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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Research Project #426035

Research Project: Associating Genotype, Phenotype, and Digital Images for Cotton Genetic Resources

Location: Crop Germplasm Research

Project Number: 3091-21000-041-01-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Apr 1, 2014
End Date: Mar 31, 2019

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.

For assembly of a digital image library, protocols will be discussed and shared to provide standardized methods for capturing images. These permanent and detailed visual records will help validate and communicate descriptor characterization and will more appropriately capture subtle variation for future identification and preservation of the extensive variation of the Collection. Samples of typical leaves, flowers, and bolls will be 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 will be loaded to GRIN-Global and CottonGen for public viewing. Accessions will be phenotypically evaluated for responses to traits of current interest to cotton researchers, including but not limited to seed quality, insect resistance, heat and drought tolerance, and water use efficiency. The germplasm collection will develop and make available uniform descriptors and techniques for morphological, production, and disease resistance investigations, and will provide historical information on the source of accessions. Standard evaluation techniques for quantitative agronomic traits will include replicated testing over environments utilizing appropriate randomization and statistical models. Information will be published in appropriate journals and outlets and data will be submitted to GRIN-Global or CottonGen as appropriate. 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 collection. Additional markers may be identified and applied to provide a denser coverage of the cotton genome and/or more robust discriminating ability among accessions. For 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 US National Cotton Germplasm Collection. In addition, seed protein and oil content have recently been measured on approximately 20% of the Gossypium accessions. This data will be analyzed and interpreted to develop a panel of accessions for association analysis. Analysis and subsequent interpretations will be published in appropriate journals and outlets.