Location: Genomics and Bioinformatics Research2010 Annual Report
1a. Objectives (from AD-416)
Utilization and development of bioinformatic and genomic tools/information to support structural analysis of plant and animal genomes. This includes the generation of DNA sequences and subsequent analysis. Development and implementation of DNA markers for development of superior cultivars (e.g., superior yield, improved quality, or resistance to the biotic or abiotic factors) or germplasm/population/species characterization. Both marker data and DNA sequences will be used for genome structure analysis.
1b. Approach (from AD-416)
The Genomics and Bioinformatics Research Unit conducts research in the area of genomics and bioinformatics for an array of species and topics. It also acts as a fully integrated component of the Mid South Area by providing genomics research support for an array of technologies and research projects. The support includes, but is not limited to high throughput DNA sequencing, gene expression analysis, bioinformatics, DNA marker development, BAC fingerprinting and high throughput genotyping with DNA marker. The centralization of these operations assures that all research projects in the MSA that could benefit from these genomic tools have access to the technology, that there is no unnecessary duplication of equipment within the Area, and there is maximum utilization and conservation of funding.
3. Progress Report
As a service research project, progress is measured by the service provided. For the reported time period these locations had significant amount of DNA sequencing (D), genotyping (G), bioinformatics (B) and/or DNA marker development (M) processed through the Laboratory: Animal Waste Management Research Unit, Service: D Aquatic Animal Health Research Unit, Service: D, B Biological Control of Pests Research Unit, Service: D Catfish Genetics Research Unit, Service: D,B,G, Commodity Utilization Research Unit, Service: D Coastal Plains Soil, Water, and Plant Research Center, Service: D Corn Host Plant Resistance Research, Service: D,B Cotton Fiber Bioscience Research Unit. Service: G Crop Genetics Research Unit, Service: D, G, B, M Crop Germplasm Research, Service: G Dale Bumpers National Rice Research Center Service: D, M Endemic Poultry Viral Disease Research Unit, Service: D,B Food Processing and Sensory Quality Research Unit, Service: D Genetics and Precision Agriculture Research, Service: G Natural Products Utilization Research Unit, Service: D, M Plant Stress and Germplasm Development Unit, Service B Southern Horticultural Laboratory, Service: G,M,B Southern Insect Management Research Unit, Service: D,G,B Soybean Genomics and Improvement, Service: D, B Subtropical Horticulture Research Station, Service: B,G,M Sugarcane Field Station, Service: D,G,M Sugarcane Research Unit, Service: G Sunflower Research Unit, Service: D Tropical Agriculture Research Station, Service: B,D,G,M DNA marker development and validation, in the form of microsatellites, have become an important output component of the unit and in the past year, markers have developed for over 18 species ranging from fungi, plants to insects. This in-house research project has a component of rice research which has been supported through various cooperative agreements (6402-21310-003-03, Mining Novel Blast Resistance Genes for Use in U.S. Breeding Programs; 6402-21310-003-04, The Mississippi Rice Variety Acceleration Breeding Project). This research has revolved around mapping novel blast resistances and the integration of DNA markers into the Mississippi rice breeding program. DNA markers, using technology advancement reported in last’s years annual report, were developed for 10 tropical tree species that are curated at the Tropical Agriculture Research Station, Mayaguez, Puerto Rico. Species for which markers were developed: Nephelium lappaceum (Rambutan) (1,362 designed markers), Manilkara zapota (sapodilla)(2,292 designed markers), Pouteria sapota (sapote)(1,124 designed markers), Litchi chinensis (lychee)(2,722 designed markers), Melicoccus bijugatus (Spanish lime) (630 designed markers), Annona reticulate and Annona squamosa (Custard apple, sugar apple) (996 designed markers), Dimorcarpus longan (longan) (3,670 designed markers), Averrhoa carambola (star fruit) (3,707), Garcinia mangostana and Garcinia cochinchinensis (mangosteen) (600 designed markers), Bambusa vulgaris var. vittata and Guadua angustifolia (bamboo) (420 designed markers).
1. Development of DNA Markers for Germplasm Conservation. Germplasm conservation is an important but expensive and difficult endeavor. This is especially true when trees are the species of interest. The USDA, ARS has germplasm collections for tropical trees but lacks the tools to characterize the genetic diversity, which is important when deciding which accessions to add to or eliminate from a collection. The unit has developed tools and procedures to cost effectively develop and validate DNA markers. DNA markers using this technology were developed for 10 species that are curated at the Tropical Agriculture Research Station, Mayaguez, Puerto Rico. The molecular markers developed in this project are now being used to characterize the germplasm of the corresponding species in three different collections (Hawaii, Florida and Puerto Rico). This should help confirm the identity of replicated accessions and determined the relative genetic diversity in the collections.
Wubben, M., Callahan, F.E., Scheffler, B.E. 2010. Transcript Analysis of Parasitic Females of the Sedentary Semi-Endoparasitic Nematode Rotylenchulus reniformis. Molecular and Biochemical Parasitology. 172:31-40.