USDA ARS National Cotton Germplasm Characterization

SUMMARY

            The USDA-ARS National Cotton Germplasm Collection (NCGC) is an essential resource for cotton breeding, research, and education.  The NCGC contains passport information on the origins of the accessions, and the Curator routinely collects standardized morphological descriptors to indicate to users the phenotypic variability and utility of the accessions.  High resolution digital images of representative plant features are captured to assemble an online digital image library.  Agronomic evaluations and genotypic diversity of accessions are also obtained through collaborations with subject matter experts.

            The online databases GRIN-Global and CottonGen are critical to communicate to their users the contents, availability, and descriptions of accessions in the NCGC.  CottonGen is unique in that it accumulates, organizes, and links information across the NCGC, other cotton collections, and research and evaluation results from trials using improved cotton germplasm and genetic resources from collections.

OBJECTIVES

The objective of this cooperative project is the coordinated characterization and evaluation of genetic and phenotypic diversity within the germplasm collection.  Sub-objectives include the development of a digital image library, phenotypic evaluation of accessions, and molecular analyses of trait associations and diversity among accessions.

PARTICIPANTS

PROTOCOLS

Morphological Descriptors

The NCGC uses a set of standardized descriptors to characterize the morphological features of all accessions for all species in the collection.  When several cotton collections existed in the United States, each collection had its own set of descriptors.  After those collections were merged to form the NCGC, a consensus, standardized set of descriptors was needed to characterize the breadth of diversity now represented in one collection.  As a result of this effort, fifty descriptors were identified.  Each descriptor has numerical categories representing the range of a given trait.  An interactive table of these descriptors and a panel of images representing each category is available on CottonGen.  When accessions are grown in College Station, TX or at the Cotton Winter Nursery in Liberia, Costa Rica (previously Tecoman, Mexico), the Curator will use these descriptors to characterize the accessions.  Data are uploaded to GRIN-Global and CottonGen for public viewing.

Digital Images

Digital images are permanent and detailed visual records that are an essential companion to the descriptor ratings.  Images can communicate subtle variation unseen in numerical descriptor ratings.  Samples of typical stems, leaves, flowers, and bolls are gathered from each accession, tagged, and quickly assembled under high resolution digital cameras.  Plant samples are laid on a measured grid background for a consistent size reference.  Images are identified by photographed tags, and then named according to accession inventory number and the year/environment of planting.  Images are uploaded to GRIN-Global and CottonGen for public viewing.  Detailed protocols will be shared to provide standardized methods for capturing images.

Agronomic Evaluations

Working with collaborators with specific expertise, accessions are phenotypically evaluated for responses to traits of interest, including but not limited to seed quality, disease resistance, insect resistance, heat and drought tolerance, and water use efficiency.  Standard evaluation techniques for quantitative agronomic traits will include replicated testing over multiple environments utilizing appropriate randomization and statistical models.  Information will be published in appropriate journals and data will be submitted to GRIN-Global or CottonGen as appropriate.

Molecular Analyses

The limitations of morphological and agronomic descriptions and evaluations are addressed with advanced molecular research tools.  Association and genetic diversity analyses will be used to investigate relationships among accessions at the molecular level.  Molecular data is currently available from 105 simple sequence repeat (SSR) markers applied to approximately 20% of the accessions in the NCGC.  Single nucleotide polymorphism (SNP) markers have been identified using different approaches and also applied to provide a denser coverage of the cotton genome and/or more robust discriminating ability among accessions and to create matrixes to determine association with phenotypic traits.

High volume instrumentation (HVI) fiber quality data (including fiber strength, length, elongation, and micronaire) from the Cotton Winter Nursery is available for the majority of accessions in the NCGC.  In addition, seed protein and oil content have been measured on approximately 20% of the NCGC accessions.  This data can be analyzed and interpreted to develop a panel of accessions for association analysis.  Analysis and subsequent interpretations will be published in appropriate journals, and data will be uploaded to GRIN-Global and/or CottonGen for public viewing.

DEVELOPED RESOURCES

• NCGC Standardized Descriptors and Rating Scales
• Cotton Trait Ontology
• Image Data
• Genotypic Data - 
• Phenotypic Data - Search Trait Descriptors

PUBLICATIONS

Hinze, L. L., P. J. Horn, N. Kothari, J. K. Dever, J. Frelichowski, K. D. Chapman, and R. G. Percy. 2015. Nondestructive Measurements of Cottonseed Nutritional Trait Diversity in the U.S. National Cotton Germplasm Collection. Crop Sci. 55:770-782. https://doi:10.2135/cropsci2014.04.0318

Hinze, L.L., Fang, D.D., Gore, M.A. et al. Molecular characterization of the Gossypium Diversity Reference Set of the US National Cotton Germplasm Collection. Theor Appl Genet 128, 313–327 (2015). https://doi.org/10.1007/s00122-014-2431-7

Lori L. Hinze, Elodie Gazave, Michael A. Gore, David D. Fang, Brian E. Scheffler, John Z. Yu, Don C. Jones, James Frelichowski, Richard G. Percy, Genetic Diversity of the Two Commercial Tetraploid Cotton Species in the Gossypium Diversity Reference Set, Journal of Heredity, Volume 107, Issue 3, May 2016, Pages 274–286, https://doi.org/10.1093/jhered/esw004

Hinze, L.L., Hulse-Kemp, A.M., Wilson, I.W. et al. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. BMC Plant Biol 17, 37 (2017). https://doi.org/10.1186/s12870-017-0981-y

Yu, J.Z., Fang, D.D., Kohel, R.J. et al. Development of a core set of SSR markers for the characterization of Gossypium germplasm. Euphytica 187, 203–213 (2012). https://doi.org/10.1007/s10681-012-0643-y

USDA-ARS NATIONAL COTTON GERMPLASM COLLECTIONS

• NCGC Asiatic Cotton Collection (USA)
• NCGC Cotton Obsolete Variety Collection (USA)
• NCGC Cotton Race Collection (USA)
• NCGC Cotton Wild Species Collection (USA)
• NCGC Gossypium barbadense Collection (USA)