Brief Summary of Minutes of Annual Meeting

In person or teleconference discussed meetings held during the year with various special interest groups:

Rosaceae Community Meetings (RosEXEC and GDR Advisory Board): October 28, 2015; January 11, 2016; April 27, 2016; August 31, 2016 Reported progress on GDR activities every quarter (report provided ahead of meetings) and plans for the next quarter to RosEXEC, the advisory board for GDR and the US Rosaeace Genomics, Genetics and Breeding Coordinating Committee. Discussed new sources of data being generated by the community through large projects and how best GDR might host and integrate. Reported on publication of a standard nomenclature for gene designation in the Rosaceae and uptake of standardization in the community and how best to keep promoting this. We also discussed outreach efforts by the GDR team to encourage journals to request data be submitted to GDR by authors.

CottonGen Cotton Breeders Workshop: Cotton Beltwide Conference, New Orleans, Jan 3, 2016 Held a 2 hour workshop for cotton breeders providing use of CottonGen for breeding, including use of the FieldBook App for collecting phenotypic data in the field. Samsung tablets with the FieldBook App were distributed to those breeders who had not already received one for evaluation. We discussed breeders’ needs for data management and analysis capability in the Tripal Breeding Management Information System being developed, as well as access to data in CottonGen. We reviewed the goals of NRSP10 as they relate specifically to CottonGen and the group agreed CottonGen was on track to meet the needs for a community database.

International Cotton Genomics Initiative Officers Meeting, San Diego, CA, Jan 10, 2016 As part of the annual in-person ICGI meeting at PAG we discussed progress in CottonGen with a focus on genomic data and resources and its role in helping coordinate cotton community through the ICGI portal hosted on CottonGen, including hosting biannual office elections and future ICGI conference organization. Committee agreed CottonGen was keeping update to date with data and tools to enable cotton genomics research.

Two day Tripal Hackathon and User Meeting: San Diego, CA, Jan 7-8, 2016 Discussion with participants about plan for Tripal under NRSP10, feedback provided and larger network of Tripal developers built. Tripal Workshop, Plant and Animal Genome Conference: San Diego, CA, Jan 10, 2016 Presentations on Tripal advances and discussion of general future needs for core Tripal and extension modules in development or needed AgBioData Meeting, Plant and Animal Genome Conference, San Diego, CA, Jan 11, 2016 Met with various participants from the agricultural database community to discuss common practices amongst databases, included discussions about NRSP10 and the Tripal platform and how adoptable it was.

GDR Users Meeting at 8^th International Rosaceae Genomics Initiative, Angers, France, June 23, 2016 After the GDR presentations, met with Rosaceae community members to discuss new developments, data acquisition, community annotation using GenSAS and functionality needed in TripalBIMS plus use of the FieldBook App. The feedback received led us to implement a new advanced search in GDR and provide input to FieldBook App developers on improved functionality needed for specialty crop breeders.

NRSP10 Open Meeting at ASHS Annual Conference, Atlanta, GA, August 9, 2016 Met with specialty crop scientists and discussed reasons for switching to Field Book from both a breeding perspective but also the database perspective and role of ontologies and standardization of data for integration and querying. We also went over the progress from the past year and the goals of NRSP10 for the next year. Had detailed discussions about use of SNP arrays and tools needed for their application to facilitate breeding.

Tripal Progress: In year 2 the major achievement in core Tripal development was the release of an alpha version of Tripal v3 in Jan 2016, set up of a demo site at http//demo.tripal.info/3.X for user exploration, and provision of a demo for stakeholders at the July Tripal users’s conference call. Web service implementation is underway in Tripal 3 which makes Tripal back-end database schema independent and helps overcome some of the limitations of having to use a chado database schema. This provides more flexibility for Tripal use and extends its utility to other genomic, genetic and breeding databases that do not want to be reliant on using Chado. In addition to work on version 3, we worked on finalizing extension modules for Tripal v2 which were developed to be easily upgraded to v3. These extension modules which will be released in November 2016 include a Chado Loader, Chado Data Display and Chado Search. These modules provide site developers with tools 1) to collect and upload data 2) to organize and display data and 3) to enable advanced search functions. Supported data types include organism, marker, QTL, Mendelian Trait Loci, germplasm, map, project, phenotype, genotype and their associated metadata. The Chado Loader module provides data collection templates and PHP loaders to enable site developers to collect and store various types of data that are required to build comprehensive genomic and genetic databases. The Chado Data Display module contains a set of Drupal/PHP templates which can be used as is or customized as desired. The Chado Search module provides comprehensive search and download functionality for sequence, gene, marker, map, QTL, phenotype, genotype and germplasm. Also included are the tools to build map data and species summary pages. The use of materialized views in the Chado Search module enables better performance as well as flexibility of data modeling in Chado, allowing existing Tripal databases with their data stored in different ways to utilize the module. These Tripal Extension modules are implemented in the Genome Database for Rosaceae (rosaceae.org), CottonGEN (cottongen.org) and Cool Season Food Legume Database (coolseasonfoodlegume.org). Other ongoing Tripal extension work includes development of a MapViewer called TripalMap, designed to replace CMap. Outreach efforts to aid community development and adoption of Tripal included: Monthly Tripal developer meetings (includes international attendees), organizing the first Tripal hackathon and the 3rd Tripal workshop at PAG 2016 , keeping the Tripal website current and providing programming support and code to other Tripal groups. At the end of year 2, Tripal was being used by over 90 databases.

GenSAS Progress: GenSAS v4.0 was released in January 2016. Major improvements completed in year 2 include; the ability to use high performance computing where jobs can be submitted to a cluster rather than just a single server (enhanced speed); functional annotation capability through the addition of the BLAST, InterProScan, Pfam, SignalP, and TargetP tools to help assign a function to the proteins encoded by the predicted gene models; as well as additional tools added for structural annotation, and integration with JBrowse and WebApollo. Major work started in year 2 for a release of GenSAS v5.0 in January 2016. It includes: (1) ability to upload sequences before project creation so sequence subsets can be created from multiple-sequence fasta files. Sequence subsets can also be filtered by sequence name or minimum size (2) ability to upload RNA-seq reads use them to train gene model predictors (Augustus, during structural step) (3) addition of the tool Tophat to enable alignment specifically for the RNA-Seq reads. Alignment tools (blast, blat, PASA, tophat) are now included as a step before structural annotation (4) structural annotation (previously labelled as the "genes" step) now also has GeneMark for prokaryotic and eukaryotic gene prediction and (5) an official genes step (OGS) was added where users can either use EvidenceModeler to create a genes consensus and use it as the OGS, or can select another data track (from gene prediction program or alignment) as the OGS. Manual curation is merged with the OGS at the end of the GenSAS protocol. It was demonstrated at several conferences (see results disseminated section). In Year 2 GenSAS was accessed by 1,135 visitors from 73 countries, with 2,333 sessions and 7,850 pages viewed.

Breeding Tools Progress: We received encouraging feedback from our 20 stakeholder breeders who had been testing or deploying the FieldBook App for collection of phenotypic data in their breeding programs. As a result, we decided to more formally collaborate with the FieldBook PI, Jesse Poland at Kansas State University, and divert funds (0.5 FTE of a developer’s salary) in years 3-5 of NRSP10 to help expedite further development relative to the expressed needs of our breeders. Following an initial needs assessment for breeding information data management tool functionality in year 1, we began BIMS design and implementation in year 2. BIMS will allow breeders to store, manage and analyze all their breeding data within a secure portal that connects their private data with all the data and tools available in their community genomics, genetics and breeding databases. We focused on working with two representative breeding programs from the 25 crops covered in the NRSP10; the peach breeding program of Dr. Kensija Gasic at Clemson University and the USDA ARS cotton breeding program of Dr. Todd Campbell in South Carolina. To gain further breeder input, we demonstrated goals and design of BIMS and FieldBook at several venues in year 2 (see the results disseminated section). These included a dedicated cotton breeder’s workshop we organized at the Cotton Beltwide conference in January 2016, the International Plant and Animal Genome Conference in January 2016, the RosBREED project participants meeting in March 2016, the International Rosaceae Genomics Conference in June 2016 and the American Society for Horticultural Science annual meeting in August 2016. By the end of year 2 the design of BIMS was decided and programming initiated.

NRSP10 Databases Progress: In year 2 we completed upgrade of the CottonGen and GDR databases to Tripal 2 and Durpal 7 with a more user-friendly design on the live site and have done the same for the Citrus (CGD) and Vaccinium (GDV) databases on the development site. We are in the process of updating the data in the latter two and will go live with the new design in year 3. Significant data and new functionality have been added to all five databases. The specific details are documented in the work completed page of each database. Use of the databases continued to increase compared with year 1 as more data and functionality was added. During the reporting period the databases were accessed as follows (as recorded by Google Analytics): GDR - accessed by 19,272 users from 152 countries, who viewed 232,162 pages; CottonGen - accessed by 9,422 users from 139 countries, who viewed 134,123 pages; CSFL - accessed by 2,982 users from 114 countries, who viewed 22,162 pages; CGD - accessed by 4,516 users from 123 countries, who viewed 24,064 pages; GDV- accessed by 1,349 users from 77 countries, who viewed 6,116 pages.

Leveraged Federal Funding: Added new NSF funded project ($2,983,307) to increase federal funding leveraged for NRSP10 efforts to $7,209,903 (listed below). This funding supports data curation efforts and additional infrastructure development for the Tripal database platform across the NRSP10 databases and adds forest/hardwood trees databases to the Tripal community of databases. This funding is important as it highlights that USDA and NSF recognize the need to support Tripal as the standard platform for database development. It further validates the importance of NRSP10 to not only provide resources for underserved crops but extend this resource-efficient, open-source database platform to other crops/animal genomics, genetics and breeding efforts.

• $2,983,307: Standards and CyberInfrastructure that Enable Big-Data Driven Discovery for Tree Crop Research. NSF PGRP, July 1, 2016 – June 30, 2019, to Dorrie Main, Sook Jung Stephen Ficklin - Washington State University; Jill Wegrzyn: University of Connecticut; Margaret Staton: University of Tennessee,　 Albert Abbott: University of Kentucky 

• $2,741,575: Genome Database for Rosaceae: Empowering Specialty Crop Research through Big-Data Driven Discovery and Application in Breeding. USDA NIFA SCRI Program, Sep 1, 2014 – Aug 31, 2019, to Dorrie Main, Sook Jung, Cameron Peace, Kate Evans, Lisa DeVetter, Nnadozie Oraguzie - Washington State University; Ksenija Gasic: Clemson University Mercy Olmstead: University of Florida 

• $1,485,021: Tripal Gateway, a Platform for Next-generation Data Analysis and Sharing. NSF DIBBS Program, Jan 1, 2015-Dec 31, 2017, to Stephen Ficklin, Dorrie Main, Sook Jung - Washington State University; Jill Wegrzyn: University of Connecticut; Margaret Staton: University of Tennessee;　 Alex Feltus: Clemson University 

Our plans for year 3 of NRSP10 are to add reference transcriptomes for all major Rosaceae species using our new Tripal RefTrans analysis pipeline; continue to add genetic, genomic and breeding data as it becomes publicly available; release the Mainlab Chado loader, search and display modules for sequence, map, marker, QTL, genotype, phenotype and germplasm; continue development of a Tripal comprehensive breeding information management system (BIMS); promote further use of the FieldBook App for more efficient collection of phenotype data by Rosaceae breeding programs and allied scientists; present GDR at relevant conferences and meetings; continue actively participating in GGB database efforts at the national and international level, including helping to organize and fund a two day AgBioData conference for the database community to develop a white paper on Agricultural Biological Database data, code and communication sharing opportunities.

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 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

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 Molecular Plant Sciences Retreat, March 5, 2016, Pullman, WA

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.

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.

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.

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, 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