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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Research Project #434423

Research Project: Advanced Genomic and Bioinformatic Tools for Accelerated Cotton Genetic Improvement

Location: Crop Germplasm Research

2021 Annual Report

Objective 1: Evaluate the cotton primary and secondary gene pools, as well as natural and synthetic cotton populations that are maintained in the USDA NPGS and cotton research community to identify useful genetic variability for industry-relevant traits, and provide information to breeders, along with augmented, and/or improved core sets of effective DNA markers. Sub-objective 1A: Augment and improve core sets of cotton SSR and SNP markers to effectively exploit the genetic variation of cotton germplasm and populations. Sub-objective 1B: Develop a core set of SSR markers for G. thurberi to allow for improved molecular characterization of this wild diploid Gossypium species. Objective 2: Sequence, refine, and annotate priority genomes of cotton species and accessions that contain genes controlling traits important to the cotton industry, and work with breeders to use these and previously identified cotton sequences to identify genomic regions for effective selections. Objective 3: Develop, improve, and manage an efficient and effective database and bioinformatics system, CottonGen, for efficiently exploiting cotton genetic variation. Objective 4: Identify key genes and genetic elements in cotton genomes, and use the information in selecting and verifying a range of priority agronomic traits, including biotic and abiotic stress resistance, and fiber and seed properties from materials contained in the USDA NPGS and cotton research community.

This project will provide the cotton industry with advanced genomic information and bioinformatic tools to enhance and accelerate the analysis and exploitation of genetic variability in the complex Gossypium genus. Current information suggests that genetic variation in cultivated cotton is limited, and that the overall structure of genetic variation in the Gossypium genus is not adequately resolved. More powerful tools are required to exploit the genetic potential of wild or uncultivated genotypes. Our recently completed genome assemblies of the Upland cotton genetic standard TM-1 and its probable progenitors provide a template for further sequencing efforts. Resequencing other cultivated and wild cotton species and/or accessions will allow comparative exploration for effective identification and manipulation of beneficial genes otherwise buried within Gossypium germplasm collections. In the current project, we will specifically develop and improve core sets of DNA markers tailored to individual cotton species, generate novel genome sequence information, and identify key genes or genetic elements linked to priority traits for improving agronomics, fiber and/or seed quality, and resistance to biotic/abiotic stresses. In cooperation with Cotton Incorporated, this project will provide support, coordination, and oversight to CottonGen, a database of genomic, genetic, and breeding resources managed by Washington State University. A primary goal of this project is to provide effective tools and information to identify and elucidate genetic variation within the U.S. National Cotton Germplasm Collection that is maintained by our sister germplasm project. New biological information developed by the project will be made publicly available in the GenBank and CottonGen databases.

Progress Report
Work under Objective 1 included ongoing analysis of polymorphism information content (PIC) of molecular tools known as single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers that were applied to cotton germplasm characterization and quantitative trait loci (QTL) mapping. Objective 1 work also genetically characterized the diploid cotton wild relative species G. thurberi. A germination protocol was optimized, and forty-seven accessions were selected for molecular characterization by comparison to a reference genome. Work under Objective 2 included public release of high-quality sequence data for G. longicalyx, a diploid wild relative of cultivated cotton, through GenBank and CottonGen databases. Genomic segments of this species were found to confer reniform nematode resistance and other valuable traits for cotton production. In addition, another diploid wild relative of cotton (G. stocksii), two nematode-resistant strains of Upland cotton (G. hirsutum), and 643 cultivated accessions of G. hirsutum and G. barbadense were genetically sequenced. Work under Objective 3 included support of and data input to the CottonGen database (managed by Cotton Inc.) which serves the broad cotton community worldwide. Thirteen new cotton genomes, approximately 11,000 genetic tools known as molecular markers, and nearly 300 molecular tools known as quantitative trait loci (QTL), 4,000 new phenotypic datapoints, and 32,000 new images (99% germplasm characterization and 100 mutant images) were added to the database. CottonGen served 358,000 pages to the user communities, and was accessed about 24,000 times by cotton researchers from 156 countries. Work under Objective 4 resulted in major progress in mapping and defining genetic control of cotton fiber/seed properties and abiotic/biotic stress tolerance for cotton improvement. In addition to fiber and seed QTL mapping and characterization using the interspecific TM-1 x 3-79 population, genetic techniques known as cotton transcriptome and methylome mapping analysis identified biological pathways and candidate genes that are differentially expressed for cell growth under alkaline stress environments. Data were also developed and analyzed for gene expression of transcription factors (TFs) between three pairs of glanded and glandless cotton lines to improve purity of cottonseed oil and protein. Overall, progress in Fiscal Year 2021 under these technologically complex and challenging objectives resulted in a much clearer understanding of the genetic make-up of commercial cottons and their wild relatives. Information developed by this project will be foundational to breeders in developing more productive and profitable cotton types for U.S. farmers.

1. Genome sequence of the diploid cotton, Gossypium longicalyx. A close relative of cultivated cotton, Gossypium longicalyx, is an African species with good resistance to the reniform nematode, a major pest that limits cotton production in many areas. Successful transfer of such resistance from this wild diploid to cultivated tetraploid cotton requires genomic knowledge and resources previously unavailable. ARS researchers at College Station, Texas, working with national and international collaborators, sequenced and assembled the genome of G. longicalyx. The assembled genome sequence and associated gene annotation, published in one of the world's most respected journals, provide plant breeders with valuable tools to effectively develop cotton cultivars that are resistant to the reniform nematode. Such resistant commercial cottons will increase productivity and profitability, and will improve environmental quality by reducing or eliminating the use of pesticides for nematode control.

2. Novel biological pathways in cotton alkaline toxicity tolerance. Alkaline toxicity, caused by accumulating chemical compounds such as sodium bicarbonate in some farmlands, threatens the growth and productivity of cotton plants. Little is known about biological pathways or genetic mechanisms of the cotton plants in response to this abiotic stress. ARS researchers at College Station, Texas, working with international collaborators, unraveled for the first time the complex biological pathways and candidate genes in cotton that are associated with cotton tolerance to sodium bicarbonate. This accomplishment is important because it has developed new knowledge that will be foundational to breeders in developing new cotton types that will not be susceptible to alkaline toxicity. Such will allow cotton to be successfully grown in alkaline soils that have historically not been conducive to cotton farming.

3. Historical selection in cotton domestication. Gossypium hirsutum and G. barbadense are the two tetraploid species cultivated for cotton, but little is known about their distinct origins from different parts of the world and their domestication from different wild populations over millennia. ARS researchers at College Station, Texas, working with national and international collaborators, sequenced 643 wild and domesticated accessions of the two species. Analysis of genetic variation cataloged from these genome sequences revealed genomic regions selected for fiber development and other traits during cotton domestication over many centuries. This work represents a significant contribution to the knowledge base of tetraploid cotton domestication under directional human selection over a long period of history, and explains to a significant degree the pathways of directed evolution that led to cotton types currently exploited in world agriculture.

Review Publications
Ashraf, J., Zuo, D., Cheng, H., Malik, W., Wang, Q., Zhang, Y., Abid, M., Yang, Q., Feng, X., Yu, J., Song, G. 2020. Improved reconstruction and comparative analysis of chromosome 12 to rectify mis-assemblies in Gossypium arboreum. Biomed Central (BMC) Genomics. 21. Article 470.
Grover, C.E., Pan, M., Yuan, D., Arick, M.A., Hu, G., Brase, L., Stelly, D.M., Lu, Z., Schmitz, R.J., Peterson, D.G., Wendel, J.F., Udall, J.A. 2020. The Gossypium longicalyx genome as a resource for cotton breeding and evolution. Genes, Genomes, Genetics. 10:1457-1467.
Fan, Y., Lu, X., Chen, X., Wang, J., Wang, D., Wang, S., Guo, L., Rui, C., Zhang, Y., Cui, R., Wang, Q., Yu, J., Ye, W. 2021. Cotton transcriptome analysis reveals novel biological pathways that eliminate reactive oxygen species (ROS) under sodium bicarbonate (NaHCO3) alkaline stress. Genomics. 113(3):1157-1169.
Yuan, D., Grover, C.E., Hu, G., Pan, M., Miller, E., Conover, J.L., Hunt, S., Udall, J.A., Wendel, J.F. 2021. Parallel and intertwining threads of domestication in allopolyploid cotton. Advanced Science. Article 2003634.
Grover, C.E., Yuan, D., Arick, M.A., Miller, E.R., Hu, G., Peterson, D.G., Wendel, J.F., Udall, J.A. 2021. The Gossypium stocksii genome as a novel resource for cotton improvement. G3, Genes/Genomes/Genetics. 11(7). Article jkab125.