Sequencing a Reference-grade Genome of the Domesticated Allotetraploid Cotton: the World's Largest Source of Renewable Textile Fiber

University Of Texas At Austin, Austin TX

Investigators

Abstract

Cotton is the world's largest source of natural textile fiber and is a main oilseed crop. The revenue resulting from annual cotton production is estimated to be $100 billion in the USA alone. Cotton is an excellent model system for studying fiber cell differentiation, cell expansion, and cellulose biosynthesis, as well as polyploid genome evolution and crop domestication. Upland or American cotton (Gossypium hirsutum L.) and Pima or Egyptian cotton (Gossypium barbadense L.) have been independently domesticated from allotetraploid species. Improving cotton fiber yield and quality will provide a sustainable alternative to petroleum-based synthetic fibers. Generating a reference-grade genome sequence for domesticated allotetraploid cotton will enable both basic and applied research that will provide new insights into fiber development and cellulose and wall biosynthesis with broad impact for biomass crops and biofuel production. Since most crops are of polyploid origin, methods and principles being developed from this project will also advance research in other crops with complex and polyploid genomes. Genomic sequence and gene expression data will be made available through public data depositories, including GenBank, GEO (http://www.ncbi.nlm.nih.gov/geo/), miRBase (http://microrna.sanger.ac.uk/), and the NCBI's SRA (http://www.ncbi.nlm.nih.gov/geo/info/seq.html). Plant materials and the final version of annotated sequence will be distributed through CottonGen (http://www.cottongen.org/icgi/home), the cotton research community website. Innovative and scalable education and training modules in plant genomics and bioinformatics will be developed for middle and high schools and undergraduate institutions in the Mississippi Delta. The effectiveness of education and outreach will be enhanced through close collaborations with Alcorn State University and Mississippi Valley State University, two Historically Black Colleges and Universities. The overall goal of this project is to develop high-quality sequence resources to address fundamental questions in crop plants that are of economic importance. The physical map-guided hybrid approach in combination with whole-genome shotgun (WGS) and genotyping-by-sequencing (GBS) is among the best strategies to sequence and assemble "gold-standard" reference-grade genomes of complex polyploid species including cotton and other important crops such as wheat. The research team has developed bacterial artificial chromosome (BAC) resources including a physical map and BAC-end sequences (BES), WGS, PacBio long reads, and single nucleotide polymorphism (SNP) data of Upland cotton (TM-1). Moreover, the critical pilot data have been generated, which are necessary in preparing a successful strategy for sequencing the allotetraploid cotton. Specifically, the project will sequence and assemble individual BAC inserts from the minimum tiling path that covers ~85% of the genome. The gaps will be filled and/or reduced by the second iteration of additional 3,000 or more BACs with integration of WGS contigs, mate-pair and PacBio long reads. The sequence contigs and scaffolds will be ordered by high-density linkage maps and BES-targeted GBS. The final sequence will consist of thirteen pairs of homoeologous pseudo-molecules, including validation by targeted GBS and BAC-fluorescence in situ hybridization. The reference-grade sequence will be annotated by Phytozome with the RNA-seq data collected from ~20 cotton tissues. This reference-grade sequence will be immediately released to the research and breeding communities to improve Upland cotton that accounts for >95% of the world cotton production. The sequence will be utilized for analyzing epigenomes and their roles in fiber development of allotetraploid cotton.