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

棉花是可再生纺织纤维的最大来源，美国是世界上最大的棉花出口国，创造了约20万个国内就业机会。提高棉花产量将有助于为美国提供就业机会、可持续农业和适应不断变化的气候。传统的育种努力已经产生了几种具有经济价值的棉花品种，如美国棉花和埃及棉花。这两个棉花品系是由两个野生物种独立结合形成的，产生的棉花品系有四组染色体（每个亲本各两组）。这种加倍的染色体被称为多倍体，这个项目的重点是了解多倍体如何塑造基因，如何用于产生改良的棉花品种。该项目利用并开发了DNA测序的尖端技术来了解多倍体。此外，本项目还为棉花育种和改良生产新的生物材料。通过与两所历史上的黑人学院和大学的积极合作，促进密西西比三角洲的科学、技术、工程和数学（STEM）教育，增强了研究目标。这些教育活动培训大学生和K-12教师掌握尖端的植物生物技术、知识和技能，以促进他们的职业发展并在课堂上使用。棉花是了解细胞分化、伸长和纤维素生物合成的良好模型系统，也是阐明多倍体基因组进化和作物驯化的良好模型系统。陆地棉（Gossypium hirsutum L.）和皮马棉（Gossypium barbadense L.）是由二倍体棉花种间杂交产生的五个或多个异源四倍体种中的两个独立驯化而成的。了解多倍体诱导的基因组结构和组织、表观遗传修饰和基因表达的变化如何使野生异源四倍体在全球棉花生产中得以选择和驯化是很重要的。项目目标是为棉花改良开发优质基因组和表观基因组资源。对驯化和野生四倍体和二倍体亲缘植物的序列特征和基因表达多样性进行比较分析，将揭示包括纤维产量、质量和环境适应性在内的农艺性状的选择和驯化的基因组特征。激光捕获显微解剖和单细胞方法将用于揭示基因组和表观基因组网络从原始真皮细胞过渡到纤维细胞。选择的候选基因在纤维发育和表观遗传途径中的功能将使用病毒诱导的基因沉默和CRISPR/cas9基因编辑工具来确定。基因组序列和表观遗传资源将发布到公共数据存储库，包括国家生物技术信息中心（NCBI）、Phytozome和CottonGen。包括染色体替代系和转基因棉花在内的植物材料将提供给棉花育种界。该项目开发的方法、原理和资源也将促进其他多倍体作物如小麦和油菜的研究。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

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.