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United States Department of Agriculture

Agricultural Research Service

Research Project: COTTON GENETIC RESOURCE MANAGEMENT

Location: Crop Germplasm Research

2013 Annual Report


1a.Objectives (from AD-416):
Objective 1: Conserve and distribute a wide diversity of cotton genetic resources and associated information to researchers and breeders worldwide. Sub-objective 1.A: Strategically expand U.S. holdings of cotton genetic resources, especially wild relatives of cotton, through germplasm exchanges and plant explorations. Sub-objective 1.B: Maintain more than 10,000 cotton accessions in the active collection. Regenerate cotton accessions at the Cotton Winter Nursery (CWN) each year, with priorities determined by user input and by seed inventory and viability. Increase the proportion of the active collection backed-up at the National Center for Genetic Resources Preservation (NCGRP). Sub-objective 1.C: Distribute on request cotton accessions and information that meet the specific needs of researchers and breeders. Sub-objective 1.D: Collect and submit data to GRIN and CottonDB. Objective 2: Strategically evaluate (phenotype) cotton genetic resources for priority biotic and abiotic stress resistance, quality factors, and other priority agronomic traits. Sub-objective 2.A: Evaluate cotton accessions in the Cotton Winter Nursery for fiber properties (strength, length, micronaire, elongation). Sub-objective 2.B: Coordinate the cooperative evaluation of cotton genetic resources for other priority agronomic traits, such as resistance to various abiotic and biotic stresses. Sub-objective 2.C: Incorporate the evaluation data collected above into GRIN, CottonDB, and other genetic resource databases. Objective 3: Characterize the genetic variability in cotton genetic resources via genotyping with leading edge genetic marker technology. Sub-objective 3.A: Genotype priority cotton accessions with SSR genetic markers, and incorporate genotypic data into GRIN, CottonDB, and/or other databases. Sub-objective 3.B: With the genotypic information obtained above, measure genetic variation within and among cotton accessions. Sub-objective 3.C: Coordinate the cooperative DNA marker characterization of the cotton germplasm collection with a core subset of portable molecular markers developed by the sister project (6202-21000-030-00D).


1b.Approach (from AD-416):
To conserve and distribute a wide diversity of cotton genetic resources (Objective 1), 400-500 new accessions will be added to the collection – primarily through germplasm exchanges with national collections held in China, France, India, Russia, and Uzbekistan. Plant explorations will also be conducted as funds for this purpose are provided by the Plant Exchange Office section of the National Germplasm Resources Laboratory. Approximately 1,000 accessions (10% of the collection) will be regenerated each year, with priority for regeneration based upon age of seed and germination rate. We will distribute upwards of 4,000 accessions per year for a total worldwide distribution of approximately 20,000 accessions over the period of this project plan. To meet the goal of evaluating cotton genetic resources for priority biotic and abiotic stress resistance, quality factors, and other priority agronomic traits (Objective 2), basic descriptor data will be collected during the grow-outs for regeneration in the Cotton Winter Nursery or in our greenhouses and specific collaborations will be established to evaluate germplasm for responses to biotic and abiotic stresses. To facilitate incorporation of evaluation data into GRIN, CottonDB, and other genetic resource databases, methods of electronic data collection and downloading into appropriate databases will be developed and cooperative efforts with managers at the Database Management Unit will be established to create new and appropriate fields within the GRIN database. More detailed or complex data will be stored in the local database until GRIN establishes the proper formats for public display. Efforts to characterize the genetic variability of the collection via genotyping with genetic marker technology (Objective.
3)are being pursued in cooperation with the sister project (6202-21000-030-00D), and are focused on developing a comprehensive set of 208 core DNA markers for evaluation. To evaluate the suitability of the markers, a standard panel of the U.S. Cotton Germplasm Collection is being used. When appropriate markers have been identified, the DNA marker profile of a preselected set of 384 accessions representing a subset of the U.S. Cotton Germplasm Collection will be scored. Genetic diversity and phylogenetic relationships will be evaluated using population genetic software such as NT-SYS and Arlequin. The 384 samples will be clustered using the computer package PAUP and/or the neighboring-joining method. Once a core set of DNA markers is established and validated on the selected subset of the U.S. Cotton Germplasm Collection, the markers will be made available to cooperators, and coordination will be provided to accomplish the work in an efficient manner to prevent duplication of effort. Standard use of the core DNA markers will enable all characterizations and evaluations of Gossypium germplasm to be pooled into a common, publicly available database for analysis and interpretation across different gene pools or germplasm sources.


3.Progress Report:
In FY 2013, seed of more than 1,000 lines of cotton were increased in the Cotton Winter Nursery in Mexico to maintain the National Cotton Germplasm Collection. The Collection filled requests for 1561 lines in response to requests from 110 individuals and institutions. During the life of this project, seed of 7379 accessions, or close to 75% of the Collection, were renewed and increased. During this period, equipment was successfully upgraded to enable electronic data capture in nearly all phases of operations. Barcoding was implemented for tracking, processing, and storage of seed; electronic data tablets were introduced to gather descriptors on field and greenhouse plantings; and a library of standardized digital images of accessions was established. More than 13,000 images were uploaded to the CottonGen database for access by the cotton research community worldwide. A project initiated in FY 2010 to determine the genetic diversity of the National Cotton Germplasm Collection continued in FY 2013, with data collection being completed and significant data analyses accomplished. During the life of this project, data was collected on 2,300 lines from the Collection using 105 molecular tools known as SSR molecular markers. As a continuation and expansion of this diversity study, an investigation of the diversity within the A and D diploid genomes of cotton was initiated. DNA was extracted from 866 A-genome and 48 D genome accessions. A preliminary set of 188 SSR markers were selected for the A genome, and marker selection is in progress for the D genome and will be completed in work under the successor project. In work to characterize the composition of cotton seed, measurement of oil and protein percentages on 2,300 accessions was completed. This project expired in FY 2013, but was replaced by 6202-21000-037-00D which is expanding upon the work of the precursor project.


4.Accomplishments
1. Creation of random mating populations increases availability of genetic resources for cotton improvement. The availability of useful genetic diversity in the U.S. National Cotton Germplasm Collection is often restricted by associations with deleterious traits or poor agronomic backgrounds. ARS scientists at College Station, Texas, drew from germplasm resources within the Collection to create four distinctive germplasm populations with broad ranges of diversity. Using random mating among multiple parents possessing like traits, populations were created for short stature and early maturity (Dwarf GP), high fiber quality (Fiber GP), the glandless plant trait (Glandless GP), and wild race stock variation (Race GP). This mixing of genetic material has created a wide range of genetic diversity that is easily accessible by cotton breeders and others in the cotton research community and represents a useful resource for development of improved cotton types for productive use by U.S. farmers.

2. Renewal of seed and characterization of lines preserves cotton resources for the future. Seed of almost 10,000 cotton accessions must be renewed on a 10-year cycle to maintain the genetic diversity present in the U.S. National Cotton Germplasm Collection and to continue to provide cotton researchers worldwide with critical germplasm for research and crop improvement efforts. ARS scientists at College Station, Texas, using plantings in the Cotton Winter Nursery in Mexico, fields at College Station, and greenhouses increased more than 1,000 important accessions in FY 2013. An additional 1,024 accessions were grown in the field at College Station for characterization and digital imaging, and several hundred accessions comprising representatives of another 40 species of Gossypium were grown year round in greenhouses. The Cotton Winter Nursery remains as the most critical support operation for the worldwide cotton research and development communities.


Review Publications
Sreenath, R., Campbel, L.M., Pandeya, D., Puckhaber, L.S., Stipanovic, R.D., Wedegaertner, T.C., Hinze, L.L., Rathore, K.S. 2013. RNAi-mediated ultra-low gossypol cottonseed trait: Performance of transgenic lines under field conditions. Journal of Biotechnology. 11:296-304.

Fang, D.D., Hinze, L.L., Percy, R.G., Li, P., Deng, D.D., Thyssen, G.N. 2013. A microsatellite-based genome-wide analysis of genetic diversity and linkage disequilibrium in Upland cotton (Gossypium hirsutum L.) cultivars from major cotton-growing countries. Euphytica. 191:391-401.

Ulloa, M., Abdurakhmonov, I.Y., Perez-M, C., Percy, R.G., Stewart, J. 2013. Genetic diversity and population structure of cottons (Gossypium spp.) of the New World assessed by SSR markers. American Journal of Botany. 91:251-259.

Last Modified: 4/16/2014
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