Source: TEXAS A&M UNIVERSITY submitted to
TOOLS FOR GENOMICS-ASSISTED BREEDING IN POLYPLOIDS: DEVELOPMENT OF A COMMUNITY RESOURCE
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
NEW
Funding Source
Reporting Frequency
Annual
Accession No.
1023566
Grant No.
2020-51181-32156
Project No.
TEX09849
Proposal No.
2020-02585
Multistate No.
(N/A)
Program Code
SCRI
Project Start Date
Sep 1, 2020
Project End Date
Aug 31, 2024
Grant Year
2020
Project Director
Byrne, D.
Recipient Organization
TEXAS A&M UNIVERSITY
750 AGRONOMY RD STE 2701
COLLEGE STATION,TX 77843-0001
Performing Department
Horticultural Sciences
Non Technical Summary
This proposal addresses the research in plant breeding, genetics, genomics, focus area. Polyploid specialty crops contribute significantly to food, fiber and ornamental production, with an annual US crop value over $9 billion and many times greater globally. Despite the importance of polyploid crops, the implementation of genomics-assisted breeding in these crops has lagged compared to diploid species. The major impediments to using genomic tools, based on extensive researcher and stakeholder consultations, are the limited availability of software suitable for polyploids (most tools are developed for diploid crops), technical expertise, and training. The present project addresses these deficiencies by developing computational tools for QTL analysis, genomic selection and haplotype analysis in polyploid crops; training polyploid breeders and geneticists to use these tools; and applying the tools for genomics-assisted breeding in public breeding programs for potato, blackberry, turfgrass, kiwi, sweetpotato and rose. A key output of the project is a Polyploid Breeding Community Resource web site to serve as a repository of the computational toolsets, genomic information, training datasets from several crops, and training materials. Success in this project will enable the routine use of genomic tools to accelerate the rate of genetic gain in a wide array of polyploid crop breeding programs, which will lead to cultivars with higher quality, greater productivity, and more resilience to biotic and abiotic stress. The project will have a long-term positive impact on specialty crop industries by training a new generation of plant breeders capable of using advanced computational tools for polyploid crops.
Animal Health Component
0%
Research Effort Categories
Basic
30%
Applied
50%
Developmental
20%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2012410108140%
2012410108040%
2012410302020%
Goals / Objectives
Goals/ObjectivesObjective 1. Develop computational tools for genomics-assisted breeding in polyploid crops. As highlighted in the introduction, over the past decade, a number of tools have been developed for linkage and QTL mapping in polyploid species. Objective 1 extends the functionality of these tools to more complex situations. Broadly speaking, there are two approaches to QTL mapping. The first involves association analysis to exploit linkage disequilibrium in arbitrary collections of germplasm (Obj. 1a) and the second uses linkage and QTL analysis of complex mating designs as well explores genomic selection (Obj. 1b). Obj 1c will develop sequence haplotyping approaches and their use in breeding. The subobjectives are as follows.Obj. 1a. Enhanced methods for genome-wide association studies (Endelman)Obj. 1b. Linkage/QTL analysis and genomic selection in multi-parent populations (Zeng and Mollinari)Obj. 1c. Polyploid haplotype assembly from short reads (Thomson)Objective 2. Validate computational tools for genomics-assisted breeding in public breeding programs for potato, blackberry, turfgrass, sweetpotato, kiwifruit and rose.One of the weaknesses of new and existing software is the lack of extensive validation on a range of polyploid crops. Thus, this project will fill this gap and systematically test the software using six polyploid crops representing a range of preferential pairing propensity, interspecific diversity, heterozygosity, chromosome number, genome size and genomic data/resource availability. Validation work will focus on 5 main areas.Obj. 2a. Allele dosage assignment.Obj. 2b. Genome-Wide Association. Obj. 2c. Linkage and QTL Analysis. Obj. 2d. Genomic Selection.Obj. 2e. Sequence-based haplotyping. Objective 3. Train polyploid breeders and geneticists to use and validate current and new computational tools. This will address training and extension needs of the polyploid crop breeding community by preparing and delivering short-courses and workshops on a yearly basis and establishing the Tools for Polyploids Community Resource. Workshops and short-courses will be prepared and delivered to breeders and associated scientists working on polyploid crops at annual meetings. The three sub objectives are:3a. Develop written documentation of software tools (Computational group):3b. Prepare and conduct annual short courses for polyploid breeders and geneticists.3c. Develop a Tools for Polyploids Community Resource web page (Main).
Project Methods
Methods:This project will develop software that extends the functionality of the current tools for QTL mapping (association analysis to exploit linkage disequilibrium in arbitrary collections of germplasm (Obj. 1a) and linkage and QTL analysis of complex mating designs) and genomic selection (Obj. 1b). Additional software will be developed to utilize sequence haplotyping approaches in polyploid breeding programs (Obj 1c). Computational tools developed will be systematically assessed for their performance over multiple crops leading to a feedback loop with the software developers towards optimization to facilitate the breeding of polyploid crops.Efforts:Annual training workshops (instruction manuals, hands-on instruction, presentations)Tools for Polyploid website (repository of training materials etc.)Email and social media to keep clientele apprised of progress and products available.Evaluations:Annual surveys about the use of genomic-assisted breeding and cultivars released.Surveys of annual workshop attendees about knowledge gained and financial importance of new software for polyploid crop breeding.The impact of the Tools for Polyploid Community Resource website will be measured by use metrics (visits, downloads, citations, etc.).The impact of the software developed and validation done will be measured by the number of scientific articles published and their citation metrics.

Progress 09/01/20 to 08/31/21

Outputs
Target Audience:Raising awareness and implementation of the constantly improving computation tools is essential to increase their use and subsequently accelerate the breeding progress of a wide diversity of polyploid crops including root/tuber crops (28%, potato, sweetpotato, yam), fruit (29%, blackberry, blueberry, banana, coffee, kiwifruit, strawberry), turfgrass, forage, sugarcane (19%), ornamentals (9%. Rose. chrysanthemum), vegetables (11%, legumes, asparagus, mint, basil), cereal (4%) and a few forest tree species. Our audience is young (64% less than 40 years old) and with no experience (90%) with the software. Many were either postdocs, graduate students (40%) or young breeders. Their training is essential to incorporating these tools into the breeding programs of the future. The expertise of our audience was on breeding/genetics (40%), computational genetics (20%), molecular genetics (25%) as well as entomology, plant pathology and plant physiology. The breeding programs ranged from small (1000 seedling per year) to very large (over 100,000 seedlings per year) representing both private (37%) and public (63%) programs. Fifty-four percent of our audience is from North America(38 states and Canada) and 46% from international locations, mainly South America, Europe and Africa but also Asia and Oceania. There was high participation from International Research Station (CGIAR) scientists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The major training event for polyploid crop breeders, their support people (bioinformatists, computational geneticists, molecular geneticists, plant pathologists, entomologists), post doctoral associates and graduate students was the 2021 Tools for Polyploids Training Workshop which was done as an online conference. This included presentations about the current computational tools for genotyping, map construction and QTL identification followed by question and answer sessions for each software suite. The attendance was superb with 353 people registering and a mean attendance over all three days of 250 participants. The 16 presentations were recorded and put on the Tools for Polyploids Youtube (https://www.polyploids.org/workshoppresentations) channel. They have received 1,137 views. and subsequent questions and trouble shooting was handled via the Tools for Polyploids SLACK channel (279 subscribers). In addition, Jeff Endelmann gave a presentation to the potato group about the use of genomic selection in their breeding programs and various PIs, graduate students and post doctoral researchers participated in professional meetings (PAG, ASHS, American Potato Society etc). How have the results been disseminated to communities of interest?During the first year of the project we have communicated progress to our scientific colleagues (7 journal articles, 4 non referred articles, 25 presentations). The major communication event for polyploid crop breeders, their support people (bioinformatists, computational geneticists, molecular geneticists, plant pathologists, entomologists), post doctoral associates and graduate students was the 2021 Tools for Polyploids Training Workshop which was done as an online conference. This included presentations about the current computational tools for genotyping, map construction and QTL identification followed by question and answer sessions for each software suite. The attendance was superb with 353 people registering and a mean attendance over all three days of 250 participants. The 16 presentations were recorded and put on the Tools for Polyploids Youtube (https://www.polyploids.org/workshoppresentations) channel. They have received 1,137 views. and subsequent questions and trouble shooting was handled via the Tools for Polyploids SLACK channel (279 subscribers). The Tools for Polyploids web site (https://www.polyploids.org/) serves as a repository of information about the project (1,738 visitors since January 2021) as well as a project management tool. The most popular section are the recorded presentations from the first conference which are used as a guide in using the software. The Tools for Polyploid Twitter account (Twitter @toolsforpolyploids, 139 followers) as well as periodic email alerts/surveys (400 people on mailing list) are used to keep our clientele informed of our activities and other polyploid related activities. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Objective 1. Develop computational tools for genomics-assisted breeding in polyploid crops. Obj. 1a. Enhanced methods for genome-wide association studies GWASpoly was improved by optimizing the control of the genome-wide false positive rate, enhancing the calculation of the kinship matrix, using the ggplot2 package, including a plotting function for LD, enhancing the ability to filter QTL output based on a specified LD window, and updating the vignette to illustrate the new features. Obj. 1b. Linkage/QTL analysis and genomic selection in multi-parent populations The interoperability among the programs such as MAPpoly, QTLpoly, polymapR, polyqtlR, updog, polyRAD and fitPoly was improved. MAPpoly updates include the addition of the probabilistic computation of two-point recombination frequencies used in polymapR for dosage-based probabilistic map construction, the fast implementation for plot large recombination frequency matrices, the functions to plot genetic information content (GIC), to read VCF and fitPoly files, probabilistic information, to upload datasets from the R packages updog, polyRAD and to import/export map results from/to polymapR, and the implementing of a multiparental mapping strategy for polyploid species. QTLpoly improvements include support for linkage maps constructed by MAPpoly and polymapR, a final QTL model that can be used to implement genomic prediction and the ongoing expansion of QTLpoly to support multiparental and multi-generational breeding populations. VIEWpoly is being developed to produce a graphical representation of the genetic map which shows marker names, parental dosages, and the linkage phase configuration of the allelic variants With QTLpoly it shows estimated positions, effects, and supporting intervals of QTL along the genome. polyqtlR has been updated to include new visualizations of chromosomal pairing patterns across populations, automated co-factor analyses and multi-QTL model building. Obj. 1c. Polyploid haplotype assembly from short reads Developed "MCHap" for assembly of micro-haplotypes in polyploids using Markov chain Monte Carlo simulation and standard bioinformatics file formats to ensure compatibility with existing software. This software assembles known multi-allelic SNPs into haplotypes within pre-defined genomic loci, calls or recalls genotypes based upon sets of known haplotypes across the genome and reports full posterior distributions for haplotype assemblies. It is designed to be run in parallel across multiple genomic loci for efficient use in an HPC environment. Objective 2. Validate computational tools Obj. 2a. Allele dosage assignment fitPoly use was facilitated by consolidating a set of software tools for data formatting and curation into the R package fitPolyTools. SNP-calling (GATK, freebayes, TASSEL, DeepVariant and proprietary software) and dosage calling (GATK, freebayes, updog, polyRAD and superMASSA) pipeline comparisons using sequence data are being performed using Workflow Description Language with the support of Docker/Singularity containers to facilitate higher accessibility, interoperability, reproducibility, and reusability of the pipelines. The comparisons will assess the marker position compatibility between methods, genome coverage and genetic map quality. Obj. 2b. Genome-Wide Association GWASpoly was used on roses, blackberries, potatoes, and turfgrass this past year to identify marker-traits associations for disease resistance, productivity, plant architecture, flowering type, and fruit/ tuber quality. In rose, the GWASpoly results were congruent with QTL scans. Obj. 2c. Linkage and QTL Analysis Linkage maps and QTL analysis using Mappoly/polymapR and/or QTLpoly/polyqtlR have been done in roses, blackberry and sweet potato. Comparisons of polymapR/MAPpoly for linkage mapping and polyqtlR/QTLpoly for QTL analysis with tetraploid rose families reveal software differences in the ease of use, computational demand, map quality and QTL positioning. The multiparental joint mapping function of MAPpoly was tested on crosses between three sweetpotato varieties: Beauregard, Tanzania, and New Kawogo (723 genotypes, 28.220 SNPs). A joint map and the haplotype reconstruction was consistent with previous work with biparental populations (Pereira et al., 2020). Work continues to improve the efficiency of the function by lowering the computational resources needed. Obj. 2d. Genomic Selection Potato breeding programs in New York, Minnesota, Maine, Oregaon, Texas and Wisconsin collected performance and genotype data on seedlings and variety checks to initiate genomic selection with the coordination of Jeff Endelman. Endelman has delivered training in the use of the StageWise genomic selection software suite to the collaborating potato breeders (see StageWise case studies (https://github.com/jendelman/StageWise). Obj. 2e. Sequence-based haplotyping Comparative Subsequence Sets Analysis (CoSSA). which uses set-theoretic operations on k-mers to identify haplotype-specific variants in heterozygous individuals is being tested to assess its utility to identify haplotypes for KASP marker development for a late blight R gene in potato. The beta version 0.5.1 of MCHap been successfully used to haplotype 800 tetraploid kiwi samples across ~10,000 loci (PFR). Objective 3. Train polyploid breeders and geneticists 3a. Develop written documentation of software tools The tutorials and reference manuals for the software have been updated and can be found at the following locations: GWASpoly and StageWise at https://github.com/jendelman. MAPpoly athttps://cran.r-project.org/web/packages/mappoly/mappoly.pdf, and vignette at https://rpubs.com/mmollin/tetra_mappoly_vignette QTLpoly athttps://raw.githubusercontent.com/guilherme-pereira/QTLpoly/master/docs/qtlpoly_0.2.1.pdf and vignette athttps://guilherme-pereira.github.io/QTLpoly/1-tutorial, and the tutorial athttps://guilherme-pereira.github.io/QTLpoly/2-tetraploid_example.html. polymapR at https://cran.r-project.org/web/packages/polymapR/index.html polyqtlR at https://cran.r-project.org/web/packages/polyqtlR/index.html 3b. Prepare and conduct annual short courses Online conference. January 12-15th, 2021. The attendance was superb with 353 people registering and a mean attendance over all four days of 250 participants. Sixteen presentations about the current computational tools for genotyping, map construction and QTL identification were followed by question and answer sessions. The recorded presentations were put on the Tools for Polyploids Youtube (https://www.polyploids.org/workshoppresentations) channel (1,137 views). Subsequent questions and trouble shooting was handled via the Tools for Polyploids SLACK channel (279 subscribers). Starting with a group of which ~90% were not familiar with the software presented, 90% were extremely or moderately satisfied with the presentations and about 50% of the participants were planning to use the software presented in the coming year. 3c. Develop a Tools for Polyploids Community Resource web page The website (polyploids.org) currently holds project information (history, participants, activities), software links, recorded presentations, recent publications, and news articles related to the project. We are working towards creating a space to house project members' data and serve as a one-stop-shop for each team to share their progress. Since its creation in January 2021 it has had 1,738 visitors. 75% of the visitors are younger than 44 and hail from North America (73%) and various countries in South America, Europe Asia, and Oceania. The most popular feature are the recorded presentations from the 2021 Tools for Polyploids Training Workshop (Tools for Polyploids). Associated social media include the Twitter @toolsforpolyploids account created in November of 2020. It currently has 139 followers and 1,107 profile visit per month.

Publications

  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Bourke, P.M., Voorrips, R.E., Hackett, C.A., van Geest, G., Willemsen, J.H., Arens, P., Smulders, M.J.M., Visser, R.G.F., Maliepaard, C. Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR. 2021, Bioinformatics (Advance access) https://doi.org/10.1093/bioinformatics/btab574
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Benson, C.W., Mao, Q., Huff, D.R., 2020. Global DNA methylation predicts epigenetic reprogramming and transgenerational plasticity in Poa annua L. Crop Sci. Special Issue: Int. Turfgrass Res. Conf. https://doi.org/10.1002/csc2.20337.
  • Type: Journal Articles Status: Submitted Year Published: 2021 Citation: Reis NS, Mollinari M, Oliveira GK, Pereira G da S, Vieira MLC. (2021) Meiosis in polyploids and implications for genetic mapping, a review (submitted)
  • Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Oloka MB, Pereira G da S, Amankwaah VA, Mollinari M, Pecota KV, Yada B, Olukolu BA, Zeng Z-B, Yencho CG. (2021) Discovery of a major QTL for root-knot nematode (Meloidogyne incognita) resistance in cultivated sweetpotato (Ipomoea batatas) Theor. Appl. Genet. https://doi.org/10.1007/s00122-021-03797-z\\
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Pereira G da S, Mollinari M, Qu X, Thill C, Zeng Z-B, Haynes K, Yencho CG. (2021) Quantitative trait locus mapping for common scab resistance in a tetraploid potato full-sib population. Plant Disease https://doi.org/10.1094/PDIS-10-20-2270-RE
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Pereira G da S, Mollinari M, Schumann MJ, Clough ME, Zeng Z-B, Yencho CG. (2021) The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv.' Atlantic-derived F1 population. Heredity - accepted (2020) https://doi.org/10.1038/s41437-021-00416-x
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Gemenet DC, Lindqvist-Kreuze H, Olukolu BA, De Boeck B, Pereira G da S, Mollinari M, Zeng Z-B, Yencho CG, Campos H. Sequencing depth and genotype quality: Accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops. (2021) Theor. Appl. Genet. https://doi.org/10.1007/s00122-020-03673-2
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: David Byrne. Tools for Polyploids  Introduction. Workshop on Tools for Genomics-Assisted Breeding in Polyploids. 1/13/2021. 96 views. https://www.youtube.com/watch?v=Srng3B-H2Nw
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Maria Caraza-Harter, Jeekin Lau, Gabriel Gesteira, Cristiane Taniguti, Filipe Matias. Computational Support. Workshop on Tools for Genomics-Assisted Breeding in Polyploids. 1/13/2021. 67 views. https://www.youtube.com/watch?v=I8-4u6aPc5w&t=23s
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Dorreen Main, Delany Baum. Community Website. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2021. 30 views. https://www.youtube.com/watch?v=YouphPF0lEo&t=19s
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Marcelo Mollinari. SuperMASSA. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2021. 45 views. https://www.youtube.com/watch?v=vw78gpg7Fsg
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Lindsay Clark. polyRAD. Workshop on Tools for Genomics-Assisted Breeding in Polyploids. 1/13/2021. 104 views. https://www.youtube.com/watch?v=vjwFBspNpRc&t=23s
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Roeland Voorrips. fitPoly. Workshop on Tools for Genomics-Assisted Breeding in Polyploids. 1/13/2021. 59 views. https://www.youtube.com/watch?v=-sP4quBOXpA&t=32s
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Roeland Voorrips. Overview of Genotype Calling. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2021. 66 views. https://www.youtube.com/watch?v=qLYpRaXAddQ&t=33s
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Marcelo Mollinari. Overview of Linkage Maps. Workshop on Tools for Genomics-Assisted Breeding in Polyploids. 1/14/2021. 74 views. https://www.youtube.com/watch?v=Y9QjpBTJxRQ&t=39s
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Peter Bourke. polymapR. Workshop on Tools for Genomics-Assisted Breeding in Polyploids.1/14/2021. 87 views. https://www.youtube.com/watch?v=UzKnfQAiy8w
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Marcelo Mollinari. MAPpoly. Workshop on Tools for Genomics-Assisted Breeding in Polyploids. 1/14/2021. 78 views. https://www.youtube.com/watch?v=NifLfBsQshQ&t=108s
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Jeffrey Endelman. PolyOrigin. Workshop on Tools for Genomics-Assisted Breeding in Polyploids. 1/14/2021. 70 views. https://www.youtube.com/watch?v=fr3FHdkGrKc
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Chris Maliepaard. Overview of QTL Analysis. Workshop on Tools for Genomics-Assisted Breeding in Polyploids. 1/15/2021. 52 views. https://www.youtube.com/watch?v=BNz31rK60HE
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Peter Bourke. polyqtlR. Workshop on Tools for Genomics-Assisted Breeding in Polyploids.1/15/2021. 46 views. https://www.youtube.com/watch?v=EBJfBxieS30
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Guilherme da Silva Pereira. QTLpoly. Workshop on Tools for Genomics-Assisted Breeding in Polyploids. 1/15/2021. 94 views. https://www.youtube.com/watch?v=B1i3TqYGzOw&t=82s
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Jeffrey Endelman. diaQTL. Workshop on Tools for Genomics-Assisted Breeding in Polyploids. 1/15/2021. 47 views. https://www.youtube.com/watch?v=iOxckvAWCnU&t=58s
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Jeffrey Endelman. GWASpoly Workshop on Tools for Genomics-Assisted Breeding in Polyploids. 1/15/2021. 122 views. https://www.youtube.com/watch?v=rsqWnUEuak8
  • Type: Other Status: Published Year Published: 2021 Citation: Huff, D.R. 2021. NIFA-USDA Impact Feature April 22, 2021. Golf Course Turfgrass Species 'Remembers' if it was Mowed, Develops Differently. https://nifa.usda.gov/impacts
  • Type: Theses/Dissertations Status: Published Year Published: 2021 Citation: Pandey, J. (2021). Molecular characterization, genome-wide association studies, and genomic selection of advanced potato clones from the Texas A&M potato breeding program. Ph.D. Dissertation. College Station, TX, July 9, 2021.
  • Type: Other Status: Published Year Published: 2021 Citation: Shannon, L. 2021 Potato Field Research in North Dakota and Minnesota, Valley Potato Grower, July/August issue - http://www.valleypotatogrower.com/flipbookJulyAug2021mag/flipbook/?page=12
  • Type: Other Status: Published Year Published: 2021 Citation: Huff, D.R., M. Sheltra, and C. Benson. 2021. Developing Tools for Modern Breeding in Genetically Complex Crops. Feature article. Pennsylvania Turfgrass 10(1):12-16.
  • Type: Other Status: Published Year Published: 2021 Citation: Huff, D.R., C. Benson, and M. Sheltra. 2021. Notable accomplishments from the Turfgrass Breeding and Genetics program over the past year. Pennsylvania Turfgrass 10(3):20.
  • Type: Other Status: Published Year Published: 2020 Citation: Mollinari, M. 2020. Genetic Mapping in Polyploids: from genotyping to haplotype reconstruction. 2020 Guest teaching in Statistical Genomics  Federal University of Goi�s, (on-line seminar) Goiania GO, Brazil
  • Type: Other Status: Published Year Published: 2021 Citation: .Riera-Lizarazu, O. 2021. Delving into Genomics-Assisted Breeding on Roses. Department of Horticultural Science, University of Minnesota (Virtual Seminar), St. Paul, MN, April 28
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Riera-Lizarazu, O., P. Klein, M. Yan, Z. Rawandoozi, E. Young, S. Kang, J. Lau, and D. Byrne. 2020. Towards Genomics-Assisted Breeding in Roses: Improving Resistance to Fungal Diseases and Flower Productivity. 10th Rosaceae Genomics Conference, December 9-11 and 16-18, Barcelona, Spain (Virtual). C0137
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Byrne, D. H. and O. Riera-Lizarazu. 2020. The status of genomics-assisted breeding of Rosaceae polyploid crops? 10th Rosaceae Genomics Conference, Virtual Conference via Barcelona, Spain, Dec. 10, 2020.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Riera-Lizarazu, O., P. Klein, and D. Byrne. 2020. Towards Genomics-Assisted Rose Breeding in Texas. 32nd Annual Texas Plant Protection Conference. December 8-10, Conroe, TX (Virtual)
  • Type: Theses/Dissertations Status: Published Year Published: 2021 Citation: Lau, Jeekin. 2021. Genetic analysis and QTL discovery in tetraploid garden roses: A study of disease and horticultural traits. Ph.D dissertation, Texas A&M University, May 2021.
  • Type: Other Status: Published Year Published: 2021 Citation: Shannon, L 2021. Sequencing, Math, and Avoidance: a few approaches to autotetraploid breeding, Laura Shannon, Plant Breeding Center UMN seminar series spring 2021 - https://www.youtube.com/watch?v=w0QL5titNv4&t=7s
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Endelman J. 2021. StageWise: Two-stage analysis of multi-environment trials for genomic selection. Annual Meeting of the Potato Association of America. July 27, 2021.
  • Type: Other Status: Published Year Published: 2020 Citation: Mollinari, M. 2020. Unraveling Polyploid Inheritance Using Ultra-Dense Multilocus Mapping. Computational Genetics Discussion Group  Roslin Institute - University of Edinburgh, (on-line seminar) Scotland, UK.
  • Type: Other Status: Published Year Published: 2020 Citation: Mollinari, M. 2020. Unraveling Polyploid Inheritance Using Ultra-Dense Multilocus Mapping. Genetics & Genomics Initiative Seminar  North Carolina State University, (on-line seminar) Raleigh, USA.\
  • Type: Other Status: Published Year Published: 2020 Citation: Mollinari, M. 2020. Genetic Mapping in Polyploids: from genotyping to haplotype reconstruction. GEN Webinar Series  Federal University of Lavras, (on-line seminar) Lavras MG, Brazil
  • Type: Other Status: Published Year Published: 2021 Citation: Byrne, D. H. 2021. Breeding garden roses for sustainable landscapes. Seminar presented to the Indian Horticultural Institute, Bamgalore, India. Hosted by Dr. Tejaswini, ornamental breeder. 73 attendees including 20 students and researchers from throughout India. June 16, 2021. Presented online via Google Talks.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Chizk, T.M., M. Worthington, R. Threlfall, H. Ashrafi, R. Aryal, and J.R. Clark. 2021. Genome wide association study (GWAS) in tetraploid blackberry for improvement of fruit morphological and shipping characteristics. Presentations from the Annual Conference of the American Society for Horticultural Science, August 5-9, Denver, CO. ASHS Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Johns, C.A., M. Worthington, T.M. Chizk, L.D. Nelson, R. Aryal, H. Ashrafi, J.R. Clark. 2021. Genetic control of internode length in blackberry. Presentations from the Annual Conference of the American Society for Horticultural Science, August 5-9, Denver, CO. ASHS Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Worthington, M. 2021. Integrating Applied Cultivar Development and Molecular Breeding in the Arkansas Fruit Breeding Program Presentations from the Annual Conference of the American Society for Horticultural Science, August 5-9, Denver, CO. ASHS Oral Presentation.
  • Type: Other Status: Published Year Published: 2020 Citation: Millar, T., S, Thomson, and J. McCallum. 2020 Signals of selection in polyploid Actinidia,. December 2020. Plant and Food Research, New Zealand virtual seminar. June 2021.
  • Type: Other Status: Published Year Published: 2021 Citation: Thomson, S., T. Millar, J. McCallum, A. Nath, E. Popowski, M. Knaebel, A. Grande, A. Catanach. 2021. Kiwifruit applied genetics, parallel genotyping programme. Plant and Food Research, New Zealand virtual seminar. June 2021.
  • Type: Other Status: Published Year Published: 2021 Citation: Thomson, S., T. Millar, J. McCallum, A. Nath, E. Popowski, M. Knaebel, A. Grande, A. Catanach.. 2021 Kiwifruit parallel genotyping platforms. presentation at the Plant and Food Research, New Zealand Kiwifruit Breeders meetings. March 2021
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Gill, H., J. Lau, L. Whiteley, Q. Fu, N. Anderson, D.H. Byrne, and O. Riera-Lizarazu. 2021. Identification of genetic determinants for a flower color transition phenotype in tetraploid roses. In: Abstracts of Presentations from the Annual Conference of the American Society for Horticultural Science, August 5-9, Denver, CO. Poster
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Fu, Q, N. Anderson, H. Gill, D.H. Byrne, and O. Riera-Lizarazu. 2021. Identification of rose germplasm with Rdr1 gene for black spot resistance. American Society for Horticultural Science, August 5-9, Denver, CO. Poster
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Godwin, C., M. Worthington, R. Aryal, H. Ashrafi, R. Threlfall, and J.R. Clark. 2021. Genetic control of acidity and sweetness in blackberry. American Society for Horticultural Science, August 5-9, Denver, CO. ASHS Poster Presentation.
  • Type: Websites Status: Published Year Published: 2021 Citation: Tools for Genomics-Assisted Breeding for Polyploids website at https://www.polyploids.org/
  • Type: Websites Status: Published Year Published: 2021 Citation: Tools for Genomics-Assisted Tools for Polyploids youTube channel at https://www.youtube.com/channel/UC2ZwtDkUDrFBlhIa9cD_DTQ