Progress 10/01/06 to 09/30/09
Outputs
OUTPUTS: We have generated cDNA libraries from reniform nematode infested and uninfested cotton plants of several genotypes, and sequenced randomly selected cDNA clones using an ABI454 sequencer. We obtained a total of over 2,000,000 reads and developed the bioinformatic tools to use these to analyze nematode infested gene expression. We previously concluded that a set of genes are up-regulated and down-regulated during nematode infestation. We are building an online cotton functional genomics database, and plan on adding our nematode data to this web page. We have also begun introgression of reniform resistance using the LONREN source, and have selected advanced lines from crosses between LONREN and adapted germplasm. Analysis of our heat stress gene expression data sets continued during 2009. We have made preliminary determination of the set of differentially expressed mRNA sequences in DPL90 and in germplasm accession TX337, and during the first quarter we began to identify these differentially expressed sequences, determine primers for PCR amplification of these, and we are beginning RT-PCR analysis to verify the differential expression. A new graduate student has had difficulty preparing RNA from all of the 5 TX heat tolerant partental genotypes we previously identified to expand this analysis from TX337 to the other accessions. We seem to have now worked through the difficulties and are moving forward. We expect to have additional samples submitted for sequencing by the end of the year. Bioinformatic analysis of the heat stress data has expanded to include more recently obtained data from Illumna sequencing. The original data was obtained using an ABI 454 sequencing. The Illumna sequencer generates many more sequences (circa 5,000,000 primary reads per run compared to the circa 70,000 reads per run from the ABI454. It turns out that it is possible to harvest both small regulatory RNA expression data and mRNA expression data from the Illumina runs. Thus, we are presently involved in this added analysis, and expect completion in 2010 which should lead to at least 2 publications and the opportunity to seek national funding for this effort. This added data was deemed necessary since a large number of the new cDNA sequences obtained from the ABI 454 sequencer were single read sequences. We are hopeful that the Illumina data will supplement the ABI data making it unnecessary to do additional ABI sequencer runs. Additionally, work continues on the preparation of a web site to share these data with the cotton research community once we have completed our publication of this information, and the development of the tools for this website. We have encountered a setback in growning plants for screening of F2 populations from crosses of DPL90 with 5 heat tolerant accessions. The initial F2 plants that had been screened using chlorophyll fluorescence were involved in a "2,4-D" spill at the AU Plant Research Greenhouse that totally destroyed our plants. This seriously set back our work, but at this point we are establishing new populations to continue this work with the funding cited above. PARTICIPANTS: Not relevant to this project. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Some of the cotton accessions that were identified in previous studies by our group as having moderate resistance to reniform nematode proved to be susceptible upon further examination. Therefore, we have abandoned these genotypes in our molecular studies and have shifted our attention to other resistance sources, such as LONREN, a G. longicalyx introgression source of resistance. Future studies and breeding efforts will be focused on the LONREN source of resistance.
Impacts
Breeding for resistance to biotic and abiotic stresses in plants is extremely difficult using standard breeding techniques. Incorporation of traits from exotic germplasm is a long-term process. We are working to develop molecular techniques to speed up transfer of resistance, and to measure the impact of exotic germplasm on yield and fiber quality of cotton. In the meantime, we are also utilizing currently available genetic resources (LONREN source) with good reniform nematode resistance to develop good adapted lines with resistance using conventional techniques. These efforts, together with efforts to develop superior cotton cultivars with improved yield and fiber quality traits will help improve profitability of cotton in the Southeastern U.S.
Publications
- Cole, C. B., D. T. Bowman, F. M. Bourland, W. D. Caldwell, B. T. Campbell, D. E. Fraser, and D. B. Weaver. 2009. Impact of heterozygosity and heterogeneity on cotton lint yield stability. Crop Sci. 49: 1577-1585.
- Weaver, D. B., R. S. Badger, and E. van Santen. 2009. Genetic correlations among agronomic and fiber quality traits in six upland cotton populations. pp. 642-646 In S. Boyd, M. Huffman, D. Richter, and B. Robertson (ed.) Proc.Beltwide Cotton Conf. San Antonio, TX.
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Progress 01/01/08 to 12/31/08
Outputs
OUTPUTS: Two reniform nematode-resistant accessions (PI 165358 and PI 530110) were hybridized reciprocally to four adapted cultivars (Suregrow 747, Delta Pearl, Paymaster 1218, and FiberMax 966). Three population structures were advanced: BC1F1:3 lines, with backcrosses to both adapted and unadapted parents, and F2:4 lines. 1200 lines representing these types were advanced in the field in single-row plots in 2008. Evaluation of these materials was begun late in 2008, using greenhouse-grown plants in 10 replications per line. Single plants were inoculated with reniform juveniles, and after 60 days, reniform numbers and root mass were determined. This project will continue into 2009. Using these same lines, we have selected a subset of 120 lines, 5 lines each for each of the cultivar/backcross combinations. Thus we have lines with 0 (adapted parents), 25 (backcrossed one time to adapted parent), 50 (F2-derived lines), 75 (backcrossed one time to unadapted parent), and 100% (exotic accessions) exotic germplasm. Single replication short-row plots of these were sampled in 2008 for fiber properties and some agronomic traits (boll size and lint percentage), and replicated plots will be grown at two locations in 2009 from seed produced in 2008. Progress in development of populations using heat-tolerant accessions has lagged behind, due to the slow flowering nature of the heat-tolerant accessions. During 2008, we were able to grow F1 plants of crosses between Deltapine 90 and 4 heat-tolerant accessions, PI's 165350, PI501467, PI501468, and PI607759. Plants were long in flowering, and we have just completed harvest of all but one of the F2 populations. These will be used to begin transfer of the heat tolerance trait, and study inheritance and gene expression. For both the heat tolerance trait and reniform nematode resistance, we subjected the resistant/tolerant accessions and the parents to stress, and collected RNA samples on a time-line basis for up to 3 days following the stress. RNA was then subjected to Massive Parallel Signature Sequencing, to look for gene products being up- or down-regulated following stress. Data are currently being interpreted. PARTICIPANTS: Not relevant to this project. TARGET AUDIENCES: Target audience is the cotton breeding community. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Breeding for resistance to biotic and abiotic stresses in plants is extremely difficult using standard breeding techniques. Incorporation of traits from exotic germplasm is a long-term process. We are working to develop molecular techniques to speeds up transfer of resistance, and to measure the impact of exotic germplasm on yield and fiber quality of cotton.
Publications
- Cambell, B. T., D. T. Bowman, and D. B. Weaver. 2008. Heterotic effects in topcrosses of modern and obsolete cotton cultivars. Crop Sci. 48:593-600.
- Wallace, T. P., D. Bowman, B. T. Campbell, P. Chee, O. A. Gutierrez, R. J. Kohel, J. McCarty, G. Myers, R. Percy, F. Robinson, W. Smith, D. M. Stelly, J. M. Stewart, P. Thaxton, M. Ulloa and D. B. Weaver. 2008. Status of the USA cotton germplasm collection and crop vulnerability. Genet Resourc Crop Evol.:http://www.springerlink.com/content/h104458583277730).
- Campbell, B.T., D.T. Bowman, and D.B. Weaver. 2007. Effects of heterosis in Upland cotton. In Proceedings of the World Cotton Research Conference 4, Lubbock, TX.
- Campbell, B.T., D.T. Bowman, and D.B. Weaver. 2008. Trivial sources of heterosis in cotton In Proceedings of the International Cotton Genome Initiative (ICGI International Conference. Anyang, China.
- Robinson, A. F., P. Agudelo, C. A. Avila, A. A. Bell, F. E. Callahan, C. G. Cook, N. D. Dighe, O. A. Gutierrez, R. W. Hayes, J. N. Jenkins, J. T. Johnson, R. Kantety, G. W. Lawrence, K. S. Lawrence, L. Mangineni, J. C. McCarty, M. A. Menz, W. A. Meredith, Jr., R. L. Nichols, R. T. Robbins, E. Sacks, B. Scheffler, G. L. Sciumbato, C. W. Smith, J. L. Starr, D. M. Stelly, S. R. Stetina, J. McD. Stewart, P. M. Thaxton, T. P. Wallace, D. B. Weaver, M. J. Wubben, and L. D. Young. 2007. Development of reniform nematode resistance in upland cotton. In Proceedings of the World Cotton Research Conference 4, Lubbock, TX.
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Progress 01/01/07 to 12/31/07
Outputs
OUTPUTS: Two reniform nematode-resistant accessions (PI 165358 and PI 530110) were hybridized reciprocally to four adapted cultivars (Suregrow 747, Delta Pearl, Paymaster 1218, and FiberMax 966). F1 plants were self-pollinated to create the F2 generation and also backcrossed to both the adapted and unadapted parent, creating BC1F1 plants. Using greenhouse and winter nursery facilities, these were then self-pollinated to create the BC1F2 generation. Both the BC1F2 and the F2 were grown in the field this summer and self-pollinated, to create a series of BC1F2:3 and F2:3 lines for future evaluation. We have approximately 150 and 92 F2:3 lines/population and 63 and 16 BC1F2:3 lines/population for PI 165358 and PI 530110, respectively. Thus we have more than 1200 lines available and ready for selection, inheritance studies, mapping studies, and evaluation using both standard phenotyping and molecular phenotyping. These populations will also provide genetic materials for exciting studies
in completely unrelated areas, including germplasm enhancement. Such studies are sorely lacking in cotton. Progress in population development involving the heat-tolerant accessions is well behind that of the nematode-resistant accessions. There are two primary reasons for this. Population development was started much later, and efforts to hybridize the heat-tolerant accessions with adapted germplasm have been delayed due to flowering response of the heat-tolerant accessions. These accessions are tropical in origin and can take over a year to reach the flowering stage, even under short days. We have succeeded in making one hybridization, producing several F1 plants that are currently being grown in the field and greenhouse. We will have limited F2 seed of one population by 2008. In terms of development of molecular markers for both heat stress and nematode resistance, we have spent most of the effort on the project to date developing techniques for evaluation of proteomic markers and
for examining mRNA expression data using microarrays. To date we have successfully obtained high quality cotton RNA, from control genotypes, and have explored various methods of protein preparation for proteomic analysis. While we are presently preparing the RNA samples for further analysis (which we expect to complete within weeks), we have had less success in obtaining consistent protein results for proteomic analysis. Our newly acquired students expect to explore a set of new techniques that will hopefully give us more consistent results, and we hope to have assessed protein markers for heat stress by the first of the year. At the present time it appears that obtaining protein markers for nematode resistance may be more problematic. We will spend a great deal of time during the next year improving these techniques.
PARTICIPANTS: David B. Weaver (Principle Investigator) Robert D. Locy Kathy Lawrence Narendra K. Singh
TARGET AUDIENCES: Target audience is the cotton breeding community.
Impacts
Breeding for resistance to biotic and abiotic stresses in any crop plant is extremely difficult using standard plant breeding techniques. We will develop a method that will make the selection of plants with these traits much easier, so that cultivars can be developed that have resistance to reniform nematode and extreme heat.
Publications
- Weaver, D. B., K. Lawrence, and E. van Santen. 2007. Reniform nematode resistance in upland cotton germplasm. Crop Sci. 47:19-24.
- Weaver, D. B., R. S. Badger, and E. van Santen. 2007. Selection and inbreeding method effects on upland cotton yield and fiber properties. pp. 2136-2139 In S. Boyd, M. Huffman, D. Richter, and B. Robertson (ed.) Proc.Beltwide Cotton Conf. New Orleans, LA.
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