@article{andres_coneva_frank_tuttle_samayoa_han_kaur_zhu_fang_bowman_et al._2017, title={Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.)}, volume={114}, DOI={10.1101/062612}, abstractNote={Abstract}, number={1}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Andres, R. J. and Coneva, V. and Frank, M. H. and Tuttle, J. R. and Samayoa, L. F. and Han, S. W. and Kaur, B. and Zhu, L. L. and Fang, Hui and Bowman, D. T. and et al.}, year={2017}, pages={E57–66} }
 @inbook{stiff_tuttle_graham_haigler_2016, place={Cham, Switzerland}, series={Sustainable Development and Biodiversity}, title={Cotton Fiber Biotechnology: Potential Controls and Transgenic Improvement of Elongation and Cell Wall Thickening}, volume={13}, ISBN={9783319445694 9783319445700}, ISSN={2352-474X 2352-4758}, url={http://dx.doi.org/10.1007/978-3-319-44570-0_8}, DOI={10.1007/978-3-319-44570-0_8}, abstractNote={Cotton is grown on five continents as an economically important crop. Its long, fine, seed fibers are one of the most highly used natural fibers, providing a high-quality spinnable fiber to the textile industry. The cotton fiberCotton fiber undergoes a complex, staged developmental program, resulting in a single cell that is 1.8–5 cm long with a thick wall composed of about 95 % cellulose. Biotechnological improvements have either directly or indirectly enhanced the fiber properties that are important for spinning, including length, bundle strength, and maturity. These experiments have generally targeted carbohydrate metabolism, cell wall structure, and hormone signaling. In this chapter, we present a brief review of cotton fiber developmentCotton fiber development with a focus on processes affecting elongation and cell wall thickening. We discuss rigorous criteria for evaluating studies on transgenic cotton fiber and mention the challenges of performing such research in the public sector. We highlight selected genetic engineering experiments that have resulted in improved cotton fiber quality Cotton fiber quality and discuss future prospects for use of biotechnology to improve cotton fiberCotton fiber and its competitiveness with synthetic fibers.}, booktitle={Fiber Plants}, publisher={Springer International Publishing}, author={Stiff, Michael R. and Tuttle, J. Rich and Graham, Benjamin P. and Haigler, Candace H.}, editor={Ramawat, K. and Ahuja, M.Editors}, year={2016}, pages={127–153}, collection={Sustainable Development and Biodiversity} }
 @article{tuttle_nah_duke_alexander_guan_song_chen_scheffler_haigler_2015, title={Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation}, volume={16}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/s12864-015-1708-9}, DOI={10.1186/s12864-015-1708-9}, abstractNote={The morphogenesis of single-celled cotton fiber includes extreme elongation and staged cell wall differentiation. Designing strategies for improving cotton fiber for textiles and other uses relies on uncovering the related regulatory mechanisms. In this research we compared the transcriptomes and metabolomes of two Gossypium genotypes, Gossypium barbadense cv Phytogen 800 and G. hirsutum cv Deltapine 90. When grown in parallel, the two types of fiber developed similarly except for prolonged fiber elongation in the G. barbadense cultivar. The data were collected from isolated fibers between 10 to 28 days post anthesis (DPA) representing: primary wall synthesis to support elongation; transitional cell wall remodeling; and secondary wall cellulose synthesis, which was accompanied by continuing elongation only in G. barbadense fiber. Of 206 identified fiber metabolites, 205 were held in common between the two genotypes. Approximately 38,000 transcripts were expressed in the fiber of each genotype, and these were mapped to the reference set and interpreted by homology to known genes. The developmental changes in the transcriptomes and the metabolomes were compared within and across genotypes with several novel implications. Transitional cell wall remodeling is a distinct stable developmental stage lasting at least four days (18 to 21 DPA). Expression of selected cell wall related transcripts was similar between genotypes, but cellulose synthase gene expression patterns were more complex than expected. Lignification was transcriptionally repressed in both genotypes. Oxidative stress was lower in the fiber of G. barbadense cv Phytogen 800 as compared to G. hirsutum cv Deltapine 90. Correspondingly, the G. barbadense cultivar had enhanced capacity for management of reactive oxygen species during its prolonged elongation period, as indicated by a 138-fold increase in ascorbate concentration at 28 DPA. The parallel data on deep-sequencing transcriptomics and non-targeted metabolomics for two genotypes of single-celled cotton fiber showed that a discrete developmental stage of transitional cell wall remodeling occurs before secondary wall cellulose synthesis begins. The data showed how lignification can be transcriptionally repressed during secondary cell wall synthesis, and they implicated enhanced capacity to manage reactive oxygen species through the ascorbate-glutathione cycle as a positive contributor to fiber length.}, number={1}, journal={BMC Genomics}, publisher={Springer Science and Business Media LLC}, author={Tuttle, John R. and Nah, Gyoungju and Duke, Mary V. and Alexander, Danny C. and Guan, Xueying and Song, Qingxin and Chen, Z. Jeffrey and Scheffler, Brian E. and Haigler, Candace H.}, year={2015}, month={Jun} }
 @inbook{tuttle_haigler_robertson_2015, title={Virus-Induced Gene Silencing of Fiber-Related Genes in Cotton}, volume={1287}, ISBN={9781493924523 9781493924530}, ISSN={1064-3745 1940-6029}, url={http://dx.doi.org/10.1007/978-1-4939-2453-0_16}, DOI={10.1007/978-1-4939-2453-0_16}, abstractNote={Virus-Induced Gene Silencing (VIGS) is a useful method for transient downregulation of gene expression in crop plants. The geminivirus Cotton leaf crumple virus (CLCrV) has been modified to serve as a VIGS vector for persistent gene silencing in cotton. Here the use of Green Fluorescent Protein (GFP) is described as a marker for identifying silenced tissues in reproductive tissues, a procedure that requires the use of transgenic plants. Suggestions are given for isolating and cloning combinations of target and marker sequences so that the total length of inserted foreign DNA is between 500 and 750 bp. Using this strategy, extensive silencing is achieved with only 200–400 bp of sequence homologous to an endogenous gene, reducing the possibility of off-target silencing. Cotyledons can be inoculated using either the gene gun or Agrobacterium and will continue to show silencing throughout fruit and fiber development. CLCrV is not transmitted through seed, and VIGS is limited to genes expressed in the maternally derived seed coat and fiber in the developing seed. This complicates the use of GFP as a marker for VIGS because cotton fibers must be separated from unsilenced tissue in the seed to determine if they are silenced. Nevertheless, fibers from a large number of seeds can be rapidly screened following placement into 96-well plates. Methods for quantifying the extent of silencing using semiquantitative RT-PCR are given.}, booktitle={Methods in Molecular Biology}, publisher={Springer New York}, author={Tuttle, John R. and Haigler, Candace H. and Robertson, Dominique}, year={2015}, pages={219–234} }
 @article{tuttle_haigler_robertson_2012, title={Method: low-cost delivery of the cotton leaf crumple virus-induced gene silencing system}, volume={8}, ISSN={1746-4811}, url={http://dx.doi.org/10.1186/1746-4811-8-27}, DOI={10.1186/1746-4811-8-27}, abstractNote={We previously developed a virus-induced gene silencing (VIGS) vector for cotton from the bipartite geminivirusCotton leaf crumple virus (CLCrV). The original CLCrV VIGS vector was designed for biolistic delivery by a gene gun. This prerequisite limited the use of the system to labs with access to biolistic equipment. Here we describe the adaptation of this system for delivery by Agrobacterium (Agrobacterium tumefaciens). We also describe the construction of two low-cost particle inflow guns. The biolistic CLCrV vector was transferred into two Agrobacterium binary plasmids. Agroinoculation of the binary plasmids into cotton resulted in silencing and GFP expression comparable to the biolistic vector. Two homemade low-cost gene guns were used to successfully inoculate cotton (G. hirsutum) and N. benthamiana with either the CLCrV VIGS vector or the Tomato golden mosaic virus (TGMV) VIGS vector respectively. These innovations extend the versatility of CLCrV-based VIGS for analyzing gene function in cotton. The two low-cost gene guns make VIGS experiments affordable for both research and teaching labs by providing a working alternative to expensive commercial gene guns.}, number={1}, journal={Plant Methods}, publisher={Springer Science and Business Media LLC}, author={Tuttle, John and Haigler, Candace H and Robertson, Dominique}, year={2012}, pages={27} }