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INVESTIGATOR: SRIPATHI, V.

PERFORMING INSTITUTION:
ALABAMA A&M UNIVERSITY
4900 MERIDIAN STREET
NORMAL, ALABAMA 35762

UNDERSTANDING EPIGENOMIC VARIATION IN DIPLOID COTTON, GOSSYPIUM HERBACEUM IN RESPONSE TO ABIOTIC STRESS

NON-TECHNICAL SUMMARY: Project summary: Heat, drought and salinity stresses lead to metabolic toxicity, membrane disorganization, generation of reactiveoxygen species (ROS), inhibition of photosynthesis and altered nutrient acquisition. This effort will identify underlying genetic and epigenetic mechanisms linked to abiotic tolerance inherent in Gossypium herbaceum. The study responds to the accentuated needs of the farmers by climate change. This research proposal is based on four-tiered objectives: 1. Expand genomic sequence coverage of an underexplored diploid cotton, G. herbaceum and develop a reference A1 genome; 2. Understanding epigenomic variation in diploid cotton, G. herbaceum, in response to abiotic stress (heat-, drought-, and salinity-stress) by utilizing Whole Genome BiSulphite Sequencing (BS-Seq) and Chromatin Immunoprecipitation-Sequencing (ChIP-Seq); 3. Identification of regulatory mechanisms associated with gene expression by utilizing comparative genomics; and 4. Train two PhD level graduate students and four undergraduate students, while expanding AAMU's capabilities in emerging sphere of epigenetic investigations. The expected outcomes of this project are: a) providing a draft genome (>96%) of G. herbaceum; b) providing gold-standard (108 methylated sites) stressed and un-stressed methylome patterns of G. herbaceum to plant community; c) decipher components of tolerance mechanisms, their regulation and control of gene expression by signaling networks and transcriptional regulators; d) data generated from this effort will be shared to public and published in high-quality journals; and e) The broader impact is the information generated will help in developing abiotic stress resistant cultivars by applying plant breeding strategies and in training next generation scientists in advanced STEM fields.

OBJECTIVES: Long-term Goals: The proposed project is a new application with long-term goals of the participating institution, Alabama A&M University (AAMU), with active research for the past five decades on agriculturally important crops. The Center for Molecular Biology (CMB) at Alabama A&M University has a well-established sequencing facility for supporting inter-institutional and inter-departmental genomic needs. CMB has a two-decade history in applied genomic research, particularly in deciphering molecular mechanisms associated with abiotic and biotic plant-stress responses. Such an impressive track record alone is not sufficient enough as new approaches and advances are driving the field of molecular biology. Therefore, additional capacity building is needed if one must train undergraduate and graduate students in cutting-edge technologies. The inherent genetic potential of some species to tolerate stress can be tapped by screening genomes. Crop production is increasingly challenging as terrestrial land plants are forced to grow under modified soil conditions due to global climate change. Understanding genomic and epigenomic variation in land plants under abiotic stresses will aid in unraveling key regulatory mechanisms associated with abiotic tolerance and adaptation. Through this project, AAMU aims to advance its long-term goals by expanding research in cotton using a diploid, underexplored parental species, Gossypium herbaceum applying novel approaches available in post-genomics era, train two graduate and four undergraduate students in conducting comprehensive research in understanding genomic and epigenomic landscapes of G. herbaceum, and to tap its inherent genetic potential linked to traits associated with abiotic stress tolerance. A holistic approach as proposed here that integrates genomic, transcriptomic and epigenomic resources in cotton will provide better understanding of these underlying molecular mechanisms. The advanced research as proposed here not only benefit the stake holders but also in training young minds who aspire to pursue their careers in STEM disciplines, which is integrated in the project objectives. The geographical location of AAMU also adds weight to this project as it is located in the most important cotton producing belt of the US, the Tennessee river delta. This project is in response to requests for development of effective and alternative strategies for genetic improvement and sustainable production of cotton to better serve its stakeholders. This is a single institution and applied research application belonging to program code "EQ", and directly or indirectly addresses CBG priority areas j, g & e; discipline code N2, B2; NIFA challenge areas b & c within NIFA priorities 1 & 3.Major Goal: The goal of this research effort is to identify underlying genetic and epigenetic mechanisms linked to abiotic stress tolerance that is inherent to G. herbaceum by utilizing existing resources in an effective manner and to make the data generated in this effort publicly available, which facilitates the cotton breeders in developing abiotic tolerant genotypes based genomic and epigenomic information rather than just relying on genetic information alone.Objectives: 1. Expand genomic sequence coverage of an underexplored diploid cotton, G. herbaceum.2. Understanding epigenomic variation in diploid cotton, G. herbaceum, in response to salinity stress (abiotic) by utilizing BS-Seq and ChIP-Seq.3. Identification of regulatory mechanisms associated with gene expression by utilizing comparative genomics.4. Train two PhD level graduate students and four undergraduate students, while expanding AAMU's capabilities in emerging sphere of epigenome research.