NRSP_OLD_10: Database Resources for Crop Genomics, Genetics and Breeding Research

(National Research Support Project Summary)

Status: Inactive/Terminating

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SAES-422 Reports

03/26/2018

Bassil, N., Davis, T., Zhang, H., Ficklin, S., Mittmann, M., Webster, T., Mahoney, L., Wood, D., Alperin, E., Rosyara, U., Koehorst-van Putten, H., Monford, A., Amaya, I., Denoyes, B., Sargent, D., Bianco, L., van Dijk, T., Pirani. A., Iezzoni, A., Main, D., Peace, C., Yang, Y., Whitaker, V., Verma, S., Bellon, L., Brew, F., Herrera, R., van de Weg, E. (2015). Development and Preliminary Evaluation of a 90K Axiom SNP Array for the Allo-octoploid Cultivated Strawberry Fragaria x ananassa. BMC Genomics 16:155.

Bett, K., Ramsay, L., Chan, C., Sharpe, A.G., Cook, D.R., Penmetsa, R.V., Chang, P., Coyne, C.J., McGee, R., Main, D., Vandenberg, A. (2015) Len Gen: The International Lentil Genome Sequencing Project. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego

DeVetter, L., Main, D., Jung, S., Cheng, C-H., Lee, T., Blenda, A., Yu, S., Zheng, P., Yu, J., Ficklin, S.P., Evans, K.M., Peace, C., Oraguzie, N., Gasic, K., Olmstead, M. (2015) Resources available for Rubus research through the Genome Database for Rosaceae. Abstracts of the XIth International Rubus and Ribes Symposium; Jun 21-24, 2015; Asheville, NC.

Ficklin, S.P., Lee, T., Humann, J.L., Cheng, C.H., Wegrzyn, J., Neale, D., Main, D. (2015) GenSAS: A web-Based Platform for Automated and Manual Curation of Genomic Sequence. Abstracts of the International Plant and Animal Conference XXIII; January 10-14, 2015; San Diego

Ficklin, S.P., Sanderson, L-A., Cheng, C-H., Jung, S., Bett, K., Main, D. (2015) Tripal Overview and Future Developments. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego

Grau, E., Wytko, C., Soto, B., Jung, S., Wang, K., Watts, N., Staton, M., Main, D., Wegrzyn, J., Feltus, F., Ficklin, S.P. (2015) Abstracts of the Galaxy Community Conference; July 6-8, 2015; Norwich, UK.

Humann, J., Jung, S., Zheng, P., Cheng, C-H., Lee, T., Frank, M., McGaughey, D., Scott, K., Yu, J., Ficklin, S.P., Sanad, M.N.M.E., Hough, H., Coyne, C., McGee, R., Main, D. (2015) Cool Season Food Legume Genome Database: An up to date resource enabling genetics, genomics and breeding research in chickpea, faba bean, lentil and pea. Abstracts of the North American Pulse Improvement 2015 Biannual Meeting; November 4-6, 2015; Niagara Falls, Canada

Humann, J.L., Ficklin, S.P., Lee, T., Cheng, C-H., Jung, S., Wegrzyn, J.L., Neale, D., Main, D. (2015) GenSAS: An Easy-to-Use, Web-Based Solution for Specialty Crop Genome Annotation. Abstracts of the American Society for Horticultural Science Conference; August 4-7, 2015; New Orleans

Iezzoni, A., Peace, C., Bassil, N., Coe, M., Finn, C., Gasic, K., Luby, J.J., Main, D., McFerson, J., Norelli, J.L., Olmstead, M., Whitaker, V.M., Yue, C. (2015) RosBREED: Combining Disease Resistance with Horticultural Quality in New Rosaceae Cultivars. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego

Iezzoni, I., Peace, C.P., Bassil, N., Coe, M., Finn, C.E., Gasic, K., Hokanson, S.C., Luby, J.J., Main, D., McFerson, J.R., Norelli, J., Olmstead, M., Whitaker, V.M., Yue, C. (2015) rosBREED2: More Traits, Additional Crops, Expanded Germplasm, New Science. Abstracts of the American Society for Horticultural Science Conference; August 4-7, 2015; New Orleans

Jung, S., Ficklin, S.P., Lee, T., Cheng, C-H., Blenda, A., Yu, J., Zheng, P., Ru, S., Peace, C., Evans, K.M., Oraguzie, N., DeVetter, L., Abbott, A.G., Gasic, K., Olmstead, M., Main, D. (2015) How to Use GDR, the Genome Database for Rosaceae. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego

Jung, S., Piaskowski, J., Ficklin, S.P., Cheng, C-H., Zheng, P., Olmstead, M., Abbott, A.G., Cedex, d'O., Chen, C., Mueller, L., Gmitter, F.G. jr, Main, D. (2015) Citrus Genome DB Updates. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego

Jung, S., Yu, J., Lee, T., Cheng, C-H., Ficklin, S.P., Main, D. (2015) CottonGen: Converting Legacy Sites to Tripal. Abstracts of International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego

Main, D., Ficklin, S.P., Lee, T., Humann, J.L., Cheng, C-H., Wegrzyn, J., Neale, D. (2015) GenSAS. Abstracts of the International Plant and Animal Conference XXIII; January 10-14, 2015; San Diego

Main, D., Jung, S. (2015) Introducing NRSP10L Database Infrastructure for Specialty Crops. Abstracts of the American Society for Horticultural Science Conference; August 4-7, 2015; New Orleans

Main, D., Jung, S., Ficklin, S.P., Cheng, C-H., Lee, T., Zheng, P., Humann, J.L., Yu, J., Blenda, A., Scott, K., Byrd, M., Hough, H., DeVetter, L., Evans, K., Peace, C., Gasic, K., Olmstead, M., Cai, L., Coe, M. (2015) Genome Database for Rosaceae – Utilizing Tripal, an Open-Source Database Platform for Genomics, Genetics and Breeding Research. Abstracts of the Crop Science Society of America/American Society of Agronomy/ Soil Society of America Annual Meeting; November 15-18, 2015; Minneapolis.

Main, D., Jung, S., Lee, T., Ficklin, S.P., Cheng, C.H., Blenda, A., Yu, J., Zheng, P., Humann, J., Peace, C., Evans, K., Oraguzie, N., Olmstead, M., Gasic, K. (2015) GDR: A Resource for Rosaceae Breeding. Abstracts of the National Association of Plant Breeders Annual Meeting, July 27-30, 2015; Pullman, WA

Main, D., Jung, S., Lee, T., Ficklin, S.P., Cheng, C-H., Blenda, A., Yu, J., Zheng, P., Humann, J., Peace, C., Evans, K., Oraguzie, N., Olmstead, M., Gasic, K. (2015) GDR: Updates and Future Development. WA Apple Genomics, Genetics and Genomics Meeting; Jan 27, 2015; Wenatchee.

Main, D., Jung, S., Lee, T., Ficklin, S.P., Cheng, C-H., Blenda, A., Yu, J., Zheng, P., Humann, J., Peace, C., Evans, K., Oraguzie, N., Olmstead, M., Gasic, K. (2015) GDR: A Community Database for Rosaceae Genomics, Genetics and Breeding Research. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego

Paul, R., Kuruganti, S., Stevens, K., Gonzalez-Ibeas, D., Martinez-Garcia, P.J., Liechty, J., Vasquez-Gross, H., Grau, E., Loopstra, C., Zimin, A., Holtz-Morris, A., Koriabine, M., Yorke, J.A., Crepeau, M., Puiu, D., Salzberg, S.L., deJong, P.J., Mockaitis, K., Main, D., Langley, C.H., Neale, D., Wegrzyn, J. (2015) Genome Annotation and Repeat Sequence Characterization in Sugar Pine (Pinus lambertiana). Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego

Ru, S., Main, D., Evans, K., Peace, C. (2015). Current applications, challenges, and perspectives of marker-assisted seedling selection in Rosaceae tree fruit breeding. Tree Genetics and Genomes 11:8.

Sanderson, L-A., Ficklin, S.P., Main, D., Bett, K. (2015) Extending Tripal for Specialized Display and Management of Diversity and Breeding data. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego

Sidhu, G., Mohan, A., Zheng, P., Dhaliwal, A.K., Main, D., Gill, K.S. (2015). Sequencing-Based High Throughput Mutation Detection in Bread Wheat. BMC Genomics 16(1):962.

Verde, I., Shu, S., Jenkins, J., Zuccolo, A., Dettori, M.T., Dardick, C., Rossini, L., Grimwood, J., Pirona, R., Goodstein, D.M., Dondini, L., Vendramin, E., Martinez-Gomez, P., Silva, H., Micali, S., Falchi, R., Scalabrin, S., Bassi, D., Main, D., Orellana, A., Vizzotto, G., Tartarini, S., Meisel, L., Abbott, A.G., Morgante, M., Rokhsar, D.S., Schmutz, J. (2015) The Peach v2.0 Release: An Improved Genome Sequence for Bridging the Gap Between Genomics and Breeding in Prunus. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego

Wegrzyn, J., Stevens, K., Paul, R., Gonzalez-Ibeas, D., Martinez-Garcia, P.J., Liechty, J., Vasquez-Gross, H., Kuruganti, S., Grau, E., Loopstra, C., Zimin, A., Yorke, J.A., Crepeau, M., Puiu, D., Holt, C., Yandell, M., Salzberg, S.L., deJong, P.J., Main, D., Langley, C.H., Neale, D. (2015) Sugar Pine Annotation. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego

Xu, J., Yu, J., Kohel, R., Percy, R., Beavis, W., Main, D., Yu, J. (2015). Distribution and evolution of cotton fiber development genes in the fibreless G. raimondii genome. Genomics 106:61-69.

Yu, J., Jung, S., Cheng, C-H., Ficklin, S.P., Lee, T., Zheng, P., Jones, D.C., Percy, R.G., Main, D. (2015) CottonGen: The Community Database for Cotton Genomics, Genetics and Breeding Research. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego

Yu, L-X., Zhang, T., Zheng, P., Li, Y., Main, D., Greene, S.L. (2015). Identification of Loci Associated with Drought Resistance Traits in Heterozygous Autotetraploid Alfalfa (Medicago sativa L.) Using Genome-Wide Association Studies with Genotyping by Sequencing. PloS One 10(9):e0138931

Yu, M., Holdsworth, W., Cheng, P., Grusack, M.A., Mazourek, M., Coyne, C.J., Main, D., McGee, R.J. (2015) Genome-wide SNP identification, linkage map construction and QTL mapping for mineral nutrients in pea. Abstracts of the North American Pulse Improvement 2015 Biannual Meeting; November 4-6, 2015; Niagara Falls, Canada

05/16/2018

Jung, S., Lee, T., Yu, J., Ficklin, S.P., Main, D. (2016). Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. Database (Oxford) baw010.

Ma, Y., Myers, J.R., Mazourek, M., Coyne, C.J., Main, D., Humann, J.L., McGee, R. (2016). Development of SCAR markers linked to sin-2, the stringless pod locus in pea (Pisum sativum L.). Molecular Plant Breeding 36(7):1-10.

Shin, S.S., Zheng, P., Fazio, G., Mazzola, M., Main, D., Zhu, Y. (2016). Transcriptome changes specifically associated with apple (Malus domestica) root defense response during Pythium ultimum infection. Physiological and Molecular Plant Pathology 94:16-26.

Ru, S., Hardner, C., Carter, P., Evans, K., Main, D., Peace, C. (2016) Modeling of genetic gain from marker-assisted seedling selection in clonally propagated crops. Horticulture Research 3, 16015.

Sidhu, G., Mohan, A., Zheng, P., Dhaliwal, A.K., Main, D., Gill, K.S. (2015). Sequencing-Based High Throughput Mutation Detection in Bread Wheat. BMC Genomics 16(1):962.

Bett K, Ramsay L, Chan C, Sharpe AG, Cook DR, Penmetsa RV, Chang P, Coyne CJ, McGee R, Main D, Edwards D, Kaur S, Vandenberg A (2016) Lentil 1.0 and Beyond. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego, USA.

Ficklin SP, Sanderson L-A, Cheng C-H, Soto B, Wytko C, Jung S, Feltus A, Bett K, Main D (2016) Deliver Searchable Genomic, Genetic and Related Data Online Using Tripal. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.

Ficklin SP, Sanderson L-A, Cheng C-H, Wytko C, Soto B, Clytus M, Bett K, Main D (2016) The Future of Tripal: intuitive content creation, flexible data storage and web services. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.

Gasic K, Rife T, Poland JA, Jung S, Evans KM, Oraguzie N, DeVetter LW, Peace C, Olmstead MA, Main D (2016) Evaluation of Field Book: An Open-source Android App for Collecting Phenotypic Data in a Peach Breeding Program. Abstracts of the 8th International Rosaceae Genomics Conference; June 21-24, 2016; Angers, France.

Gasic K, Rife T, Poland JA, Jung S, Evans KM, Oraguzie N, DeVetter LW, Peace C, Olmstead MA, Main D (2016) Evaluation of Field Book: An Open-source Android App for Collecting Phenotypic Data in a Peach Breeding Program. Abstracts of the American Society for Horticultural Science Conference; August 7-11, 2016; Atlanta, USA.

Grau E, Demurijan SA, Vasquez-Gross H, Gessler D, Staton M, Jung S, Feltus A, Main D, Ficklin SP, Neale D, Wegrzyn J (2016) TreeGenes: Enabling Visualization and Analysis in Forest Tree Genomics. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.

Humann JL, Ficklin SP, Lee T, Cheng C-H, Jung S, Wegrzyn J, Neale D, Main D (2016) GenSAS v4.0: An Easy-to-Use, Web-Based Platform for Structural and Functional Genome Annotation and Curation. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.

Humann JL, Ficklin SP, Lee T, Cheng C-H, Jung S, Wegrzyn J, Neale D, Main D (2016) Gensas v5.0: An Easy-to-use, Web-based Platform for Individual or Collaborative Structural and Functional Genome Annotation and Curation. Abstracts of the American Society for Horticultural Science Conference; August 7-11, 2016; Atlanta, USA.

Humann JL, Jung S, Zheng , Cheng C-H, Lee T, Frank M, McGaughey D, Scott K, Yu J, Ficklin SP, Sanad MNME, Hough H, Coyne C, McGee R, Main D (2016) Cool Season Food Legume Genome Database: An Up-to-Date Resource Enabling Genetics, Genomics and Breeding Research in Pea, Lentil, Faba Bean and Chickpea. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.

Humann JL, Jung S, Zheng P , Cheng C-H, Lee T, Frank M, McGaughey D, Scott K, Yu J, Ficklin SP, Sanad MNME, Hough H, Coyne C, McGee R, Main D (2016) Cool Season Food Legume Genome Database: An up-to-Date Resource Enabling Genetics, Genomics and Breeding Research in Pea, Lentil, Faba Bean and Chickpea. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.

Humann, J, JungS, Zheng P, ChengC-H, Lee T, Frank M, McGaughey D, Scott K, Yu J, Ficklin SP, Sanad MNME,, Hough H, Coyne C, McGee R, Main D(2015) Cool Season Food Legume Genome Database: An up to date resource enabling genetics, genomics and breeding research in chickpea, faba bean, lentil and pea. Abstracts of the North American Pulse Improvement 2015 Biannual Meeting; November 4-6, 2015; Niagara Falls, Canada

Jung S, Cheng C-H, Lee T, Ficklin SP, Blenda A, Yu J, Scott, K, Byrd M, Ru S, Zheng P, Humann JL, DeVetter L, Peace C, Evans KM, Gasic K, Olmstead M, Coe M, Abbott AG, Main D (2016) GDR, the Genome Database for Rosaceae: New Data and Functionality. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.

Jung S, Lee T, Chen C-H, Gasic K, Campbell BT, Evans KM, Peace C, Main D (2016) GDR Breeding Information Management Systems. Abstracts of the 8thInternational Rosaceae Genomics Conference; June 21-24, 2016; Angers, France.

Jung S, Lee T, Cheng C-H, Yu J, Gasi K, Campbell BT, Evans KM, Peace C, Main D (2016) TripalBIMS: the Breeding Information Management System in Tripal. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.

Jung S, Lee T, Cheng C-H, Yu J, Gasic K, C Evans KM, Peace C, Main D (2016) Development of TripalBIMS: a Breeding Information Management System in Tripal. RosBREED Participants Meeting; March 7-9, 2016; East Lansing, USA.

Jung, S., Bassett, C., Bielenberg, D.C., Cheng, C-H., Dardick, C., Main, D., Meisel, L., Slovin, J., Troggio, M., Schaffer, R.J. (2015) A standard nomenclature for gene designation in the Rosaceae. Tree Genetics & Genomes 11(5): 108

Jung, S., Lee, T., Yu, J., Ficklin, S.P., Main, D. (2016). Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. Database (Oxford) baw010.

Long-Xi Yu, Zheng P, Ho J, Bhamidimarri S, Main D (2016) A Whole Genome Association Study on Verticillium Wilt Resistance in Heterozygous Autotetraploid Alfalfa (Medicago sativa L.). Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.

Ma Y, Holdsworth B, Cheng P, Mazourek M, Coyne C, Main D, McGee R (2016) Genome-wide SNP identification, linkage map construction and QTL mapping for mineral nutrients. Poster presentation at WSU Academic Showcase, March 25, 2016, Pullman, WA

Main D (2016) Progress in the Genome Database for Rosaceae: Empowering Specialty Crop Research through Big-Data Driven Discovery and Application in Breeding and NRSP 10 Database Resources for Crop Genomics, Genetics and Breeding Research. Presentation to the Specialty Crop Committee Annual Meeting; August 2, 2016, Portland, USA.

Main D, Jung S, Cheng C-H, Lee T, Ficklin SP, Blenda A, Yu J, Scott, K, Byrd M, Ru S, Zheng P, Humann JL, DeVetter L, Peace C, Evans KM, Gasic K, Olmstead M, Coe M, Abbott AG (2016) Introduction to RGC8 GDR Workshop. Abstracts of the 8th International Rosaceae Genomics Conference; June 21-24, 2016; Angers, France.

Main D, Jung S, Cheng C-H, Lee T, Zheng P , Ficklin SP, Humann JL, Yu J, Blenda A, Scott K, Byrd M, DeVetter L, Peace C, Evans KM, Gasic K, Olmstead M, Coe M, Abbott AG (2016) Genome Database for Rosaceae: Updates and New Directions. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.

Main D, Jung S, Cheng CH, Lee T, Ficklin SP, Gasic K, Yu J, Humann JL, Zheng P, Scott K, Evans KM, Peace C, DeVetter L, Oraguzie N, Olmstead M (2016) Genome Database for Rosaceae: A Resource for Genomics, Genetics and Breeding Research. Abstracts of the American Society for Horticultural Science Conference; August 7-11, 2016; Atlanta, USA.

Main D, Jung S, Cheng CH, Lee T, Ficklin SP, Lee T, Humann JL, Yu J, Zheng P, Peace C, Evans KM, Gasic K, Olmstead M, DeVetter LW, Kahn M, Mcferson JR, Abbott A, Bassil N (2016) Resources available for Fragaria research through the Genome Database for Rosaceae. Abstracts of the 8th International Strawberry Symposium; August 13-17, 2016; Quebec, Canada.

Main D, Jung S, Ficklin SP, Cheng C-H, Lee T, Zheng P, Humann P, Yu J, Blenda A, Scott K, Byrd M, Hough H, Wasko DeVetter L, Evans K, Peace C, Gasic K, Olmstead M, Cai L, Coe M (2015) Genome Database for Rosaceae – Utilizing Tripal, an Open-Source Database Platform for Genomics, Genetics and Breeding Research. Abstracts of the Crop Science Society of America/American Society of Agronomy/ Soil Society of America Annual Meeting; November 15-18, 2015; Minneapolis.

Main D, Jung S, Kahn M, Peace C, Mcferson J (2016) Overview of NRSP and Planned Tripal development. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.

Main D, Jung S, Lee T, Cheng C-H, Yu J, Gasic K, Campbell BT, Evans KM, Peace C (2016) TripalBIMS: development of a Breeding Information Management System. Abstracts of Cotton Breeders Workshop, 2016 Cotton Beltwide Conference; January 5-7, 2016; New Orleans, USA.

Main D, Rife T, Poland JA, Gasic K, Jung S, Campbell BT, Evans KM (2016) Introduction to Field Book: An Open-source Android App for Collecting Phenotypic Data in a Breeding Programs. Abstracts of Cotton Breeders Workshop, 2016 Cotton Beltwide Conference; January 5-7, 2016; New Orleans, USA.

Main D, Yu J, Jung S, Cheng CH, Lee T, Zheng P, Humann JL, McGaughey D, Hough H, Ficklin SP, Campbell BT, Percy RG, Jones DC (2016) Overview of CottonGen for Breeders. Abstracts of Cotton Breeders Workshop, 2016 Cotton Beltwide Conference; January 5-7, 2016; New Orleans, USA.

Olmstead M, Iezzoni AF, Peace CP, Bassil N, Coe M, Finn CE, Gasic K, Luby JJ, Main D, McFerson JR, Norelli JL, Whitaker VM, Yue C, Sebolt A (2016) Successful Networking to Create International Collaborations in the Rosaceae Community. Abstracts of the American Society for Horticultural Science Conference; August 7-11, 2016; Atlanta, USA, USA.

Reid R, Brown A, Main D, Broewer C, Walstead RN, Chen Y (2016) Blueprints for Blueberry: A Genome Assembly and Annotation. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.

Ru, S., Hardner, C., Carter, P., Evans, K., Main, D., Peace, C. (2016) Modeling of genetic gain from marker-assisted seedling selection in clonally propagated crops. Horticulture Research 3, 16015.

Sanderson L-A, Ficklin SP, Main D, Bett K (2016) Tripal v2: An Overview. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.

Sidhu, G., Mohan, A., Zheng, P., Dhaliwal, A.K., Main, D., Gill, K.S. (2015). Sequencing-Based High Throughput Mutation Detection in Bread Wheat. BMC Genomics 16(1):962.

Yu J, Jung S, Cheng CH, Lee T, Buble K, Zheng P, Humann JL, McGaughey D, Hough H, Ficklin SP, Camobell BT, Percy RG, Jones DC, Main D (2016) Updates to CottonGen: The Community Database for Genomics, Genetics and Breeding Research in Cotton. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego, USA.

Yu J, Jung S, Cheng CH, Lee T, Buble K, Zheng P, Humann JL, McGaughey D, Hough H, Ficklin SP, Campbell BT, Percy RG, Jones DC , Main D (2016) CottonGen: Current Functionality and Future Direction. 2016 World Cotton Research Conference 6 and 2016 ICGI Conference; May 2-6, 2016;. Goiânia, Brazil

Yu J, Jung S, Cheng CH, Lee T, Zheng P, Humann JL, McGaughey D, Hough H, Ficklin SP, Campbell BT, Percy RG, Jones DC , Main D (2016) New Breeding Data and Tools in CottonGen: The Community Resource for Cotton Genomics, Genetics and Breeding Researches. Abstracts of the Cotton Improvement Conference, 2016 Cotton Beltwide Conference; January 5-7, 2016; New Orleans, USA.

Yu M, Holdsworth W, Cheng P, Grisack MA, Mazourek M, Coyne C, Main D, McGee RJ (2015) Genome-wide SNP identification, linkage map construction and QTL mapping for mineral nutrients in pea. Abstracts of the North American Pulse Improvement 2015 Biannual Meeting; November 4-6, 2015; Niagara Falls, Canada

05/17/2018

Gasic, K., Jung, S., Cheng, C.H., Lee, T., Zheng, P., Yu, J., Humann, J., Evans, K., Peace, C., DeVetter, L., Mcferson, J., Coe, M.I. and Main, D. Resources in the Genome Database for Rosaceae for Peach Research. Acta Horticulturae (in press).

Jung, S., Lee, T., Cheng, CH., Humann, J., Yu, J., Ficklin, S.P. and Main, D. (2017). Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases. Database (Oxford) bax092.

Iezzoni, A., Peace, C., Main, D., Bassil, N., Coe, M., Finn, C., Gasic, K., Luby, J., Hokanson, S., McFerson, J., Norelli, J., Olmstead, M., Whitaker, V., Yue, C. (2017). RosBREED 2: Progress and future plans to enable DNA-informed breeding in the Rosaceae. Acta Horticulturae.2017.1172.20.

Ma, Y., Coyne, C.J., Main, D., Pavan, S., Sun, S., Zhu, Z., Zong, X., Leitao, J., McGee, R.J. (2017). Development and validation of breeder-friendly KASPar markers for er1, a powdery mildew resistance gene in pea (Pisum sativum L.). Molecular Breeding 37:151.

Ma, Y., Coyne, C.J., Grusack, M., Mazourek, M., Cheng, P., Main, D., McGee, RJ. (2017) Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.) BMC Plant Biology 17(1):43

Yu, L.X., Zheng, P., Zhang, T., Rodringuez, J., Main, D. (2017) Genotyping‐by‐sequencing‐based genome‐wide association studies on Verticillium wilt resistance in autotetraploid alfalfa (Medicago sativa L.). Molecular Plant Pathology 18(2):187-194

Main, D., Jung, S., Lee, T., Cheng, C-H., Zheng, P., Humann, J.L., Ru, S., Scott, K., Frank, M., Yu, J., Gasic, K., McFerson, J., Evans, K.M., Peace, C.P., DeVetter, L., Coe, M. and Kahn, M. 2017. GDR: New Data and New Functionality. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA

Jung, S., Lee, T., Cheng, C-H., Zheng, P., Humann, J.L., Ru, S., Scott, K., Frank, M., Yu, J., Gasic, K., McFerson, J., Evans, K.M., Peace, C.P., DeVetter, L., Coe, M., Kahn, M and Main, D. 2017. Using GDR: An Overview. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA

Jung, S., Lee, T., Cheng, C-H., Zheng, P., Humann, J.L., Ru, S., Scott, K., Frank, M., Yu, J., Gasic, K., McFerson, J., Evans, K.M., Peace, C.P., DeVetter, L., Coe, M., Kahn, M and Main, D. 2017. Newly Designed Genome Database for Rosaceae (GDR). Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA

Campbell, J.D., Campbell, E., Jung, S., Main, D., Poelchau, M., Walls, R. and Harper, L.S. 2017. AgBioData: A Consortium of Agricultural Biological Databases. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA

Buble, K., Jung, S., Humann, J.L., Cheng, C-H., Lee, T., Ficklin, S.P., Yu, J. and Main, D. 2017. Development of TripalMap. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA

Lin, Q., Herndon, N., Grau, E., Ficklin. S.P., Staton, M., Jung, S., Main, D., Feltus, A. and Wegrzyn, J.L. 2017. A Novel Tripal Database Module and Workflow to Facilitate Variant Mapping and Detection in Non-Model Plant Species. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA

Ficklin, S.P., Cheng, C.H., Watts, N., Chen, M., Wytko, W., Soto, B., Sanderson, L.A., Jung, S., Wang, K-H., Staton, M., Main D., Feltus, A. and Wegrzyn, J.L. 2017. Tripal Introduction and Core Development Efforts. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA

Yu, J., Jung, S., Cheng, C.H., Lee, T, Zheng, P., Humann, J., McGaughey, D., Frank, M., Hough, H., Campbell, B.T., Percy, R.G., Jones, D.C., Main, D. 2017. CottonGen: An upto-date Resource for Cotton Genomics, Genetics and Breeding Research. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA

Jung, S., Cheng, C-H., Lee, T., Ficklin, S.P., Yu, J., Humann, J.L. and Main, D. 2017. Mainlab Chado Loader, Chado Data Display and Chado Search for Sequence, Map, Marker, QTL, Genotype, Phenotype and Germplasm Data. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA

Gasic, K., Jung, S., Lee, T., Cheng, C-H., Yu, J., Campbell, T., Evans, K.M., Peace, C. and Main, D. (2016). Use of FieldBook and BIMS for Rosaceae Breeding. RosBREED Participants Meeting; March 6-8, 2017; East Lansing, USA

Humann, J.L., Piaskowski, J., Jung, S., Cheng, C-H., Lee, L., Frank, M., Scott K., Zheng, P., Flores, M., Saha, S., Mueller, L.A., Gmitter, F.G. jr, Abbott, A.G., and Main, D. 2017. Resources in the Citrus Genome Database that enable basic, translational, and applied research. 5th International Research Conference on Huanglongbing, Mar. 15-17, 2017, Orlando, FL. Journal of Citrus Pathology, 2017, 4(1):20.

Jung, S., Cheng, C-H., Lee, T., Ficklin, S.P., Yu, J., Humann, J.L. and Main, D. (2017) Development of Database Resources and Tools for Crop Genomics, Genetics and Breeding Research. Abstracts of the International Plant and Animal Genome Asia Conference XXV; May 29-30, 2017; Seoul, South Korea

Jung, S., Cheng, C-H., Lee, T., Ficklin, S.P., Yu, J., Humann, J.L. and Main, D. (2017) Development of Database Resources and Tools for Crop Genomics, Genetics and Breeding Research. Abstracts of the 2017 Plant and Breeding Symposium; June 3-4, 2017; Seoul, South Korea

Jung S., Lee, T., Gasic, K., Campbell, B.T., Cheng C-H., Yu, Y., Humann, J.L., Evans, K., Peace, C., and Main, D. 2017. TripalBMS: the Breeding Management System in Tripal for efficient management of private breeding data that are integrated with public genomic and genetic data. 2017. Proceedings of the American Society of Plant Biologist Annual Meeting; June 24-28, 2017; Honolulu, HI

Main, D., Humann, J.L., Lee, T., Ficklin, S.P., Cheng, C-H., Hough, H., Jung, S., Wegrzyn, J.L., and D.B. Neale. 2017. Structural and functional annotation of model and non-model organisms with GenSAS v5.0, a web-based annotation platform. Proceedings of the American Society of Plant Biologist Annual Meeting; June 24-28, 2017; Honolulu, HI

Main, D., Jung, S., Kahn, M., Peace, C., and J. McFerson. 2017. National Research Support Project 10. American Society of Plant Biologist Annual Meeting June 24-28, 2017, Honolulu, HI

Gasic, K., Jung, S., Lee, T., Cheng, C-H., Zheng, P., Humann, J.L., Ru, S., Scott, K., Frank, M., Yu, J., McFerson, J., Evans, K.M., Peace, C.P., DeVetter, L., Coe, M., Kahn, M. and Main, D., (2017). Peach Resources in the Genome Database for Rosaceae. Proceedings of the IX International Peach Symposium; July 2-6, 2017; Bucharest, Romania

Gasic, K., Lee, T., Jung, S., and Main, D. 2017. A Breeders Perspective on Using the Breeding Information Management System for Fruit Breeding. Proceedings of the ASHS Annual Conference; September 19-22, Waikoloa, HI

Jung S., Lee, T., Cheng, C.H., Zheng, P., Humann, J.L., Yu, J., Scott, K., Frank, M., McGaughey, D., Hough, H., Gasic, K., Evans, K., Peace, C., McFerson, J., Coe, M., and Main, D,. 2017. Resources for Breeders in the Genome Database for Rosaceae. . Proceedings of the ASHS Annual Conference; September 19-22, Waikoloa, HI

Bassil, N., Jung, S., Cheng, C-H., Lee, T., Zheng, P., and Main, D., 2017. NRSP10 Resources for Small Fruit Research. Proceedings of the ASHS Annual Conference; September 19-22, Waikoloa, HI

Humann, J.L., Lee, T., Ficklin, S.P., Cheng, C-H., Hough, H., Jung, S., Wegrzyn, J.L., and D.B. Neale. 2017. Using Gensas for Specialty Crop Community Genome Annotation. Proceedings of the ASHS Annual Conference; September 19-22, Waikoloa, HI

Humann, J., Piaskowski, J., Jung, S., Cheng, C-H., Lee, L., Frank, M., Scott K., Zheng, P., Flores, M., Saha, S., Mueller, L.A., Gmitter, F.G. jr, Abbott, A.G., and Main, D. 2017. Citrus Genome Database: Resources That Enable Basic, Translational, and Applied Research. Proceedings of the ASHS Annual Conference; September 19-22, Waikoloa, HI

Staton, M., Chen, M., Almsaeed, A., Condon, B., Yu, J., Henry, W., Wegrzyn J.L., Main, D., Ficklin, S.P. 2017. Using Tripal As a Project Database: The Hardwood Genomics Project. Proceedings of the ASHS Annual Conference; September 19-22, Waikoloa, HI

Peace, C., Vanderzande, S., Iezzoni, A., Jung, S., and Main, D. 2017. NRSP10 Resources for Translational Tree Fruit Research. Proceedings of the ASHS Annual Conference; September 19-22, Waikoloa, HI

Main, D., Jung, S., Kahn, M., Peace, C., and J. McFerson. 2017. What Is NRSP10 and What Can It Do for Specialty Crop Research. Proceedings of the ASHS Annual Conference; September 19-22, Waikoloa, HI

Campbell B.T., Lee, T., Jung, S., Yu, J., Jones, D., and Main, D. 2017. A Breeders Perspective on using the Breeding Information Management System for Cotton Breeding. Proceedings of the 2017 Cotton Breeders Tour, September 24-26, Arizona.

Udall, J., Yu, J., Jung, S., Cheng, C.H., Lee, T, Zheng, P., Humann, J., McGaughey, D., Frank, M., Hough, H., Campbell, B.T., Percy, R.G., Jones, D.C., Main, D. 2017. CottonGen: An An Overview for Breeders. Proceedings of the 2017 Cotton Breeders Tour, September 24-26, Arizona.

06/08/2019

Jung, S., Lee, T., Cheng, C-H., Buble, K., Zheng, P., Yu, J., Humann, J.L., Ficklin, S.P., Gasic, K., Scott, K., Frank, M., Ru, S., Hough, H., Evans, K., Peace, P., DeVetter, L., McFerson, J., Coe, M., Wegrzyn, J.L., Staton, M., Main D. (2018) 15 years of GDR: New data and functionality in the Genome Database for Rosaceae. Nucleic Acids Research 47(D1), D1137-D1145.

Falk, T., Herndon, N., Grau, E., Buehler, S., Richter, P., Zaman, S., Baker, E.M., Ramnath, R., Ficklin, S., Staton, M., Feltus, F.A., Jung, S., Main, D., Wegrzyn, J.L. (2018) Growing and cultivating the forest genomics database, TreeGenes. Database, bay084.

Harper, L., Campbell, J., Cannon, E., Jung, S., Poelchau, M., Walls, R.L., Andorf, C.M., Arnaud, E., Berardini, T., Birkett, C., Cannon, S., Carson, J., Condon, B., Cooper, L., Dunn, N., Elsik, C., Farmer, A., Ficklin, S.P., Grant, D., Grau, E., Herndon, N., Hu, Z-L., Humann, J.L., Jaiswal, J., Jonquet, C., Laporte, M.A., Larmande, P., Lazo, G., McCarthy, F., Menda, N., Mungall, C., Munoz-Torres, M., Naithani, S., Nelson, R., Nesdill, D., Park C., Reecy, J., Reiser, L., Sanderson, L-A., Sen, T.Z., Staton, M., Subramaniam, S., Tello-Ruiz, M.K., Unda, V., Unni, D., Wang, L., Ware, D., Wegrzyn, J.L., Williams, J., Woodhouse, M., Main, D. (2018). AgBioData Consortium Recommendations for Sustainable Genomics and Genetics Databases for Agriculture. Database, bay088.

Herndon, N., Falk, T., Grau, E.S., Jung, S., Ficklin, S., Main, D., Staton, M.E., Wegrzyn, J.L. (2018) Association Mapping for Forest Trees with CartograTree. Studies on the Semantic Web, 33, Chapter 8, 137-149. IOS Press eBooks (Ed. Anne E. Thessen)

Humann, J. L., Lee, T., Ficklin, S., & Main, D. Structural and Functional Annotation of Eukaryotic Genomes with GenSAS. Gene Prediction (pp. 29-51). Humana, New York, NY (in press).

McFerson, J., Jung, S., Cheng, C-H., Lee, T., Zheng, P., Evans, K., Peace, C., Main, D. (2017) Tree Fruit Breeding and Big Data Get together in the Genome Database for Rosaceae. Presentation at the Washington State Tree Fruit Association Annual Meeting, Dec 5, 2017, Kennewick, WA, USA.

Main, D., Yu, J., Jung, S., Cheng, C.H., Lee, T., Humann, J. Zheng, P., McGaughey, D., Frank, M., Scott, K., Hough, H., Campbell, B.T., Mohan, A., Udall, J., Percy, R.G., Jones, D. (2018). Using CottonGen for Crop Improvement. Proceedings of the National Cotton Council Beltwide Cotton Conference, January 3-5, 2018, San Antonio, Texas, USA.

Campbell, J.D., Cannon, E., Jung, S., Main, D., Poelchau, M., Walls, R., Harper, L.C. (2018). AgBioData: Identifying and Meeting Common Goals in the Management of Agricultural Biological Data. Proceedings of the International Plant & Animal Genome Conference XXVI, January 13-17, 2018, San Diego, CA, USA.

Poelchau, M., Campbell, J.D., Cannon, E., Jung, S., Main, D., Walls, R., Harper, L.C. (2018). Challenges and Recommendations for Genomics, Genetics and Breeding Databases from the AgBioData Consortium. Proceedings of the International Plant & Animal Genome Conference XXVI, January 13-17, 2018, San Diego, CA, USA.

Jung, S., Lee, T., Cheng, C-H., Ficklin, S.P., Yu, J., Humann, J., Main, D. (2018). Mainlab Chado Module, a Tripal Module for Loading Map, Marker, QTL, Genotype, Phenotype and Germplasm Data. Proceedings of the International Plant & Animal Genome Conference XXVI, January 13-17, 2018, San Diego, CA, USA.

Buble, K., Jung, S., Humann, J., Cheng, C-H., Lee, T., Ficklin, S.P., Yu, J., Main, D. (2018). TripalMap Mapviewer 1.0. Proceedings of the International Plant & Animal Genome Conference XXVI, January 13-17, 2018, San Diego, CA, USA.

Main, D., Buble, K., Lee, T., Jung, S., Humann, J., Yu, M., Ficklin, S.P., Gasic, K., Campbell, B.T. (2018). Updates on Tripal Mapviewer and the Tripal Breeding Information Management System (BIMS). Proceedings of the International Plant & Animal Genome Conference XXVI, January 13-17, 2018, San Diego, CA, USA.

Jung, S., Lee, T., Cheng, C-H., Zheng, P., Yu, J., Humann, J., Gasic, K., Frank, M., Scott, K., Evans, K.M., Peace, C., Devetter, L., McFerson, J., Kahn, M., Main, D. (2018). Using GDR for Translational Research. Proceedings of the International Plant & Animal Genome Conference XXVI, January 13-17, 2018, San Diego, CA, USA.

Jung, S., Lee, T., Cheng, C-H., Gasic, K., Campbell B.T., Main, D. (2018). Using the Tripal Breeding Information Management System (BIMS) to Enable Efficient Management of Phenotypic and Genotypic Data. Proceedings of the International Plant & Animal Genome Conference XXVI, January 13-17, 2018, San Diego, CA, USA.

Ficklin, S.P., Cheng, C-H., Spoor, S., Chen, M., Almsaeed, A., Mills, N., Watts, N., Wytko, C., Grau, E., Herndon, N., Soto, B., Wang, K-C., Feltus, A., Staton, M., Wegrzyn, J., Jung, S., Main, D. (2018) The Tripal Gateway Project: Supporting Exchange, Transfer and Analysis of Large-Scale Data for Online Biological Databases. Proceedings of the International Plant & Animal Genome Conference XXVI, January 13-17, 2018, San Diego, CA, USA.

Jung, S., Lee, T., Yu, J., Humann, J.L., Hough, H., Main, D. (2018). Breeding Information Management System Training Workshop Presentations. Breeders Workshop at the RosBREED Participants Meeting, March 5, 2018, East Lansing, MI, USA.

Buehler S., Falk T., Grau E.S., Herndon N., Zaman S., Main D., Jung S., Ficklin F., Staton M., Wegrzyn J.L. (2018). Tripal Sequence Similarity Search provides efficient protein sequence similarity search for Tripal sites. Proceedings of the Bioinformatics Open Source Conference, June 25-30. 2018, Portland, OR, USA.

Main, D. (2018). CottonGen: A Database Resource for Genomics, Genetics and Breeding Research. Proceedings of the International Cotton Genome Initiative (ICGI) Research Conference, May 31 - June 4, 2018, Edinburgh, Scotland, United Kingdom.

Yu, J., Lee, T., Jung, S., Campbell, B.T., Gasic, K., Humann, J., Hough, H., Jones, D., Percy, R., Main, D. (2018). CottonGen BIMS for effective and efficient management of breeding data. Proceedings of the International Cotton Genome Initiative (ICGI) Research Conference, May 31 - June 4, 2018, Edinburgh, Scotland, United Kingdom.

Cheng, C.H., Yu, J., Jung, S., Zheng, P., Humann, J., Lee, T., McGaughey, D., Mohan, A., Frank, M., Hough, H., Udall, J., Jones, D., Main, D. (2018). How to Effectively Search and Download Data in CottonGen. Proceedings of the International Cotton Genome Initiative (ICGI) Research Conference, May 31 - June 4, 2018, Edinburgh, Scotland, United Kingdom.

Zheng, P., Jung, S., Cheng, Cheng, C.H., Yu, J., Hough, H., Udall, J., Jones, D., Main, D. (2018). Visualization of Conserved Syntenic Blocks Among Six Cotton Genomes in CottonGen. Proceedings of the International Cotton Genome Initiative (ICGI) Research Conference, May 31 - June 4, 2018, Edinburgh, Scotland, United Kingdom.

Buble, K., Yu, J., Jung, S., Humann, J., Cheng, C.H., Lee, T., Hough, H., McGaughey, D., Frank, M., Main, D. (2018). Using TripalMap for Genetics Research. Proceedings of the International Cotton Genome Initiative (ICGI) Research Conference, May 31 - June 4, 2018, Edinburgh, Scotland, United Kingdom.

Jung, S., Lee, T., Cheng, C-H., Buble, K., Zheng, P., Yu, J., Humann, J.L., Ficklin, S.P., Gasic, K., Scott, K., Frank, M., Ru, S., Hough, H., Evans, K., Peace, P., DeVetter, L., McFerson, J., Coe, M., Wegrzyn, J.L., Staton, M., Main D. (2018). Genome Database for Rosaceae: A Resource for Genomic, Genetic and Breeding Research. Proceedings of the 9th International Rosaceae Genomics Conference, June 26-30, 2018. Nanjing, China.

Hardner, C., Satish, K., Main, D., Hayes, B., Peace, C. (2018). Global Genomic Prediction of Performance. Proceedings of the 9th International Genomics Conference, June 26-30, 2018. Nanjing, China.

Jung, S., Lee, T., Cheng, C-H., Buble, K., Zheng, P., Yu, J., Humann, J.L., Gasic, K., Scott, K., Frank, M., Ru, S., Hough, H., Evans, K., Peace, P., DeVetter, L., McFerson, J., Coe, M., Main D. (2018) Genome Database for Rosaceae: resource for genomic, genetic and breeding research. ‎July 5th 2018, Chungbuk National University, Cheongju, South Korea.

Main, D., Harper, L., Jung, S., Campbell, J.D., Cannon, E., Poelchau, M., Walls, R. (2018) AgBioData Visioning and Implementation. Proceedings of the ASPB Annual Conference; July 14-18, 2018, Montreal, Canada

NRSP10 databases and Tripal brochures at AgBioData Booth. ASPB Annual Conference; July 14-18, 2018, Montreal, Canada

Staton, M (2018). Tripal v3, the Collaborative Online Database Platform Supporting an International Community of Plant Genome Databases. Proceedings of the ASHS Annual Conference; July 31-Aug 4, 2018, Washington, D.C., USA.

Jung, S., Lee, T., Cheng, C-H., Buble, K., Zheng, P., Yu, J., Humann, J.L., Gasic, K., Scott, K., Frank, M., Ru, S., Hough, H., Crabb J., Evans, K., Peace, P., DeVetter, L., McFerson, J., Coe, M., Jahn, M., Main D. (2018). New Data and Functionality in NRSP10 Databases. Proceedings of the ASHS Annual Conference; July 31-Aug 4, 2018, Washington, D.C., USA.

Rife, T., Poland, J.A. (2018). Integrating Free Mobile Apps into Specialty Crop Breeding and Horticultural Programs. Proceedings of the ASHS Annual Conference; July 31-Aug 4, 2018, Washington, D.C., USA.

Gasic, K., Lee, T., Jung, S., Humann, J.L.,Yu, J., Hough, H., Campbell, B.T., Peace, P., Evans, K., Main D. (208). Using the Tripal Breeding Information Management System to Improve Breeding Efficiency. Proceedings of the ASHS Annual Conference; July 31-Aug 4, 2018, Washington, D.C., USA.

Peace, C., Hardner, C., Lee, T., Jung S., Main, D. (2018) Extending the Tripal Breeding Information System to Combine International Data for Global Performance Predictions. Proceedings of the ASHS Annual Conference; July 31-Aug 4, 2018, Washington, D.C., USA.

Main, D., Jung, S., Humann, J.L., Peace, C., Gasic, K., Kanh, M., McFerson, J. (2018). NSRP10 - the Next Five Year Plan: Furthering Integration of Big Data, Tools and Analysis Capability to Enable Specialty Crop Research Discovery and Improvement. Proceedings of the ASHS Annual Conference; July 31-Aug 4, 2018, Washington, D.C., USA.

Plant Breeding Coordinating Committee SCC-80 (2018). U.S. Public Plant Breeding Capacity. Proceedings of the National Association of Plant Breeders Annual Meeting, August 7-10, Guelph, Canada.