Source: AGRICULTURAL RESEARCH SERVICE submitted to
GENOMICS AND BIOINFORMATICS RESEARCH IN CATFISH, COTTON, AND SOYBEANS
Sponsoring Institution
Agricultural Research Service/USDA
Project Status
TERMINATED
Funding Source
Reporting Frequency
Annual
Accession No.
0406486
Grant No.
(N/A)
Project No.
6402-21310-001-00D
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Oct 1, 2002
Project End Date
Sep 30, 2007
Grant Year
(N/A)
Project Director
SCHEFFLER B E
Recipient Organization
AGRICULTURAL RESEARCH SERVICE
(N/A)
STONEVILLE,MS 38776
Performing Department
(N/A)
Non Technical Summary
(N/A)
Animal Health Component
50%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011710108020%
2011820108020%
2013910108026%
3043710108021%
3043910108013%
Goals / Objectives
Broad objectives of this research project are to develop bioinformatics and genomics tools/databases to support genomics research primarily on catfish, cotton, and soybeans. The MSA Genomics Laboratory also makes available facilities, instrumentation, and trained personnel for supporting other genomics research, particulary in the MSA, as part of the overall ARS Genomics Program. The utilization of information derived from genomics research requires the design and implementation of effective bioinformatics and genomics tools (e.g. microarrays, biophotonics, DNA sequencing, genotyping) and infrastructure for the collection, storage, analysis, visualization, and public dissemination of information derived from studies of species of agricultural importance. In addition to research activities, this project also includes coordinating interactions with other key collaborating sites involved in agricultural bioinformatics (e.g. Beltsville, Maryland; Clay Center, Nebraska; Ft. Pierce, Florida; Cornell, New York; Mississippi State University, Mississippi; Iowa State University, Iowa).
Project Methods
All activities conducted under this project will support basic and applied genomics and bioinformatics problems limiting production primarily of catfish, cotton and soybeans. Supported research projects will be conducted by scientists in multiple research units throughout the Mid South Area. Approaches will support technical and operational responsibility for genomics and bioinformatics aspects of Area research; provide input into the initial planning and design of experiments to facilitate genomic and statistical analyses and development of data by the project scientists; and identify, evaluate and install a variety of highly specialized genomics and bioinformatics equipment and computer programs. As part of this project, novel technologies that utilize non-invasive technologies (e.g. biophotonics) for visualization (imaging at the molecular level using light, heat, and/or fluorescing signatures) of gene expression, invasiveness of bacteria or hormone-receptor interactions in living livestock will be developed.

Progress 10/01/02 to 09/30/07

Outputs
Progress Report Objectives (from AD-416) Broad objectives of this research project are to develop bioinformatics and genomics tools/databases to support genomics research primarily on catfish, cotton, and soybeans. The MSA Genomics Laboratory also makes available facilities, instrumentation, and trained personnel for supporting other genomics research, particulary in the MSA, as part of the overall ARS Genomics Program. The utilization of information derived from genomics research requires the design and implementation of effective bioinformatics and genomics tools (e.g. microarrays, biophotonics, DNA sequencing, genotyping) and infrastructure for the collection, storage, analysis, visualization, and public dissemination of information derived from studies of species of agricultural importance. In addition to research activities, this project also includes coordinating interactions with other key collaborating sites involved in agricultural bioinformatics (e.g. Beltsville, Maryland; Clay Center, Nebraska; Ft. Pierce, Florida; Cornell, New York; Mississippi State University, Mississippi; Iowa State University, Iowa). Approach (from AD-416) All activities conducted under this project will support basic and applied genomics and bioinformatics problems limiting production primarily of catfish, cotton and soybeans. Supported research projects will be conducted by scientists in multiple research units throughout the Mid South Area. Approaches will support technical and operational responsibility for genomics and bioinformatics aspects of Area research; provide input into the initial planning and design of experiments to facilitate genomic and statistical analyses and development of data by the project scientists; and identify, evaluate and install a variety of highly specialized genomics and bioinformatics equipment and computer programs. As part of this project, novel technologies that utilize non- invasive technologies (e.g. biophotonics) for visualization (imaging at the molecular level using light, heat, and/or fluorescing signatures) of gene expression, invasiveness of bacteria or hormone-receptor interactions in living livestock will be developed. Accomplishments PLANT RESPONSE TO RUST PATHOGEN: Soybean rust is a major threat to U.S. soybean production. Since research on the pathogen is limited due to quarantine restrictions, the Soybean Genomics and Improvement Unit (Beltsville/BARC) initiated a project on common bean infected with rust. The project combined genomic and proteomic analysis, with the Mid South Area Genomics Laboratory (MGL)performing sequence analysis on libraries containing both bean and rust clones. Since the source of the DNA was a mixture of the two species, it was the responsibility of the MGL to bioinformatically separate the DNA sequences by species. Impact: The high quality sequences allowed for reliable and in depth proteomic analysis. It also identified unique pathogen genes related to key developmental stages. This accomplishment addresses National Program 301 (NP 301) �Plant Genetic Resources, Genomics, and Genetics Improvement�, Action Plan Problem Statement 3A �Genetic Theory and Methods of Crop Improvement�. Technology Transfer Number of Non-Peer Reviewed Presentations and Proceedings: 2 Number of Newspaper Articles,Presentations for NonScience Audiences: 2

Impacts
(N/A)

Publications

  • Rinehart, T.A., Scheffler, B.E., Reed, S.M. 2005. Estimating genetic diversity within the hydrangea genus using molecular markers. Southern Nursery Association Research Conference, pp656-659.
  • Perera, O.P., Blanco C.A., SchefflerB.E., and Abel C.A. 2007. Characteristics of 13 ploymorphic microsatellite makers in the corn earworm, Helicovepa zea (Lepidoptera: Noctuidae). Mol. Ecol. Notes. doi: 10.1111/j.147-8286.2007.01806.x
  • Cooper, B., Neelan, A., Campbell, K., Lee, J., Liu, G., Garrett, W.M., Scheffler, B.E., Tucker, M.L. 2007. Protein Accumulation Changes Associated with Germination of the Uromyces appendiculatus Uredospore. Molecular Plant-Microbe Interactions. 20(7):857-866.
  • Perera O. P., Snodgras G.L., Scheffler B.E., Gore J., and Abel C. A. 2007. characterization of eight ploymorphic microsatelliet markers in the tarnished plant bug, Lygus lineolaris (Palisot de Beauvois). Mol. Ecol. Notes. doi: 10.1111/j.1471-8286.2007.01747.x
  • Wang, X., Trigiano, R.N., Windham, M.T., Devries, R., Scheffler, B.E., Rinehart, T.A., Spiers, J.M. 2006. A simple and effective procedure for discovering microsatellites from small insert libraries. Molecular Ecology Notes. Vol 7. pp 558-561
  • Scheffler, J.A., Scheffler, B.E., Ray, J.D., Taliercio, E.W. 2006. On the hunt for new molecular markers: evaluating soybean (glycine max) ssr's for cotton (gossypium hirsutum). Indian Society for Cotton Improvement. Vol 31: 79-87


Progress 10/01/05 to 09/30/06

Outputs
Progress Report 1. What major problem or issue is being resolved and how are you resolving it (summarize project aims and objectives)? How serious is the problem? Why does it matter? Advancements in the genetic improvement of catfish, cotton, soybeans, or other important commodities can be enhanced through a multi-disciplinary approach that includes the use of genomic and bioinformatic tools. Such tools can also be used in analyzing pests. Genomic tools such as marker assisted breeding, gene expression profiling, and DNA sequencing provide a wealth of data that must be managed and analyzed using bioinformatic tools. In order to enhance the capabilities of ARS researchers the MSA Genomics Laboratory was developed to provide an interactive facility with cost effective means for marker assisted breeding and DNA sequencing. The Laboratory also provides a centralized location for gene expression profiling. 2. List by year the currently approved milestones (indicators of research progress) The scientists in the Mid South Area (MSA) are in need of high throughput DNA sequencing analysis for expressed sequence tag (EST) libraries and bacterial artifical chromosome (BACs), and marker assisted breeding. Outsourcing of this analysis was not cost effective or unavailable at the time. Establishment of this technology at the needed throughput rate at each location was cost prohibitive and is technically challenging. Therefore, the MSA Genomics Laboratory was created to handle the scientific needs of MSA scientists. Development of the Genomics Laboratory provides ARS scientist access to the latest technology in these areas and increases the amount of sample throughput while at the same time of decreasing their operating costs. As a service orientated project, this project does not go through the OSQR process and therefore does not have specific milestones. 4a List the single most significant research accomplishment during FY 2006. BAC fingerprinting of the catfish genome: National Program 106. Problem: There is limited knowledge of the catfish genome and this information would be valuable for efforts to improve catfish production. Accomplishment: High throughput BAC fingerprinting technique was used to develop 7X genome coverage of catfish. This information is being used to develop a physical map of the catfish genome. Impact: A physical map is a major milestone in the characterization of a genome will greatly assistance in marker assisted breeding and candidate gene isolation through markers. 4b List other significant research accomplishment(s), if any. 1. Survey of the cotton genome: National Program 301. Problem: The cotton genome is known to be relatively large and it contains a significant amount of repetitive DNA. Using present technology it will be costly to determine the whole genome sequence. However there are alternative strategies that would allow for the determination of the DNA sequence of the most of the genes in cotton. Accomplishments: Working with Orion Genomics, a pilot experiment was conducted based on ~20,000 DNA sequences, to determine how well and costly GeneThresher technology from Orion would work to uncover the genes in the two types of cotton grown in the USA and their progenitor species. Impact: Based on this information it is now possible to strategy to have part or all of the cotton genome sequenced. 2. QTL-mapping in cotton using linkage disequilibrium: National Program 301. Problem: QTL-mapping is extremely time-consuming, high-risk and expensive work; prohibitively expensive if dozens, let alone hundreds or thousands, of germplasm accessions are to be examined. Accomplishments: Use of linkage disequilibrium (LD) based association mapping circumvents the need for large F2 or RI mapping populations by making use of information contained within the genetic recombinations that have occurred in cotton genome during the course of recent evolution. By this method, certain alleles at a marker locus can be associated with alleles at a linked locus affecting a trait of interest. LD was conducted on a number of cultivars and exotic cotton lines. Impact: The final data should identify key areas in the cotton genome that have been selected by independent breeders over time. 3. Analysis of rust infection in legumes: National Program 301. Problem: Soybean Asian Rust is a major threat to US soybean production and there is limited molecular information on the pathogen or how the plant responds to the pathogen. Studies on Soybean Asian Rust are difficult because of the need for permits and quarantine facilities. Accomplishment: 20,000 ESTs from common bean infected with the rust pathogen Uromyces appendiculatus were sequenced from both directions. With other ARS scientists and the University of Missouri. Impact: This data will help in determining legume responses to rust infections, which in turn will act a baseline for studying virulence factors when similar studies can be completely completed with soybean plants infected with Soybean Asian Rust. 4d Progress report. No additional information for this time period. 5. Describe the major accomplishments to date and their predicted or actual impact. Genetic knowledge of Catfish at the DNA level is limited. Catfish Genetics Research Unit scientists submitted 18816 DNA samples for sequencing and 16416 multiplexed samples for genotyping. To date, this has led to submission of 7833 EST sequences to GenBank. Increased knowledge of genes in the form of BACs and ESTs sequences will assist in the development of microarrays and permit identification of genes controlling economically important traits. National Program 106. A BAC fingerprinting technique was developed for use on the ABI 3730XL sequencer. National Program 106. There is limited knowledge of cotton at the DNA level. While several studies have looked at related species little has been published for Gossypium hirsutum. cDNA libraries was developed and ~70,000 final ESTs were derived from them. National Program 301. Three soybean BACs were completely sequenced to study ancient gene duplication events and subsequent evolution of the region. National Program 301. 6. What science and/or technologies have been transferred and to whom? When is the science and/or technology likely to become available to the end- user (industry, farmer, other scientists)? What are the constraints, if known, to the adoption and durability of the technology products? None for this time period. 7. List your most important publications in the popular press and presentations to organizations and articles written about your work. (NOTE: List your peer reviewed publications below). "A Wealth of Genetics Technology Under One Roof" was published in the July 2006 issue of Agricultural Research magazine. "Pegging a Troublesome Change in Hydrilla" was published in the November 2005 issue of Agricultural Research magazine.

Impacts
(N/A)

Publications

  • Blenda, A.V., Scheffler, J.A., Scheffler, B.E., Palmer, M., Lacape, J., Jesudurai, C., Jung, S., Muthukumar, S., Yellambalase, P., Ficklin, S., Staton, M., Eschelman, R., Ulloa, M., Saha, S., Burr, B., Lui, S., Zhang, T., Fang, D., Yu, J., Pepper, A.E., Kumpatla, S.P., Jacobs, J., Tomkins, J. P., Cantrell, R.G., Main, D. 2006. Cmo: a cotton microsatellite database resource for gossypium genomics. Biomed Central (BMC) Genomics.7:132
  • Patel, M.R., Scheffler, B.E., Wang, L., Willett, K.L. 2006. Effects of benzo(a)pyrene exposure on killfish (fundulus heteroclitus) aromatase activities and mrna. Aquatic Toxicology. 77(3):267-278.
  • Tabanca, N., Douglas, A.W., Bedir, E., Dayan, F.E., Kirimer, N., Baser, H. K., Aytac, Z., Khan, I.A., Scheffler, B.E. 2005. Patterns of essential oil relationships in pimpinella (umbelliferae) based on phlyogenetic relationships using nuclear and chloroplast sequences. Plant Genetic Resources. 3(2):149-169.
  • Techen, N., Khan, I.A., Pan, Z., Scheffler, B.E. 2006. The use of polymerase chain reaction (pcr) for the identification of ephedra dna in dietary supplements. Planta Medica. 72: 241-247.
  • Taliercio, E.W., Allen, R.D., Essenberg, M., Nguyen, H., Patil, M., Payton, P.R., Phillips, A., Pierce, M., Scheffler, B.E., Turley, R.B., Wang, J., Zhang, D., Scheffler, J.A. 2006. Analysis of ests from multiple gossypium hirsutum tissues. Genome. Vol. 49: p. 306-319.
  • Willett, K.L., Ganesan, S., Patel, M., Metzger, C., Quiniou, S.M., Waldbieser, G.C., Scheffler, B.E. 2005. In vivo and in vitro cyp1b mrna expression in channel catfish. Marine Environmental Research.
  • Arias, R.S., Dayan, F.E., Michel, A., Howell, J., Scheffler, B.E. 2006. Characterization of a higher plant herbicide-resistant phytoene desaturase and its use as a selectable marker. Plant Biotechnology Journal. 4: 263- 273.


Progress 10/01/04 to 09/30/05

Outputs
1. What major problem or issue is being resolved and how are you resolving it (summarize project aims and objectives)? How serious is the problem? What does it matter? Advancements in the genetic improvement of catfish, cotton, soybeans, or other important commodities can be enhanced through a multi-disciplinary approach that includes the use of genomic and bioinformatic tools. Such tools can also be used in analyzing pests. Genomic tools such as marker assisted breeding, gene expression profiling, and DNA sequencing provide a wealth of data that must be managed and analyzed using bioinformatic tools. In order to enhance the capabilities of ARS researchers the Mid South Area (MSA) Genomics Laboratory was developed to provide an interactive facility with cost-effective means for marker assisted breeding and DNA sequencing. The Laboratory also provides a centralized location for gene expression profiling. 2. List the milestones (indicators of progress) from your Project Plan. The scientists in the MSA are in need of high throughput DNA sequencing analysis for Expressed Sequence Tag(EST) libraries and Bacterial Artificial Chromosomes (BACs), and marker assisted breeding. Outsourcing of this analysis was not cost effective or unavailable at the time. Establishment of this technology at the needed throughput rate at each location was cost prohibitive and is technically challenging. Therefore, the MSA Genomics Laboratory was created to handle the scientific needs of MSA scientists. Development of the Genomics Laboratory provides ARS scientist access to the latest technology in these areas and increases the amount of sample throughput while at the same time of decreasing their operating costs. 3a List the milestones that were scheduled to be addressed in FY 2005. For each milestone, indicate the status: fully met, substantially met, or not met. If not met, why. 1. General throughput for sequencing and genotyping were increased, compared to past fiscal year (FY) and the facility has increased its capacity to handle the MSA needs. Alterations to existing techniques resulted in a decease of consumables and thus a reduction in expenditures compared to past FY. Milestone Fully Met 3b List the milestones that you expect to address over the next 3 years (FY 2006, 2007, and 2008). What do you expect to accomplish, year by year, over the next 3 years under each milestone? It is anticipated that there will be a continued increase in the number of samples submitted for both sequencing and fragment analysis in the coming years and new methodologies will need to be developed to handle the increase at a cost effective level. Gene expression profiling experiments will be increased for several species researched in the MSA using microarrays developed within house, by collaborators, or commercially. 4a What was the single most significant accomplishment this past year? Application of high-throughput DNA marker technology in sugarcane breeding: Sugarcane has a unique problem in the development of hybrid and breeding material in knowing if the resulting seed is the result of a cross between the selected individuals or is due to pollen contamination or self fertilization of the female. A high-throughput method was developed to genotype F1 seedlings before they were planted in the field. 21504 reactions were processed in a short period of time. The process should increase the productivity of the breeding program by eliminating bad crosses. This work is conducted with the Sugarcane Research Unit, Houma, LA. 4b List other significant accomplishments, if any. 1. Development of Molecular Markers for Hydrangea: Public DNA databases contain little information on hydrangea. In order to develop DNA markers to assist in breeding programs and act as identifiers in varieties, a marker enhanced genomics, DNA library was created by Small Fruit Research Unit in Stoneville, MS. The clones from the library were sequenced and potential markers identified. 192 markers were developed and tested on several hydrangea species. At least 60 markers are proving useful in the program at Poplarville. 2. Tall fescue/endophyte interaction: Problem: The important forage grass, tall fescue (Festuca arundinacea Schreb.), has demonstrably greater adaptive advantages to environmental stresses when symbiotic with its fungal endophyte, Neotyphodium coenophialum (E+) compared to aposymbiotic tall fescue (E-). Objectives: Analyze the mechanism of cross- talk between plant and endophyte which should allow more refined control of endophyte benefits and detriments through management practices or molecular techniques. Accomplishments: As a first step cDNA's from a normalized library constructed from inflorescences of Festuca pratesis (meadow fescue) infected with the endophyte, Neotyphodium uncinatum, are being sequenced by Forage-Animal Production Research Unit. To date over 12,000 sequences have been done at Mid South Area Genomics facility in Stoneville, MS, run by the Catfish Genetic Research Unit. Sequence analysis revealed that this normalized library is composed of a high number of single copy cDNAs (82% unigenes), and 75% of the genes have homology to plant genes, 15% with homology to fungal genes and 10% of which the origin is not possible to determine or unknown, or previously uncharacterized. Impact: Sequence analysis is the first step in the analysis of the fescue endophyte interaction. The work will ultimately allow for the understanding and manipulation of fescue persistence and quality. 4d Progress report. This report documents research conducted under Specific Cooperative Agreement 6402-21310-001-02N, Genethresher methylation filtering pilot projects in Gossypium hirsutum, barbadense, raimondii, and arboretum, with Orion Genomics. There is limited knowledge of cotton at the genomic DNA level. While several studies have looked at some of the DNA through EST analysis this does not provide whole genome coverage nor does it provide information on the regulatory regions of the genes. Since Gossypium hirsutum (the predominant form of cultivated cotton) is a tetraploid and its relative genome size is large it is not anticipated that the genome will be sequenced in the near future. Most of the genome is probably due to the presence of non-gene regions. In order to obtain the gene rich regions without sequencing the whole genome a filtering method could be used to remove the non-gene regions. The goal of the project is to determine the gene enrichment, or "filter power," and genome reduction achieved through the application of GeneThresher methylation filtering technology by Orion Genomics in the following: Gossypium hirsutum cv TM-1, Gossypium barbadense 3-79, Gossypium raimondii, and Gossypium arboreum Var. Stephens Coll. as a Pilot Project. The GeneThresher methylation filtering technology has been applied to Gossypium hirsutum cv TM-1 and Gossypium arboreum Var. Stephens Coll. by Orion Genomics. Sequencing of the clones from these libraries will begin at the MSA Genomics Laboratory when libraries for all four species are available. This pilot project will discover how much of the genomes of the four cotton species is composed of non-gene regions. This information can in turn be used to determine how many clones will need to be sequenced in a cotton genome project to determine the DNA sequence of most of the genes in cotton. 5. Describe the major accomplishments over the life of the project, including their predicted or actual impact. Genetic knowledge of Catfish at the DNA level is limited. Catfish Genetics Research Unit scientists submitted 18816 DNA samples for sequencing and 16416 multiplexed samples for genotyping. To date, this has led to submission of 7833 EST sequences to GenBank. Increased knowledge of genes in the form of BACs and ESTs sequences will assist in the development of microarrays and permit identification of genes controlling economically important traits. A BAC fingerprinting technique was developed MSA Genomics Laboratory for use on the ABI 3730XL sequencer. There is limited knowledge of cotton at the DNA level. While several studies have looked at related species little has been published for Gossypium hirsutum. A normalized library was developed by Crop Genetic and Production Research Unit from young ovules (1-2 days after pollination), 30,000 final ESTs were derived from this library. Two soybean BACs were completely sequenced in conjunction with Corn Insects and Crop Analysis of Soybean Research Unit of Ames, Iowa, to study ancient gene duplication events and subsequent evolution of the region. 6. What science and/or technologies have been transferred and to whom? When is the science and/or technology likely to become available to the end- user (industry, farmer, other scientists)? What are the constraints, if known, to the adoption and durability of the technology products? In conjunction with Crop Genetics and Production Research Unit, all publicly available SSR markers for cotton were run on the Cotton Incorporated sponsored CMD panel. The data is being made publicly available through the CMD database (http://www.mainlab.clemson.edu/cmd/). 7. List your most important publications in the popular press and presentations to organizations and articles written about your work. (NOTE: List your peer reviewed publications below). Presentation: The Roadmap to the Cotton Genome, by Brian Scheffler at the International Cotton Genome Initiative Workshop. Hyderabad, India. October 2004.

Impacts
(N/A)

Publications


    Progress 10/01/03 to 09/30/04

    Outputs
    1. What major problem or issue is being resolved and how are you resolving it (summarize project aims and objectives)? How serious is the problem? What does it matter? Advancements in the genetic improvement of catfish, cotton, soybeans, or other important commodities can be enhanced through a multi-disciplinary approach that includes the use of genomic and bioinformatic tools. Such tools can also be used in analyzing pests. Genomic tools such as marker assisted breeding, gene expression profiling, and DNA sequencing provide a wealth of data that must be managed and analyzed using bioinformatic tools. In order to enhance the capabilities of ARS researchers the MSA Genomics Laboratory was developed to provide an interactive facility with cost effective means for marker assisted breeding and DNA sequencing. The Laboratory also provides a centralized location for gene expression profiling. 2. List the milestones (indicators of progress) from your Project Plan. The scientists in the MSA are in need of high throughput DNA sequencing analysis for EST libraries and BACs, and marker assisted breeding. Outsourcing of this analysis was not cost effective or unavailable at the time. Establishment of this technology at the needed throughput rate at each location was cost prohibitive and is technically challenging. Therefore, the MSA Genomics Laboratory was created to handle the scientific needs of MSA scientists. Development of the Genomics Laboratory provides ARS scientists access to the latest technology in these areas and increases the amount of sample throughput while at the same time of decreasing their operating costs. 3. Milestones: A. General throughput for sequencing and genotyping were increased compared to past FY. Alterations to existing techniques resulted in a decease of consumables and thus a reduction in expenditures. B. It is anticipated that there will be a continued increase in the number of samples submitted for both sequencing and fragment analysis in the coming years and new methodologies will need to be developed to handle the increase at a cost effective level. Gene expression profiling experiments will be increased for catfish and cotton using microarrays developed within house, by collaborators, or commercially. Genotyping capacity will be increased and bioinformatics support will be expanded. 4. What were the most significant accomplishments this past year? A. There is limited knowledge of cotton at the DNA level. While several studies have looked at related species, little has been published for Gossypium hirsutum. Eight cDNA libraries were developed by Earl Taliercio (6402-21000-029-00) from young fibers and ovules, stems, and roots; 26,000 final ESTs were derived from them. Dr. Taliercio has shared this information with Paxton Patton so they could be annotated for the development of cotton microarrays sponsored by Cotton Incorporated and the data will be released to the public database GenBank in the near future. The data was screened for new SSRs which are presently being tested. B. Two soybean BACs were completely sequenced in conjunction with Randy Shoemaker CRIS 3625-21000-039-00, to study ancient gene duplication events and subsequent evolution of the region. The Major Histocompatibility Complex is a key element of the immune system. It is composed of the Major Histocompatibility Class I genes and the Major Histocompatibility class II genes. One BAC clone (from Sylvie Quiniou and Geoff Waldbieser: CRIS 6402-31000-006-00D) containing all MHC II genes and sequenced it using transposons or by direct sequencing on the clone with specific primers. A BAC fingerprinting technique was developed by Sylvie Quiniou (CRIS 6402-31000-006-00D) and MSA Genomics Laboratory for use on the ABI 3730XL sequencer. C. None D. This report documents research conducted under specific cooperative agreement 6402-21310-001-01S "Biophotonics - the Application of novel imaging methodologies to livestock production research" with Mississippi State University. Additional details can be found in the report for the parent project 6402-31000-001-00D "Genomics and bioinformatics research in catfish, cotton, and soybeans". There is a critical need for technological innovations that will permit production-based questions to be asked and answered in the context of the whole organism. Traditionally, new molecular and biotechnological advances have not addressed matters that can be translated back to the live animal in a production-based setting. Thus the interface between our understanding of the molecular and cellular realm through artificial manipulations in the laboratory have not always corresponded to the "real-world" responses of the whole animal - for example, in the feedlot, dairy or swine unit. While Mississippi and other states in the southern region have unique challenges related to their livestock production environments (e.g., heat stress in dairy cattle), disease, pre-harvest food safety issues, and other aspects of production animal agriculture are problems faced nationally and globally. To make broader strides forward in production animal agriculture, technological advances at the whole animal level are critical to our future understanding of how to solve production-based problems. As part of the "Biophotonics Initiative" at Mississippi State University within the Mississippi Agricultural and Forestry Experiment Station (MAFES), novel technologies that utilize the photon (light), thermal signatures (heat) and fluorescence are being adapted to cellular- and molecular- based strategies to permit live animal imaging of a variety of physiological processes. These non-invasive technologies (e.g., Biophotonics, which uses light as an indicator beacon of molecular events) will enable the expression of genes, invasiveness of bacteria or hormone- receptor interactions to be visualized in the living animal, in real-time, under traditional livestock production environments. This initiative has established the Facility for Organismal and Cellular Imaging (FOCI) within the Department of Animal and Dairy Science which brings faculty with expertise in functional imaging together with scientists working in the animal and veterinary sciences to develop novel imaging systems and paradigms aimed at specific production-based problems. The first year of the Biophotonics Initiative has resulted in an increase in the research infrastructure within FOCI which has enabled new research aims in the areas of pathogen detection and pathogen tracking (within normal production situations and as applied to pre- and post-harvest food safety research) in swine and sheep, the applications of fluorescence monitoring systems for evaluating bovine embryo development and viability, and great strides have been achieved in the applications of digital infrared thermography for assessing wound healing in horses, evaluating heat stress and thermal tolerance in cattle, udder function and mastitis detection in dairy cattle, and lameness in herbivores (e.g., equine and bovine). Linkages with existing research groups in engineering and physics at Mississippi State University have also been established, which should facilitate the development of novel imaging technologies as applied to large animal models of production agriculture. When one considers the national impact of production losses to the livestock industries (for example, infections of the mammary gland in dairy cattle; mastitis results in a $2 billion loss in production to dairy producers), the spread of Salmonella bacteria in swine (livestock diseases cost our economy $17.5 billion nation-wide) or the impact of early embryonic failure to beef cattle operations (a loss of $1.4 billion to cattle producers nation-wide), the need for scientific advancements to address these and other livestock production issues becomes apparent. Results from this initiative will not only develop new models to advance scientific progress in reproductive biology, food safety, animal health and environmental physiology, but will also address critical questions which heretofore have not been addressable previously in living animals. The greatest impact as a result of the first year of research as part of this initiative is likely the expanded potential applications of digital infrared thermography for clinical diagnostics in production animal agriculture. Early detection of conditions of lameness or mastitis detection could save cattle producers nation-wide millions of dollars once the critical windows for measurement and assessment have been defined, aims that are part of on-going research through the "Biophotonics Initiative". 5. Describe the major accomplishments over the life of the project, including their predicted or actual impact. Genetic knowledge of Catfish at the DNA level is limited. Catfish Genetics Research Unit scientists submitted 18816 DNA samples for sequencing and 16416 multiplexed samples for genotyping. To date, this has led to submission of 7833 EST sequences to GenBank. Increased knowledge of genes in the form of BACs and ESTs sequences will assist in the development of microarrays and permit identification of genes controlling economically important traits. 6. What science and/or technologies have been transferred and to whom? When is the science and/or technology likely to become available to the end- user (industry, farmer, other scientists)? What are the constraints, if known, to the adoption and durability of the technology products? A BAC fingerprinting technique was developed by Sylvie Quiniou (CRIS 6402- 31000-006-00D) and MSA Genomics Laboratory for use on the ABI 3730XL sequencer. This information was shared with the firm ABI, University of Arizona, Clemson and U.C Davis who are utilizing the protocol. 7. List your most important publications in the popular press and presentations to organizations and articles written about your work. Scheffler, B.E. 2004. The Basis for Fluridone Resistance in Hydrilla verticillata, by Brian Scheffler at the The Aquatic Plant Management Society, Inc. 44th Annual Meeting, Tampa, Florida. July, 2004. Scheffler, J.A., Dowd, M.K., Meredith, W.R. Jr., Scheffler, B.E. (2004) New Possibilities for Some Old Genes: Improved Host Plant Resistance in Cotton, Proceedings of the World Cotton Research Conference III, Cape Town, South Africa 9-13 March 2003 p. 175-182. Scheffler, B.E., Arias, Renee S., Netherland, Michael D., Michel, Albrecht, Duke, Stephen O. and Dayan, Franck E. 2004. The Basis for Fluridone Resistance in Hydrilla verticillata. The Aquatic Plant Management Society, Inc. 44th Annual Meeting, Tampa, Florida July, 2004. Bowers, S., Gandy, S., Anderson, B., Ryan, P. and Willard, S. 2004. Assessment of pregnancy in the mare using digital infrared thermography. American Society of Animal Science/American Society of Dairy Science 2004 National Meeting (Abstract accepted and to be presented July 2004). Dickerson, T.W., Youngblood, R.C., Ryan P.L. and Willard, S.T. 2004. Use of digital infrared thermography to assess rate of wound healing in a murine model. The FASEB Journal 18(5), March 2004 (Experimental Biology 2004 Abstract #787.5). Youngblood, R.C., Dickerson, T.W., Willard, S.T. and Ryan, P.L. 2004. Methoxychlor exposure does not alter vascular endothelial growth factor receptor 2-mediated gene expression in a novel transgenic mouse wound model. The FASEB Journal 18(5), March 2004 (Experimental Biology 2004 Abstract #791.2) Schmidt, S., Hillman, P., Lee, C., Graves, K., Hostetler, D. and Willard, S. 2004. Profiling mastitis in dairy cows: A case study of natural infection and thermal responsiveness. American Society of Animal Science Southern Section, Tulsa, OK, p. 21 (Abstr. #85). Schmidt, S., Bowers, S., Dickerson, T., Graves, K. and Willard, S. 2004. Assessments of udder temperature gradients pre- and post-milking relative to milk production in Holstein cows as determined by digital infrared thermography. American Society of Animal Science/American Society of Dairy Science 2004 National Meeting. Yang, X., Owen, T.G., Scheffler, B.E., and Weston, L.A. 2004. Manipulation of root hair development and sorgoleone production in sorghum seedlings. Journal of Chemical Ecology, 30:199-213. Michel, A., Johnson, R.D., Duke, S.O., and Scheffler, B.E. 2004. Dose- response relationships of herbicides with different more of actions using Lemna paucicostata. Environmental Toxicology and Chemistry, 23:1074-1079. Techen, N., Crockett, S.L., Khan, I.A., and Scheffler, B.E. 2004. Authentication of medicial plants using molecular biology techniques to compliment conventional methods. Current Medicinal Chemistry.11:1391- 1401. Gregory Vidal, Scheffler, Brian, Michel, Albrecht and D'Surney, Steven J. 2004. Genomic and Phylogenic comparisons of the alpha globin and beta globin intergenic sequences between zebra fish (Danio rerio) and six closely related Cyprinindae species. DNA and Cell Biology, 23:325-334.

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