Progress 10/01/05 to 09/30/06
Outputs
Progress Report 4d Progress report. This report serves to document research conducted under a Reimbursable Cooperative Agreement between ARS and Alabama A&M University under a NRI grant. Additional details of research can be found in the report of the inhouse research project 6406-21000-010-00D, Germplasm Enhancement and Genetic Improvement of Cotton. Progress concluded with the 2005 Annual Report, but was not terminated because of financial management reasons. See 2005 Annual Report for last reported progress.
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Progress 06/15/03 to 06/14/06
Outputs
Progress Report Objectives (from AD-416) To discover new EST-SSR, SNP markers specific to functional genes and AFLP markers and use them to develop an integrated, high resolution physical QTL linkage genome map in cotton through multi-institutional effort with ARS, Alabama A & M and Alcorn Universities. To provide experience for minority scientists to improve the work force diversity in the biotech area. To use aneuploid cytogenetic stocks to assign linkage group markers to chromosomes. Approach (from AD-416) Identify EST-SSR and SNP makers by data mining the cotton EST database. Design specific pairs of primers specific to the EST sequence of interest. Amplify genomic DNA of several lines, sequence and compare to identify SNP markers. Alcorn University will use HPLC to screen for SNP polymorphisms. ARS will use an ABI Prism SnaPshot multiplex kit with an ABI 3100 system and Real Time PCR for screening SNP markers as per manufacturer's protocols. Alabama A & M University will use DNA sequencing to screen for SNP polymorphism. Significant Activities that Support Special Target Populations This report serves to document research conducted under a Reimbursable Cooperative Agreement between ARS and Alabama A&M University. Additional details of research can be found in the report for the in-house project 6406-21000-010-00D, "Germplasm Enhancement and Evaluation of Cotton." Progress concluded with the 2006 Annual Report, but was not terminated because of financial management reasons. See 2006 Annual Report for last reported progress.
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Progress 10/01/04 to 09/30/05
Outputs
4d Progress report. This report serves as the final report to document research conducted under a Reimbursable Agreement between the ARS Genetics and Precision Agriculture Research Unit and Alabama A&M University under an NRI grant. Additional details of research can be found in the report of the parent research project 6406-21000-010-00D, Germplasm Enhancement and Genetic Improvement of Cotton. The objectives were to discover EST-SSR and SNP markers associated with fiber genes and identify chromosome association. 133 SSR-containing consensus EST sequences were identified from 9,948 EST sequences from G. hirsutum. We discovered 1900 consensus, non-redundant sequences containing an SSR motif of at least 18-bp length from 38,598 sequences of G. arboreum in an EST database. We constructed 206 primer pairs from these non-redundant sequences and detected polymorphism among a few selected intra and interspecific cotton genotypes. This was the first report on PCR-based
EST-SSR markers in cotton. More than 50% of these EST-SSRs are associated with fiber ESTs. We have submitted a report on 84 EST-SSR primer pairs covering more than 200 SSR markers from G. hirsutum EST database to the Cotton Microsattelite Database at Cotton Incorporated. We are currently working on 200 additional EST-SSR primer pairs developed from the G. arboretum database. We have developed a SNP detection method in cotton. Work will continue to assign these markers to chromosomes. These results have expanded the knowledge of functional genomics in cotton.
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Progress 10/01/03 to 09/30/04
Outputs
4. What were the most significant accomplishments this past year? This report serves to document research conducted under a Reimbursable Cooperative Agreement between ARS and Alabama A&M University under an NRI grant. Additional details of research can be found in the report of the parent project 6406-21000-010-00D, Germplasm Enhancement and Genetic Improvement of Cotton. The objectives are to discover EST-SSR and SNP markers associated with fiber genes and identify their chromosomal locations. Research is under way to seek for fiber specific genes on chromosome substitution lines CS-B22Lo and CS-B22sh. We are growing plant materials for sampling specific aged bolls. 133 SSR-containing consensus EST sequences were identified by analyzing 9,948 EST sequences from G. hirsutum. Primers were designed for 84 and tested for polymorphism among four cotton lines belonging to G. hirsutum and G. barbadense. We discovered about 1900 consensus and non-redundant sequences
that contain an SSR motif of at least 18-bp length from 38,598 sequences of G. arboreum in an EST database. We constructed 206 primer pairs from these non-redundant sequences and detected polymorphism among a few selected intra and interspecific cotton genotypes. This is the first report on PCR-based EST-SSR markers in cotton. More than 50% of these EST-SSR's are associated with fiber EST's. We are making progress in development of a SNP detection method in cotton.
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