Project Summaries

12-178  Project Manager: D. C. Jones

DIGITIZING THE US NATIONAL GERMPLASM COLLECTION

James E. Frelichowski, USDA-ARS

A set of standardized morphological descriptors was developed by the curator. This is a long term commitment to development of the collection which will facilitate quality control, phenotypic comparisons among accessions, and data gathering across years, environments, and users. The descriptors were summarized for each commonly observed trait in drop-down menus in a spreadsheet to remove time and error associated with writing, and for instant uploading onto electronic field tablets. The file contained 36 categories (columns) of descriptors (choices within each cell/column). An example of morphological descriptors for the trait leaf color are: yellow, yellow-green, light green, dark green (typical of G. barbadense), green with red veins, sun red, red, bronze, virescent, and mottled.

A new Canon camera and accessories were purchased to complement two older models already in use and enable rapid capture of standardized, high quality, consistent images of representative tissues of each accession. A ruler grid, plain background, tripods with fixed lens distances, and a tent were constructed to consistently display sizes and color of leaf, flower, and bolls. High resolution digital images enable 'zoom in' on additional characters such as gossypol glands, surface hairs, and nectar glands for later scoring and estimate of metric characters such as size, distribution and density. Users of the collection and the Cotton Crop Germplasm Committee consider morphological characters as important for research into cotton physiology, breeding for yield improvement, and to introduce genetic variation into elite germplasm sources.

Two major field plantings of accessions of the Collection were established. The first was 1814 accessions at the Cotton Winter Nursery (CWN) in Tecoman, Colima, MX and the second was 900 accessions of obsolete cultivars in College Station, TX.

Dr. Frelichowski and his technician Janna Love traveled to the Cotton Winter Nursery from February 12, 2012 to March 4th. A representative leaf, open flower and boll were harvested from each accession and photographed. Each accession was scored for morphological descriptors using the excel file on a field tablet. The pairing of descriptors and images will allow users to understand the scoring methods and directly contribute to the digitization of the collection or submit feedback in these formats. The procedures were duplicated in the College Station summer planting. This year's planting only represents close to 1/5th of the collection.

A meeting was held at our location in College Station, November 13th for our current collaborators which include Cotton Incorporated, four ARS locations, and Texas Agrilife in Lubbock, TX (Dr. Jane Dever's research lab). The excel file format for the descriptors was accepted and we decided upon a standard format for naming images for effective uploading and referencing into the CottonGen database. 

We consider 'fully digitized' 3980 accessions meaning there are digital images and descriptor scores for this many accessions of the collection. This is the second year of this approach and thus we are including progress made in 2011 which consisted of 1074 accessions of Asiatic diploid cotton species at the CWN and 192 accessions of the four main cotton producing species in the College Station summer field planting. Because the collection is close to 10,000 accessions we are close to the halfway point of completing the collection. We are working closely with collaborators at CottonGen to finish the formatting of the images and then upload the completed work. Additional plantings are scheduled in 2013 of well over 1000 accessions to place us past the halfway mark of digitizing the Collection. Continued meetings in 2013 with our collaborators will discuss ways to close the gap more quickly.

 

Project Year: 2012
 

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