RESEARCH-PGR: Genomic and Epigenomic Analyses of Fiber Development in Allotetraploid Cottons

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Cotton is the largest source of renewable textile fiber and the U.S.A. is the world's top exporter of cotton, generating ~200,000 domestic jobs. Improving cotton production will help provide U.S. jobs, sustainable agriculture, and adaptation to a changing climate. Traditional breeding efforts have given rise to several types of economically valuable cotton strains such as American and Egyptian cotton. These two strains of cotton were independently formed by the combination of two wild species, yielding cotton strains with four sets of chromosomes (two from each parent). This doubling of chromosomes is known as polyploidy, and this project is focused on understanding how polyploidy shapes how genes are used to generate improved strains of cotton. This project leverages and develops cutting edge technologies in DNA sequencing to understand polyploidy. In addition, this project produces new biological materials for cotton breeding and improvement. The research goals are augmented by promoting Science, Technology, Engineering and Mathematics (STEM) education in the Mississippi Delta through active collaborations with two Historically Black Colleges and Universities. These educational activities train college students and K-12 teachers in cutting-edge plant biotechnology techniques, knowledge, and skills to advance their careers and use in their classrooms.Cotton is an excellent model system not only for understanding cell differentiation, elongation, and cellulose biosynthesis, but also for elucidating polyploid genome evolution and crop domestication. Upland cotton (Gossypium hirsutum L.) and Pima cotton (Gossypium barbadense L.) were independently domesticated from two of five or more allotetraploid species that arose from interspecific hybridization between diploid cotton species. It is important to understand how polyploidy-induced changes in genome structure and organization, epigenetic modifications, and gene expression have enabled selection and domestication of wild allotetraploids for worldwide cotton production. The project goal is to develop high-quality genomic and epigenomic resources for cotton improvement. Comparative analyses of sequence features and gene expression diversity among domesticated and wild tetraploid and diploid relatives will reveal genomic signatures for selection and domestication of agronomic traits, including fiber yield and quality and adaptation to the environments. Laser-capture microdissection and single-cell approaches will be used to reveal genomic and epigenomic networks during the transition from protodermal to fiber cells. Functions of the selected candidate genes for fiber development and epigenetic pathways will be determined using virus-induced gene silencing and CRISPR/cas9 gene-editing tools. Genomic sequences and epigenetic resources will be released to public data depositories, including National Center for Biotechnology Information (NCBI), Phytozome, and CottonGen. Plant materials including chromosome substitution lines and transgenic cotton will be available for the cotton breeding community. The methods, principles and resources being developed from this project will also advance the research on other polyploid crops such as wheat and canola.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.