber
mutants. While the chloroplast genome replicates like a single circular chromosome, the
mitochondrial genome can divide into subgenomic circles by means of direct repeats. We observed
that the mitochondrial subgenomes vary in relative abundance during fiber cell development. We
examined the correlation between mitochondrial gene copy number and transcript abundance and propose
that subgenome replication dynamics may support the transcriptional program of mitochondria in
developing cotton fibers.
4:40 PM - 5:00 PM
Presenters: Amanda M. Hulse Texas A&M University, Cotton SNP Chip Consortium TAMUS, UC Davis, CSIRO, CIRAD, CSIR-NBRI, USDA-ARS, CI
W223 - Development of a Cotton SNP Chip from International Consortium-based Collaborations
An international collaborative effort has developed a SNP Chip for Cotton. This Illumina Infinium genotyping assay will allow genotyping of up to 90,000 attempted bead types, with 70,000 included in the public “fixed content”. The remaining 20,000 attempted bead types are available as “add-on content”. The consortium effort has included all currently published SNP development works as well as some sets of in press SNP data sets. The fixed content will primarily target intra-specific Gossypium hirsutum SNPs, but will also contain markers which target inter-specific SNPs for G. barbadense, G. tomentosum, G. mustelinum, G. armourianum, and G. longicalyx. The inter-specific targeted SNP are all developed relative to G. hirsutum and will greatly enable introgression work. This talk will discuss the international consortium effort to develop the SNP Chip for Cotton, the data sets utilized in the effort and distribution and development of the fixed content.
5:00 PM - 5:20 PM
Presenters: Rich Tuttle North Carolina State University
W224 - Integrated Transcriptomics and Metabolomics Between 10 – 28 Days Post Anthesis in Two Species of Commercial Cotton Fiber
Cotton fiber is a tissue comprised of a single cell type that develops from the seed epidermis in discrete stages including: initiation, elongation, a transition from primary to secondary wall deposition, and secondary wall thickening. Most cotton fiber produced comes from the species Gossypium hirsutum, but Gossypium barbadense cotton fibers are longer, stronger, and finer leading to a higher value yarn. We characterized fiber development in these two allotetraploid cotton species under controlled growth conditions and used RNAseq and metabolomics (Metabolon Inc., Durham, NC) to identify differences at 10, 15, 18 21, and 28 days post anthesis. The Gossypium raimondii genome was used in combination with Gossypium arboretum ESTs as a mapping reference. 37,937 transcripts (reads per kilobases per million reads >2) were identified of which 8,842 transcripts were differentially expressed (fold change>2) between the two species during development. Metabolic profiling of the cotton fiber showed that 186 of 206 identified metabolites were differentially accumulated between the two species during fiber development. KEGG ontology was used to map both datasets to metabolic pathways. Our results indicate that the two species differ most significantly in protein biosynthesis and turnover for all timepoints and in ROS management during the transition stage and secondary cell wall deposition. Other pathways that are differentially regulated between the two species include: glutathione metabolism, nitrogen metabolism, galactose metabolism, phenylpropanoid biosynthesis, amino and nucleotide sugar metabolism, starch and sucrose metabolism, and glycolysis. This work was funded by the National Science Foundation (award #1025947).
5:20 PM - 5:40 PM
Presenters: Yong-Ling Ruan University of Newcastle
W225 - Regulation of Cotton Fiber Development by Sugar and Water
Sugar and water are two key resources pivotal for cotton fiber development. We aim to elucidate (i) the molecular basis of sugar import to, and utilization within, cotton fibers and (ii) the mechanisms underpinning water influx into and efflux from fibre cells and (iii) how different components work together to drive and terminate fiber elongation and cellulose biosynthesis. Cell biology studies revealed a transient closure of plasmodesmata (PD) during cotton fibre elongation, coinciding with high expression of sugar and K+ transporters and rapid cell expansion. The latter is driven by osmotic water influx facilitated by a set of aquaporins (PIPs and TIPs). To elucidate how imported sucrose is utilized in fibre cells to power their elongation and cellulose biosynthesis, we examined the role of sucrose synthease (Sus) and invertase (Inv), which degrade sucrose into hexoses. Transgenic analyses revealed the critical role that Sus plays in fibre elongation, whereas over-expression of Sus increased early fibre elongation and seed set. Notably, a significant amount of sucrose must also enter into vacuoles as indicated by high activity of vacuole Inv (VIN) during fibre elongation, which may play a key role in driving water influx into vacuoles mediated by TIPs. At the onset of cellulose synthesis, a novel Sus protein targets to cell wall matrix, which may be directly involved in channeling carbon from sucrose to cellulose. These findings provide novel insights into the molecular basis of fiber development and opportunities to improve fiber yield and quality.
5:40 PM - 6:00 PM
Presenters: David Stelly Texas A&M University
W226 - Brief Oral Summaries of 15 Selected Posters by the Presenting Authors