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
OTHER GRANTS
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. H.
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%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
2410 - Cross-commodity research--multiple crops;

Field Of Science
3020 - Education; 1081 - Breeding; 1080 - Genetics;
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 09/01/22 to 08/31/23

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 (31%, potato, sweetpotato, yam), fruit (31%, blackberry, blueberry, banana, coffee, kiwifruit, strawberry), turfgrass, forage, sugarcane (15%), ornamentals (12%. Rose. chrysanthemum), vegetables (7%, legumes, asparagus, mint, basil), cereal (3%) and a few forest tree species. Our audience is young (69% less than 40 years old) and with little experience (70%) with the software. About 43% are students or post-doctoral associates. 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 (24%), molecular genetics (24%) 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 (23%) and public (35%) programs. About half of our audience is from North America (38 states and Canada), The international participants were mainly from South America (6%), Europe (23%) and Africa (10%) but also Asia and Oceania. There was high participation from the International Research Station (CGIAR) scientists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The major training events for polyploid crop breeders, their support people (bioinformatists, computational geneticists, molecular geneticists, plant pathologists, entomologists), post-doctoral associates and graduate students were the 2022 pre-conference Computational Sessions (December, 3 sessions), the 2023 Tools for Polyploids Training Workshop (January) and the 2023 New Zealand Tools for Polyploids Workshop (March). The Computational Sessions were online sessions whereas the Workshops were hybrid events. This included presentations about updates of computational tools for genotyping, map construction and QTL identification, genomic selection, haplotyping from sequencing data and visualization tools. The attendance was superb with ~95 in-person and ~170 online participants. Eighteen training presentations, 10 user presentations and 9 digital posters were posted on the Tools for Polyploids (https://www.polyploids.org/workshoppresentations) Youtube channel. They have received 4,627 views (double as compared to last year) and subsequent questions and trouble shooting was handled by our computational team and software developers. In addition, various PIs, graduate students and post-doctoral researchers participated in professional meetings (Plant and Animal Genome, 11th Rosaceae Genomics Conference, American Society of Horticultural Sciences, International Rubus and Ribes Symposium, Advances in Genome Biology and Technology Conference, National Association of Plant Breeders, American Potato Society). 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 (12 journal articles, 4 journal articles in review, 1 non referred articles, 40 presentations). The major communication events for polyploid crop breeders, their support people (bioinformatists, computational geneticists, molecular geneticists, plant pathologists, entomologists), post-doctoral associates and graduate students were the 2022 pre-conference Computational Sessions (December, 3 sessions). the 2023 Tools for Polyploids Training Workshop (January) and the 2023 New Zealand Tools for Polyploids Workshop (March). The Computational Sessions were online sessions whereas the Workshops were hybrid events. This included presentations about updates of computational tools for genotyping, map construction and QTL identification, genomic selection, haplotyping from sequencing data and visualization tools. The attendance was superb with ~95 in-person and ~170 online participants. Eighteen training presentations, 10 user presentations and 9 digital posters were posted on the Tools for Polyploids (https://www.polyploids.org/workshoppresentations) Youtube channel. They have received 4,627 views.(double as compared to last year) and subsequent questions and trouble shooting was handled by our computational team and software developers. The Tools for Polyploids web site (https://www.polyploids.org/) serves as a repository of information about the project (4,227 visitors) as well as a project management tool. The most popular section is the recorded presentations. The Tools for Polyploid X account (@toolsforpolyploids, 402 followers) as well as periodic email alerts/surveys (~650 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 GWAS. COMA (convex optimization of mate allocation), a software for optimizing crossing plans to maximize the predicted merit of F1 progeny while limiting inbreeding is being finalized for release in Fall of 2023. Obj. 1b. Linkage/QTL analysis and genomic selection Reads2Map was expanded to handle polyploid species. VIEWpolyhad a new module added (Hidecan) and the interface was modified to improve the ease of use. Qploidy was developed to determine ploidy and detect aneuploidy using genomic data. MAPpoly and QTLpoly. Much has been accomplished in improving the performance of this software by increasing its speed, lowering the computer resources required, lowering the level of coding expertise to use and the designing the structure of MAPpoly 2.0 to allow the integration of user-friendly Shiny interface to increase its accessibility to a broader audience. MAPpoly and MAPoly2.0 have been enhanced by new Quality Assurance and Quality Control (QA/QC) procedures for the systematic screening of markers, individuals, and maps, by allowing the plotting of the changes made by the HMM chain as compared to raw data, by allowing the construction of maps based on data from single parents, with data from individuals derived from selfing, parents with different ploidy levels and the addition of a meiotic analysis algorithm. The output structure of MAPoly2.0 is pre-configured to seamlessly integrate with multi-parental populations, providing immediate compatibility with our in-development software, MAPpoly-MP. The increased speed of the remim2 and null_model2 runs in QTLpoly has enabled this software to run on personal computers. The multi-parental functionality for MAPpoly and QTLpoly is ready and will be soon released. polymapR has been updated to allow greater flexibility to generate linkage maps in triploid populations. polyqtlR has been updated to provide users with the option to test for both additive and dominance effects in the QTLscan function. A number of other minor updates including routing package maintenance updates were performed (e.g. to keep up with CRAN requirements). Obj. 1c. Polyploid haplotype assembly from short reads. The new versions of MChap released (https://github.com/PlantandFoodResearch/MCHap) streamline the user interface, provided updated documentation, a new tutorial and fixed a bug reported by a third-party user of the software which enables its application to larger genomic loci (several kilobases) using long-read sequencing. Currently, incorporating pedigree structure into genotype calling to improve the accuracy of autopolyploid genotype calls. This (unreleased) software function is expected to be publicly released in 2024. Objective 2. Validate computational tools. Obj. 2a. Allele dosage assignment. Obj. 2b. Genome-Wide Association. Blackberry. Developed KASP markers for primocane fruiting and thornlessness from results of a GWASpoly analysis which were used to eliminate floricane seedlings in the greenhouse before field planting. All selections are being phenotyped for floricane bloom date, intensity and timing of primocane-fruiting, berry size, BRIX, titratable acidity, and pH. These data will be used for GWAS analysis and training of genomic selection models in the next cycle Creeping bentgrass Phenotypic data was collected on the diversity panel genotypes grown in a space-plant nursery and the putting green trials. The following parameters were measured for both trials: diameter of vegetative spread, leaf color, leaf texture, shoot density. In addition, the following parameters were measured for the spaced-plant nursery site: flowering time (50% anthesis), flowering culm number, flowering culm height, flowering culm angle, inflorescence length, and estimated seed yield. DNA has been extracted from the creeping bentgrass diversity panel and DNA sequencing is to be completed this year. TAMU potato program used GWASpoly to identify genomic regions associated with free amino acids, minerals, dormancy, and heat stress-related traits. These findings will contribute to a better understanding of the genetic basis of important traits in potatoes. Obj. 2c. Linkage and QTL Analysis. The current versions and the latest development versions to analyze multi-parental populations of MAPpoly and QTLpoly have undergone extensive testing and validation in diploid (rose, pecan, Acacia crassiacarpa), tetraploid (rose, blueberry, alfalfa, kiwifruit) and hexaploidy (sweetpotato) species for ability to develop accurate maps, QTL analyses, to assess improved speed/resource needs, and to assess the effects of aneuploidy on linkage mapping and subsequent QTL analysis. Obj. 2d. Genomic Selection. The use of R package BGLR (flexible for modeling multiple random effects) for genomic prediction with environmental covariates and the use of R package randomForest for imputation of genetic marker data in autopoyploids for genomic selection was validated Six potato breeding programs (OR, ME, MN, TX, WI, NY) have phenotyped/genotyped 3 or more years of harvest and are using StageWise to utilize genomic selection models to guide them in the early generation selection of parents in their breeding programs. Obj. 2e. Sequence-based haplotyping. Software validation of MChap continued with a focus on the accuracy of genotype calls and the simulated data with respect to inbreeding coefficient and population homozygosity. Objective 3. Train polyploid breeders and geneticists 3a. Develop written documentation of software tools. Reads2Map, hidecan, MAPpoly, QTLpoly, and VIEWpoly have extensive documentation that is freely available to the polyploid community. Their official documentation is distributed alongside the packages, and comprehensive tutorials on building genetic maps using MAPpoly (https://rpubs.com/mmollin/tetra_mappoly_vignette) and performing multiple QTL analysis with QTLpoly (https://gabrielgesteira.github.io/QTLpoly/docs/1-tutorial) are also available. We presented our packages on different occasions including hands-on practices and expositive talks. All the materials, including slides, computer codes, and datasets, are publicly available under the Creative Commons License at https://github.com/mmollina/SCRI polymapR and polyqtkR vignettes have been updated. 3b. Prepare and conduct annual short courses. We held 3 pre-conference virtual software reviews (Dec. 2022), a 2-day hybrid training workshop (San Diego, Jan. 12-13, 2023) and a 1-day hybrid hands-on workshop (New Zealand, Mar. 17, 2023. The attendance was superb (~ 95 in person and ~170 remote participants). The presentations included computational tools for genotyping, map construction and QTL identification, genomic selection, haplotyping from sequencing data and visualization tools. These were complemented by user presentations (10 oral, 11 posters). 37 presentations were put on the Youtube (https://www.polyploids.org/) channel (4,627 video views. 286 subscribers). About 90% of the participants were extremely or moderately satisfied with the presentations. The participants that were planning to use the software in the coming year increased to about 64% reflecting an increased familiarity with the software presented and an increased use of genomics assisted breeding for parental, seedling and genomic selection. 3c. Develop a Tools for Polyploids Community Resource web page The website (polyploids.org) was enhanced by improving the contact form functionality allowing easy access to ask questions about workshops, website issues and other concerns. It had 4,227 visitors from North America (62%), South America (4%), Europe (16%) Asia (14%), and Oceania (2%). The X (Twitter) (@toolsforpolyploids) account currently has 402 followers and ~3,000 profile visits per month. Activity on website and X has doubled from last year with a more international audience.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jeffrey Endelman. 2023. Genetic marker imputation in polyploids. Tools for Polyploids Workshop 1/12/2023 San Diego State University, San Diego, CA.. https://youtu.be/QFv0G6szE7A
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jeekin Lau. 2023. Software comparison: QTL vs GS in a breeding context. Tools for Polyploids Workshop 1/13/2023. San Diego State University, San Diego, CA. https://www.youtube.com/watch?v=5xdfWHLRjVg
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Roeland Voorrips. 2023. Haplotype assignment in polyploids from SNP array data. Tools for Polyploids Workshop 1/13/2023. San Diego State University, San Diego, CA. https://youtu.be/z8bOhGPMpdo?si=pl_tjw1YJ0E06Ghq
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Tim Millar, Susan Thomson. 2023. Bayesian micro-haplotype assembly in autopolyploids. Tools for Polyploids Workshop 1/13/2023. San Diego State University, San Diego, CA. https://youtu.be/Udjftw3A3EQ
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jeffrey Endelman. 2023. Genomic selection with R package StageWise. Tools for Polyploids Workshop 1/13/2023. San Diego State University, San Diego, CA. https://youtu.be/upEZzKh7cHA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Marlee Labroo. 2023. Comparisons of hybrid breeding strategies in clonal polyploids. Tools for Polyploids Workshop 1/13/2023. San Diego State University, San Diego, CA. https://youtu.be/x_1zoShEL5U
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jeekin Lau. 2023. QTL Analysis and Mapping Software. Rosaceae Genomics Conference 3/17/2023. Tools for Polyploids One-Day Workshop, Nelson, NZ, https://youtu.be/7Bgmflh2ze4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Cris Taniguti and Olivia Angelin-Bonnet. 2023. VIEWpoly + HIDECAN: Usage demonstration of VIEWpoly updates and the integration with HIDECAN package. 1 hour course. Rosaceae Genomics Conference 3/17/2023. Tools for Polyploids One-Day Workshop, Nelson, NZ, https://youtu.be/uY_FVvtzoYc
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Cris Taniguti. 2023. Reads2Map: Usage demonstration in a High-Performance Computing environment. 1 hour course. Rosaceae Genomics Conference 3/17/2023. Tools for Polyploids One-Day Workshop, Nelson, NZ, https://youtu.be/rhqBllC50Ss
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Ran Wang. 2023. Genetic mapping and QTL analysis of the sex locus in tetraploid kiwiberry. Tools for Polyploids Workshop 1/12/2023. San Diego State University, San Diego, CA. https://youtu.be/sEcUo3P_60Q
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Tim Koorevaar. 2023. Construction of a strawberry breeding core collection to capture and exploit genetic variation. Tools for Polyploids Workshop 1/12/2023. San Diego State University, San Diego, CA. https://youtu.be/VSwMfWxj_qM
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Simon Fraher. 2023. Discovery of major QTL conferring resistance to root-knot nematodes in sweetpotato populations. Tools for Polyploids Workshop 1/12/2023. San Diego State University, San Diego, CA. https://youtu.be/mAxJ9aUlAkQ
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Lillian Hislop. 2023. Tools and Techniques for GWAS and Genomic Prediction in Blueberries with Breeding Insight. Tools for Polyploids Workshop 1/13/2023. San Diego State University, San Diego, CA. https://youtu.be/xTN6ofEHBXM
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Mateus Mondin. 2023. Chromosome synteny by comparative genome analysis revisit polyploid contribution to legume evolution. Tools for Polyploids Workshop 1/13/2023. San Diego State University, San Diego, CA. https://youtu.be/U2ZzkC5LgWk
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Hamid Ashrafi. 2023. Genome-wide association mapping of fruit quality-related traits in a diversity panel of blueberries. Tools for Polyploids Workshop 1/13/2023. San Diego State University, San Diego, CA. https://youtu.be/0emr_uSQwBQ
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Olivia Angelin-Bonnet. 2023. The hidecan package: visual integration of GWAS and differential expression results. Tools for Polyploids Workshop 1/13/2023. San Diego State University, San Diego, CA. https://youtu.be/FoOEV_bjP0w
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: John McCallum. 2023. Building Polyploid Statistical Genetics Workflows in R with the Targets and Future Packages. Tools for Polyploids Workshop 1/13/2023. San Diego State University, San Diego, CA. https://youtu.be/UkhQdm_HqTE
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Guilherme da Silva Pereira. 2023. Development and validation of KASP markers for marker-assisted selection in autohexaploid sweetpotato breeding. Tools for Polyploids Workshop 1/12/2023. San Diego State University, San Diego, CA. https://youtu.be/K9K6a_UzlXY?si=dfHevunDlbp_jf5Z
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Paterne Agre. 2023. Efforts towards yam breeding modernization using genomic tools. Tools for Polyploids Workshop 1/12/2023. San Diego State University, San Diego, CA. https://youtu.be/VF6MH8qkU5A?si=y1Z2LB-xqwABQDmD
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Ao Jiao. 2023. Exploration of the Genetic Background of Potato Tuber Dormancy in Response to Cold Storage. Tools for Polyploids Workshop, San Diego, CA. Poster. January 12-13, 2023. https://rb.gy/3uhzk
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Heeduk Oh. Identification of QTLs related to fruit texture at harvest and postharvest in blueberry. Tools for Polyploids Workshop, San Diego, CA. Poster. January 12-13, 2023. https://rb.gy/mnmj9
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jeewan Pandey. Genome-wide association studies of mineral content in potato tubers and identification of clones with high genomic-estimated breeding value. Tools for Polyploids Workshop, San Diego, CA. Poster. January 12-13, 2023. https://rb.gy/661ez
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Tim Millar. 2023. Haplotyping from sequence data. Rosaceae Genomics Conference 3/17/2023. Tools for Polyploids One-Day Workshop, Nelson, NZ, https://youtu.be/j5pADdrK5NY
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Beatriz Tome Gouveia.2023. Turfgrass breeding dashboard for a multi-state collaborative project. Tools for Polyploids Workshop Poster Session 1/12/23. https://rb.gy/l9lxs
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Lushan Ghimire. 2023. Identification of Genomic Regions Associated with Bacterial Wilt Resistance in Southern Highbush Blueberries Using Genome-Wide Association Study. Tools for Polyploids Workshop, San Diego, CA. Poster. January 12-13, 2023. https://shorturl.at/koAFK
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Paul Adunola.2023. Integration of Genetic and Data-Driven Methods for Optimizing Genomic Prediction in Autotetraploid Blueberries. Tools for Polyploids Workshop, San Diego, CA. Poster. January 12-13, 2023. https://shorturl.at/cqyFY
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Sanjeev Gautam. 2023. Investigating the genetic background of potato tuber defects caused by heat stress. Tools for Polyploids Workshop, San Diego, CA. Poster. January 12-13, 2023. https://shorturl.at/btxFS
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Hochhaus, T., Lau, J., Taniguti, C.H., Young, E., Byrne, D.H., Riera-Lizarazu, O. 2023. Meta-analysis of rose rosette disease resistance quantitative loci and search for candidate genes. Tools for Polyploids Workshop, San Diego, CA. Poster. January 12-13, 2023. https://shorturl.at/acpI6
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Gill H., Lau J., Whiteley L., Byrne D., and Riera-Lizarazu O. 2023. Identification of Quantitative Trait Loci Controlling Shoot Length, Internode Length, and Number of Internodes in Tetraploid Roses. Tools for Polyploids Workshop, San Diego, CA. Poster. January 12-13, 2023. https://rb.gy/fq4ch
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Sathya Jali. 2023. Elimination of Pungency in Allotetraploid Brassica juncea through Gene Editing of the Multicopy Myrosinase Gene Family. Tools for Polyploids Workshop Poster Session 1/13/23.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Soukeye Conde. 2023. Development and characterization of a unique genetic resource for allele mining and peanut improvement in Africa. Tools for Polyploids Workshop Poster Session 1/13/23.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Mollinari M., Theoretical and Practical Aspects of Linkage Analysis in Diploids and Polyploids. Presented to USDA/Breeding Insight group in Ithaca, NY. August 28-31, 2023.
  • Type: Websites Status: Published Year Published: 2023 Citation: Tools for Polyploids. https://www.polyploids.org/
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Pandey, P., D.C. Scheuring, J.W. Koym, J.B. Endelman, and M.I. Vales. 2023. Genomic selection and genome-wide association studies in tetraploid chipping potatoes. The Plant Genome. https://doi.org/10.1002/tpg2.20297
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Chizk TM, Clark JR, Johns C, Nelson L, Ashrafi H, Aryal R and Worthington ML (2023) Genome-wide association identifies key loci controlling blackberry postharvest quality. Front. Plant Sci. 14:1182790. doi: 10.3389/fpls.2023.1182790
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Robbins, Matthew D., Scott E. Warnke, P. Jeff Maughan, David R. Huff, Christopher W. Benson, Eric N. Jellen, Paul G. Johnson, and B. Shaun Bushman. Chromosome-Scale Genome Assembly and Annotation of Allotetraploid Annual Bluegrass (Poa annua L.), Genome Biology and Evolution, Volume 15, Issue 1, January 2023, evac180, https://doi.org/10.1093/gbe/evac180
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Endelman JB (2023) Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection. Theoretical & Applied Genetics 136:65. doi:10.1007/s00122-023-04298-x
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Benson CW, Sheltra MR, Maughan PJ, Jellen EN, Robbins MD, Bushman BS, Patterson EL, Hall ND, and Huff DR. Homoeologous evolution of the allotetraploid genome of Poa annua L. BMC Genomics. 2023 Jun 26, Volume 24(1):350. https://doi.org/10.1186/s12864-023-09456-5.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Lau, J., Gill, H., Taniguti, C. H., Young, E. L., Klein, P. E., Byrne, D. H., et al. 2023. QTL discovery for resistance to black spot and cercospora leaf spot, and defoliation in two interconnected F1 bi-parental tetraploid garden rose populations. Frontiers in Plant Science 14. Available at: https://www.frontiersin.org/articles/10.3389/fpls.2023.1209445
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Hochhaus, T., Lau, J., Taniguti, C. H., Young, E. L., Byrne, D. H., & Riera-Lizarazu, O. 2023. Meta-Analysis of Rose Rosette Disease-Resistant Quantitative Trait Loci and a Search for Candidate Genes. Pathogens, 12(4), 575. https://doi.org/10.3390/pathogens12040575
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Th�r�se Navarro, Alejandro; Bourke, Peter M.; van de Weg, Eric; Clot, Corentin R.; Arens, Paul; Finkers, Richard; Maliepaard, Chris (2023) Smooth Descent : A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors. Frontiers in Genetics, vol. 14, https://doi.org/10.3389/fgene.2023.1049988
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Wang, Ran; Xing, Siyuan; Bourke, Peter M.; Qi, Xiuquan; Lin, Miaomiao; Esselink, Danny; Arens, Paul; Voorrips, Roeland E.; Visser, Richard G.F.; Sun, Leiming; Zhong, Yunpeng; Gu, Hong; Li, Yukuo; Li, Sikai; Maliepaard, Chris; Fang, Jinbao (2022) Development of a 135K SNP genotyping array for Actinidia arguta and its applications for genetic mapping and QTL analysis in kiwifruit. Plant Biotechnology Journal, 21(2), p.369-380. https://doi.org/10.1111/pbi.13958
  • Type: Journal Articles Status: Under Review Year Published: 2023 Citation: Angelin-Bonnet, O., M. Vignes, P.J. Biggs, S. Baldwin and S. Thomson. 2023. Visual integration of GWAS and differential expression results with the hidecan R package. bioRxiv preprint. Doi: https://doi.org/10.1101/2023.03.30.535015 this version posted April 3, 2023.
  • Type: Journal Articles Status: Submitted Year Published: 2023 Citation: Pandey, J., D. Thompson, M. Joshi, D.C. Scheuring, J.W. Koym, V. Joshi, and M.I. Vales. Genetic architecture of tuber-bound free amino acids in potato and effect of growing environment on the amino acid content. Scientific Reports (in press)
  • Type: Journal Articles Status: Under Review Year Published: 2023 Citation: Taniguti, C. H., Taniguti, L. M.; Amadeu, R. R.; Lau, J.; de Siqueira Gesteira, G.; Oliveira, T. D. P.; Ferreira, G. C.; Pereira, G. D. S.; Byrne, D.; Mollinari, M.; Riera-Lizarazu, O.; Garcia, A. A. F. 2023. Developing best practices for genotyping-by-sequencing analysis using linkage maps as benchmarks. GigaScience (In Press). doi: 10.1101/2022.11.24.517847
  • Type: Journal Articles Status: Under Review Year Published: 2023 Citation: Zhao, D., Mejia-Guerra, K., Mollinari, M., Samac, D., Irish, B., Beil, C., & Sheehan, M. (Under review). A public mid-density genotyping platform for Alfalfa (Medicago sativa L.). Submitted to Genetic Resources.
  • Type: Journal Articles Status: Submitted Year Published: 2023 Citation: Fraher, S.; Schwarz, T.; Heim, C.; Gesteira, G.S.; Mollinari, M.; Pereira, G.S.; Zeng, Z-B.; Brown-Guedira, G.; Gorny, A.; Yencho, G.C. Discovery of a major QTL for resistance to the guava root-knot nematode (Meloidogyne enterolobii) in Tanzania an African landrace sweetpotato (Ipomoea batatas). Manuscript submitted to Theoretical and Applied Genetics.
  • Type: Theses/Dissertations Status: Published Year Published: 2023 Citation: Millar, T. R. (2023). Signals of selection within a mixed-ploidy Actinidia chinensis pedigree (Thesis, Doctor of Philosophy). University of Otago. Retrieved from http://hdl.handle.net/10523/15977
  • Type: Theses/Dissertations Status: Published Year Published: 2023 Citation: Chizk, T.M. 2023. Multiomic explorations of fruit texture and postharvest quality in blackberry and muscadine grape. Doctoral dissertation. University of Arkansas, Fayetteville.
  • Type: Theses/Dissertations Status: Published Year Published: 2023 Citation: Alejandro Therese Navarro. 2023. Harvesting data from polyploid plants: developing genetic analysis tools in strawberry. Doctoral dissertation. Wageningen University, the Netherlands, June 28, 2023.
  • Type: Other Status: Published Year Published: 2023 Citation: Huff, D.R. 2023. A Poa annua Conspiracy: Nation-wide Golf Course Evaluation Trials. Pennsylvania Turfgrass 12 (3):8-13. Cover Story.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Wu, S., Sun, H., Kitavi, M., Hamilton, J. P., Gesteira, G. S., Mollinari, M., Zeng, Z. B. et al. (2023). Advances in the development of chromosome-scale haplotype-resolved genome assemblies of hexaploid sweetpotatoes. Plant and Animal Genome Conference XXX. San Diego, CA. January 13-18, 2023. Poster.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Gesteira, G.S., Mollinari, M., Pereira, G., Olukolu, B., Oloka, B., Yencho, C., et al. (2023). Genetic mapping in interconnected hexaploid sweetpotato populations. Plant and Animal Genome Conference XXX. San Diego, CA. January 13-18, 2023. Poster.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Lau, J., C. Taniguti, P. E. Klein, D. H. Byrne, and O. Riera-Lizarazu. 2023. Linkage mapping and QTL analysis in autotetraploid rose. Plant and Animal Genome Conference XXX. San Diego, CA. January 13-18, 2023. Oral.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Taniguti, C. H., Taniguti, L. M.; Amadeu, R. R.; Lau, J.; De Siqueira Gesteira, G.; Oliveira, T. D. P.; Ferreira, G. C.; Pereira, G. D. S.; Byrne, D.; Mollinari, M.; Riera-Lizarazu, O.; Garcia, A. A. F. 2023. Selecting best bioinformatic pipeline for evaluating diploid and auto-tetraploid garden roses genotyping-by-sequence data. Plant and Animal Genome Conference XXX. San Diego, CA. January 13-18, 2023. Oral.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jiao, A., S. Gautam, J. Pandey, D.C. Scheuring, J.W. Koym, M.I. Vales. 2023. Genome-wide association studies of potato tuber dormancy in response to cold storage. Plant and Animal Genome Conference XXX. San Diego, CA. January 13-18, 2023. Poster.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Pandey, J., S. Gautam, D.C. Scheuring, J.W. Koym, and M.I. Vales. 2023. Genomic regions associated with mineral content in potato tubers and identification of clones with high genomic-estimated breeding value. Plant and Animal Genome Conference XXX. San Diego, CA. January 13-18, 2023. Poster.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Hochhaus, T., Lau, J., Taniguti, C.H., Young, E., Byrne, D.H., Riera-Lizarazu, O. 2023. Meta-analysis of rose rosette disease resistance quantitative loci and search for candidate genes. Plant and Animal Genome Conference XXX. San Diego, CA. January 13-18, 2023. Poster.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Gill H., Lau J., Whiteley L., Byrne D., and Riera-Lizarazu O. Identification of Quantitative Trait Loci Controlling Shoot Length, Internode Length, and Number of Internodes in Tetraploid Roses Plant and Animal Genome XXX Conference. January 13-18, 2023.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Gautam, S., J. Pandey, D.C. Scheuring, J.W. Koym, and M.I. Vales. 2023. Uncovering genomic regions associated with potato tuber defects under heat stress and identification of heat-tolerant clones. Plant and Animal Genome Conference XXX. San Diego, CA. January 13-18, 2023. Poster.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Navarro, A.T. 2023. Fragrance Mystery: A Volatile QTL Study Highlights the Complex Genetic Regulation of Strawberry Aroma. Plant and Animal Genome Conference XXX. San Diego, CA. January 13-18, 2023. Oral.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Koorevaar, T., J. Willemsen, P. Arens, C. Maliepaard, and R. Visser. 2023. Construction of a strawberry breeding core collection to capture and exploit genetic variation Plant and Animal Genome Conference XXX. San Diego, CA. January 13-18, 2023. Oral.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Lau, J., H. Gill, C.H. Taniguti, E. Young, P.E. Klein, D.H. Byrne, O. Riera-Lizarazu. 2023. Black Spot and Cercospora Leaf Spot Resistance in Auto-Tetraploid Garden Roses. 11th Rosaceae Genomics Conference, Nelson, New Zealand. March 13-16, 2023
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Hochhaus, T., Lau, J., Taniguti, C.H., Young, E., Byrne, D.H., Riera-Lizarazu, O. 2023. Meta-analysis and identification of candidate genes for rose rosette disease resistance quantitative loci. Poster. 11th Rosaceae Genomics Conference, Nelson, New Zealand. March 13-16, 2023
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Taniguti, C. J. Lau, A. Franco Garcia, M. Mollinari, D.H. Byren, O. Riera-Lizarazu. 2023. The challenges while building linkage maps for diploid and polyploid species with genotyping by sequencing markers. Poster. 11th Rosaceae Genomics Conference, Nelson, New Zealand. March 13-16, 2023
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Gill H., Lau J., Zhen S., Byrne D., and Riera-Lizarazu O. Genetic Determinants and Pigment Analysis of Autotetraploid Roses Exhibiting the Flower Color Transition Phenotype. Poster. 11th Rosaceae Genomics Conference, Nelson, New Zealand. March 13-16, 2023.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Rawadoozi, Z., E.L. Young, S. Kang, M. Yan, S. Noyan, Q. Fu. T. Hochhaus, M.Y. Rawandoozi, P. Klein, D.H. Byrne, and O. Rira-Lizarazu. Pedigree-based analysis in multi-parental diploid populations reveals QTLs for fungal diseases. Poster. 11th Rosaceae Genomics Conference, Nelson, New Zealand. March 13-16, 2023
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Byrne, D.H., O. Riera-Lizarazu and J. Endelman. 2023. Tools for genomics-assisted breeding in polyploids SCRI project. Oral presentation. 11th Rosaceae Genomics Conference, Nelson, New Zealand. March 13-16, 2023
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Riera-Lizarazu, O. and D.H. Byrne. 2023. Towards genomics-aided rose breeding in Texas, USA. Oral presentation. 11th Rosaceae Genomics Conference, Nelson, New Zealand. March 13-16, 2023
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Hochhaus, T., Lau, J., Taniguti, C.H., Young, E., Byrne, D.H., Riera-Lizarazu, O. 2023. Integrated Quantitative Trait Loci Mapping for Rose Rosette Disease Resistance and a Search for Candidate Genes in Rose (Rosa spp.). American Society for Horticultural Sciences Conference, Orlando, FL. Oral presentation. August 3, 2023.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Gill H., Lau J., Zhen S., Byrne D., and Riera-Lizarazu O. QTL Mapping and Pigment Analysis of Flower Color Transition Phenotype in Autotetraploid Roses American Society of Horticultural Science, Orlando, FL. July 30- August 04, 2023.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Vaughn I, Silva A, Johns C, Nelson L, Worthington M. 2023. Validation of a diagnostic marker for primocane-fruiting in blackberry. American Society for Horticultural Science Annual Conference, Orlando, FL. Oral Presentation. August 1, 2023.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jiao, A., S. Gautam, J. Pandey, D.C. Scheuring, J.W. Koym, M.I. Vales. 2023. Genome-wide association studies and genomic prediction for potato tuber dormancy. Potato Association of America 107th Annual Meeting. July 23-27, 2023. Prince Edward Island, Canada. Oral presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Vales, M.I., S. Gautam, A.M. Ifeduba, A. Jiao, J. Pandey, S. Toinga-Villafuerte, D.C. Scheuring, and J.W. Koym. 2023. Development of heat-tolerant potato varieties by the Texas A&M Potato Breeding Program. Potato Association of America 107th Annual Meeting. July 23-27, 2023. Prince Edward Island, Canada. Oral presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Yusuf M., Miller M., Stefaniak T., and Shannon L. Genomic selection for quality traits using image based tools in potato. Potato Association of America Meeting July 2023, Charlottetown, PEI, Canada
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: K. Brown-Donovan (presenter), M. H. M. L. Andrade, E. H. Tan, G. A. Porter 2023. Initial Application of Genomic Selection in the University of Maine Potato Program, Potato Association of America 107th Annual Meeting, Charlottetown, PEI, Canada
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Johns C, M Worthington, Chizk TM, Silva A, Nelson L, Hardigan M, Thompson E, Clark J. 2023. Association analysis and marker development for prickle-free blackberry canes. XIII International Rubus and Ribes Symposium. Poster Presentation. July 20, 2023. Portland Oregon
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Nelson L, Silva A, Worthington M. 2023. Implementation of marker-assisted selection in the University of Arkansas blackberry breeding program. XIII International Rubus and Ribes Symposium. Poster Presentation. July 20, 2023. Portland Oregon
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Worthington M, Chizk TM, Silva A, Johns C, Godwin C, Nelson L, Clark J. 2023. Advances in molecular breeding of blackberries in the Arkansas Fruit Breeding Program. XIII International Rubus and Ribes Symposium. Oral Presentation. July 20, 2023. Portland Oregon
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Worthington M, Chizk TM, Wang YJ, Clark JR. 2023. The potential role of polygalacturonase and pectin methylesterase in blackberry fruit softening patterns. XIII International Rubus and Ribes Symposium. Poster Presentation. July 20, 2023. Portland Oregon
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Taniguti, C. H.; Gesteira, G. S. ; Lau, J. ; Pereira, G. S. ; Byrne, D. ; Zeng, Z. B. ; Riera-Lizarazu O. & Mollinari, M. 2023. VIEWpoly: An interactive tool for mining results from genetic mapping analysis in autopolyploid species. Poster. Advances in Genome Biology and Technology Conference, San Antonio, Texas, April.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Endelman JB, Vales I, Shannon L, Porter G, De Jong W, Sathuvalli S (2023) SCRI Project: Genomics-Assisted Breeding in Polyploids. Potato EXPO, January 4-5, 2023.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Enriquez JOS, Endelman JB (2023) Genomic prediction with environmental covariates in potato. Annual Meeting of the National Association of Plant Breeders, July 17-19, 2023.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Huff, D.R. 2023. Prototype Testing of Commercial Poa annua Seed for Greens & Fairways. 2023 Northeastern Pennsylvania Golf, Lawn, Landscape, and Sports Turf Conference. Wilkes-Barre, PA. January 26, 2023.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Huff, D.R. 2023. Breeding stress tolerant varieties of bentgrass and Poa annua that require less pesticides & fewer inputs. 2023 Western Pennsylvania Golf, Lawn, Landscape, and Sports Turf Conference. Washington, PA. February 21-22, 2023.
  • Type: Other Status: Published Year Published: 2023 Citation: Huff, D.R. Jan 2023. Commercial Poa annua Seed for Greens & Fairways. Fresh Cut Grass. A 1-hour Podcast from Penn State Extension. Hosts: Jeff Fowler and Tanner Delvalle. (https://extension.psu.edu/fresh-cut-grass), Season 3, Episode 8. (https://feeds.buzzsprout.com/1715936.rss)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Cris Taniguti, Jeekin Lau, Gabriel Gesteira, Maria Caraza-Harter. 2022. Genotype Calling Support Session. Tools for Polyploids Computational Support Session. 12/6/2022. https://www.youtube.com/watch?v=k83h1MHQBBQ
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jeekin Lau, Cris Taniguti, Gabriel Gesteira, Maria Caraza-Harter. 2022. Mapping Analysis Support Session. Tools for Polyploids Computational Support Session. 12/13/2022.. https://youtu.be/sMOWV7lwmvM
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Gabriel Gesteira, Maria Caraza-Harter, Jeekin Lau, Cris Taniguti. 2022. QTL Analysis Support Session. Tools for Polyploids Computational Support Session. 12/20/2022. https://youtu.be/03ZVJW_sUQY
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: David Byrne. 2023. Workshop Introduction. Tools for Polyploids Workshop 1/12/2023. San Diego State University, San Diego, CA. https://youtu.be/ERjHuTR_pa0
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Delany Baum, Dorrie Main. 2023. Community Resource Website. Tools for Polyploids Workshop 1/12/2023. San Diego State University, San Diego, CA. https://youtu.be/enNUiie0uYg
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Taniguti, C. H., Taniguti, L. M.; Amadeu, R. R.; Lau, J.; De Siqueira Gesteira, G.; Oliveira, T. D. P.; Ferreira, G. C.; Pereira, G. D. S.; Byrne, D.; Mollinari, M.; Riera-Lizarazu, O.; Garcia, A. A. F. 2023. Reads2map: Practical and Reproducible Workflows to Build Polyploid Linkage Maps from Sequencing Data. Tools for Polyploids Workshop 1/12/2023. San Diego State University, San Diego, CA. https://youtu.be/4r6uQ-YzIMg
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Giorgio Tumino. 2023. QTL analysis for multiparental polyploid populations. Tools for Polyploids Workshop 1/12/2023. San Diego State University, San Diego, CA. https://youtu.be/X7P5FWKC0aQ
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Marcelo Mollinari, Gabriel Gesteira, Guilherme Pereira. 2023. MAPpoly and QTLpoly: interconnected sweetpotato families. Tools for Polyploids Workshop 1/12/2023. San Diego State University, San Diego, CA. https://youtu.be/s42oZucXgLA


Progress 09/01/21 to 08/31/22

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, sweet potato, yam), fruit (30%, blackberry, blueberry, banana, coffee, kiwifruit, strawberry), turfgrass, forage, sugarcane (16%), ornamentals (12%. Rose. chrysanthemum), vegetables (10%, legumes, asparagus, mint, basil), cereal (4%) and a few forest tree species. Our audience is young (68% less than 40 years old) and with little experience (90%) with the software. About 45% are students or post-doctoral associates. 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 (20%) and public (35%) programs. About half of our audience is from North America (38 states and Canada), The international participants were mainly from South America, Europe and Africa but also Asia and Oceania. There was high participation from the 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 2022 Tools for Polyploids Training Workshop. This included presentations about updates of computational tools for genotyping, map construction and QTL identification and to introduce software packages about genomic selection, haplotyping from sequencing data and visualization tools. The attendance was superb with 283 people registering and an attendance- of 250 participants. The 14 training presentations, 9 user presentations and 16 digital posters were posted on the Tools for Polyploids Youtube (https://www.polyploids.org/2022recordedpresentations) channel. They have received 2,451views. and subsequent questions and trouble shooting was handled via the Tools for Polyploids SLACK channel (310 subscribers). In addition, 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, 2 non referred articles, 30 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 2022 Tools for Polyploids Training Workshop which was done as an online conference. This included presentations about updates of computational tools for genotyping, map construction and QTL identification and to introduce software packages about genomic selection, haplotyping from sequencing data and visualization tools. The attendance was superb with 283 people registering and a mean attendance of 250 participants. Fourteen training presentations, 9 user presentations and 15 digital posters were posted on the Tools for Polyploids Youtube (https://www.polyploids.org/workshoppresentations) channel. They have received 2,451 views. and subsequent questions and trouble shooting was handled via the Tools for Polyploids SLACK channel (310 subscribers). The Tools for Polyploids web site (https://www.polyploids.org/) serves as a repository of information about the project (2,669 visitors) 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 (@toolsforpolyploids, 274 followers) as well as periodic email alerts/surveys (~450 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 GWAS. GWASpoly, had a Variant Call Format (VCF) input format incorporated to facilitate the use of GBS data. Obj. 1b. Linkage/QTL analysis and genomic selection PolyOrigin uses interconnected multi-parental tetraploid populations to connect statistical alleles from QTL models with biological alleles based on DNA sequencing and reconstruct progeny haplotypes. Its utility was demonstrated on a 3-member diallel in tetraploid potato. This ability represents a new milestone in genomics-assisted breeding for tetraploid species. MAPpoly v2.0 improved to analyze mixed ploidy levels and allelic information on single-generation interconnected populations, to avoid memory overflow in personal computers and to include a within software tutorial for ease of use. Removed third package dependencies from QTLpoly and submitted it to CRAN to facilitate installation. polymapR has improved functionality for cross-ploidy populations to analyze tetraploid x diploid crosses in ornamental, banana, and watermelon breeding. VIEWpoly provides a user-friendly and interactive interface to evaluate results from mappoly, polymapR, QTLpoly, polyqtlR, and diaQTL packages and integrate these with genomic information. PedigreeSimR, created to make the PedigreeSim software accessible from an R environment (available in SCRI project website. StageWise, a user-friendly software that can handle the complexity of the multi-year, multi-location, multi-trait datasets used in genomic selection programs was developed. The software comes with sample potato breeding datasets and tutorials to illustrate its features. Obj. 1c. Polyploid haplotype assembly from short reads. MCHap was designed to assemble micro-haplotypes in polyploids using Markov-chain Monte Carlo simulation is now publicly available. The source code for MCHap is available at https://github.com/PlantandFoodResearch/MCHap. Objective 2. Validate computational tools. Obj. 2a. Allele dosage assignment. Reads2Map a software for the comparison of dosage call software (GATK, freebayes, updog, polyRAD, and SuperMASSA) using linkage map quality as the benchmark developed for diploid genotyping-by-sequencing data is being updated to support polyploid data. Obj. 2b. Genome-Wide Association. In blackberry GWAS was performed for a wide range of fruit and plant traits measured in the panel using GWASpoly. QTL were identified and HRM marker assays suitable for MAS for fruit texture, titratable acidity, primocane height and thornlessness are being developed. TAMU potato breeding program used GWASpoly to identify QTL associated with tuber morphological traits, tuber defects and tuber dormancy. Some of the QTLs confirmed prior studies, whereas others were discovered for the first time. Nine QTLs were identified for tuber dormancy, including three on chromosome 1 and additional ones on chromosomes 3, 4, 5, 6, 9, and 12. The creeping bentgrass diversity panel (n=266) has been phenotyped for diameter of vegetative traits on both the spaced plant and putting green trials and for flowering/seed traits in the replicated spaced plant trial in 2022. The accessions have been extracted for their DNA and will soon be sequenced for genotyping. GWASpoly will be used this coming year to identify QTL and marker associations with the phenotyped traits. Obj. 2c. Linkage and QTL Analysis. polymapR, MAPpoly, polyqtlR, QTLpoly, GWASpoly, polyOrigin, diaQTL to identify and haplotype QTL for resistance to black spot (2), cercospora leaf spot (3), and rose rosette disease (2) in tetraploid rose. The haplotyped progeny enabled the selection of genotypes with resistance QTLs for multiple diseases which will be used in a breeding program to stack multiple disease resistance genes in rose to develop a disease resistant sustainable rose cultivar. polymapR and MAPpoly were shown to be efficient approaches to genetic maps for diploid rose populations. The current versions of MAPpoly and QTLpoly for bi-parental families were extensively tested in tetraploid and hexaploid species. The MAPpoly multi-parental algorithm was used to construct genetic maps in a 6x sweetpotato and a 4x alfalfa with excellent results. The sweetpotato populations were succesfully analyzed with to detect significant QTL on chromosomes 3 and 12 for beta-carotene content as previously seen in QTL studies based on biparental populations. Obj. 2d. Genomic Selection. The StageWise package(https://github.com/jendelman/StageWise) was designed to facilitate the use of genome-wide markers for genomic selection in autotetraploid (4x) species. Six potato breeding programs (OR, ME, TX, NY, MN, and WI) all have phenotyped/genotyped two or more years of harvest and are beginning to utilize the StageWise package to build genomic selection models. Obj. 2e. Sequence-based haplotyping. Validation work for MCHap has focussed on three areas: 1) Accuracy of the Dirichlet-Multinomial as a prior distribution for autopolyploid genotypes. 2) MCMC-simulations conform to their expected statistical distribution. 3) Accuracy of genotype calling using simulated data. In all cases, the validation experiments confirmed the accuracy the approaches used. Additional validation work is ongoing with he collaboration of the teams at Texas A&M University and North Carolina State University. 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://gabrielgesteira.github.io/QTLpoly/docs/1-tutorial. polymapR at https://cran.r-project.org/web/packages/polymapR/index.html polyqtlR at https://cran.r-project.org/web/packages/polyqtlR/index.html VIEWpoly at https://CRAN.R-project.org/package=viewpoly. 3b. Prepare and conduct annual short courses. Online conference. January 13-14, 2022. The attendance was superb with an attendance of 250 participants. The presentations included updates of computational tools for genotyping, map construction and QTL identification and introductions of software packages on genomic selection, haplotyping from sequencing data and visualization tools. These were complemented by user presentations (9 oral, 15 digital posters). 38 presentations were put on the Youtube (https://www.polyploids.org/) channel (2,451views). Subsequent questions and trouble shooting was handled via the Tools for Polyploids SLACK channel (310 subscribers). Over 90% of the participants were extremely or moderately satisfied with the presentations. The participants that were planning to use the software presented in the coming year increased to about 60% reflecting an increased familiarity with the software presented and an increased use of genomics assisted breeding for parental, seedling and genomic selection. 3c. Develop a Tools for Polyploids Community Resource web page The website (polyploids.org) was improved by adding an index to find pertinent videos, making the pages smartphone accessible, creating an acknowledgement page and enhancing the homepage functionality and visual appeal. It had 2,669 visitors. 75% of the visitors are younger than 44. They hail from North America (71%), South America, Europe Asia, and Oceania. The most popular feature are the recorded presentations from the Tools for Polyploids Training Workshops. The Twitter (@toolsforpolyploids) account currently has 274 followers and 1,798 profile visits per month.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Dorrie Maine, Delany Baum. Community Resource Website. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. 8 views. https://www.youtube.com/watch?v=AKYRf-rzlJE
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Peter Boruke, Chris Maliepaard, Roeland Voorrips. Polyploids Linkage and QTL Mapping with QTL Mapping with polymapoR and polyqtlR. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. 29 views. https://www.youtube.com/watch?v=lVajnpylOUw
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Jibran Tahir, Cyril Brendolise. Genetic Maze for polygenic traits in heterozygous polyploid kiwifruit population. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. 20 views. https://www.youtube.com/watch?v=n9wvENxxuoU
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Paterne Agre. Identification of QTLs Controlling Resistance to Anthracnose Disease in Water Yam. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. 7 views. https://www.youtube.com/watch?v=l4aEA7Y2-F8
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Marcelo Mollinari, Gabriel Gesteira, Cris Taniguti. MAPpoly and QTLpoly Updates. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. 96 views. https://www.youtube.com/watch?v=EjqAYzSktl0
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Cris Taniguti. Reads2Map: Practical and reproducible workflows to build linkage maps from sequencing data. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. 28 views. https://www.youtube.com/watch?v=cf1UPWADlrY
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Alejandro Therese Navarro. Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. 14 views. https://www.youtube.com/watch?v=jTpjh1ijo0g
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Jeffrey Endelman. New Software Features for GWAS in Polyploids. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. 54 views. https://www.youtube.com/watch?v=snwT7GHPOIs
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Mason Chizk. Novel Genomic Resources Enable Association Mapping in Blackberry. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. 33 views. https://www.youtube.com/watch?v=gKb3w2DYj8c
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Jeekin Lau, Cris Taniguti, David Byrne, Oscar Riera-Lizarazu. Linkage Map and QTL Mapping Software Comparisons. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. 37 views. https://www.youtube.com/watch?v=aqtooVPgzTE
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Chris Maliepaard, Roeland Voorrips, Peter Bourke. Simulation Tools: PedigreeSim and GenoSim. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/14/2022. 24 views. https://www.youtube.com/watch?v=r6o4sQ7SuW0
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Ranjana Bhattacharjee. Harnessing the Fruits of Genomics-Assisted Breeding in Clonally Propagated Crops. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/14/2022. 4 views. https://www.youtube.com/watch?v=byCZFQ0K1QM
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Tim Millar and Susan Thomson. Bayesian micro-haplotype assembly in autopolyploids. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/14/2022. 24 views. https://www.youtube.com/watch?v=OjEqqX09FdA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Jeffrey Endelman. Genomic Selection in Polyploids. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/14/2022. 76 views. https://www.youtube.com/watch?v=7ZabxVXl7Io
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Jeffrey Endelman. Genomic Selection in Potatoes. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/14/2022. 86 views. https://www.youtube.com/watch?v=64q4IPBkbsA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Patricio Munoz. Genomic Selection: Blueberry (Tetraploid) case study. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/14/2022. 58 views. https://www.youtube.com/watch?v=VEYEPMDfl-4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Olivia Angelin-Bonnet. Investigation genotype-phenotype relationships for tuber bruising in autotetraploid potatoes. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/14/2022. 23 views. https://www.youtube.com/watch?v=ANTL2ZSOnug
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Nweze Nwabueze Peter. Evaluation of Musa Accessions Indigenous to Benin Republic for Resistance to Black Sigatoka Disease. Workshop on Tools for Genomic-Assisted Breeding in Polyploids 1/14/2022. 17 views. https://www.youtube.com/watch?v=_pKF25y2cRM
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Joao Vitor Nomura. Genome-Wide Association for Drought Tolerance in Potato. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/14/2022. 116 views. https://www.youtube.com/watch?v=eBwCVDNjNB8
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: " Simon Fraher, Tanner Schwarz, Bonny Oloka, Ken Pecota, Chris Heim, Adrienne Gorny, Craig Yencho. QTL analysis of the Tanzania x Beauregard sweetpotato mapping population or resistance to Meloidogyne enterolobii. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. https://www.polyploids.org/sites/default/files/2022-02/Simon.poster.mp4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Jose Guillermo Chacon, Marcelo Mollinari, Bode Olukolu, Zhao-Bang Zeng, Gina Fernandez. Octoploid Strawberry Linkage Map from Reduce Representation Sequencing SNP Markers. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. https://www.polyploids.org/sites/default/files/2022-02/Jose%20Chacon.poster.mp4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Jeewan Pandey, Douglas Scheuring, Jeffrey Koym, Maria Isabel Vales. Genomic prediction for yield and processing traits in the tetraploid potato. Workshop on Tools or Genomics-Assisted Breeding in Polyploids 1/13/2022. https://www.polyploids.org/sites/default/files/2022-02/Jeewan%20Pandey.poster.mp4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Ao Jiao, Sanjeev Gautam, Jeewan Pandey, Douglas Scheuring, Jeffrey Koym, Maria Isabel Vales. Exploring the Genetic Control of Potato Tuber Dormancy. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. https://www.polyploids.org/sites/default/files/2022-02/Ao%20Jiao.poster.mp4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Ira Herniter, Nicholi Vorsa. Development of Genomic Resources for Cultivated Blueberry. Workshop on Tools for Genomic-Assisted Breeding in Polyploids 1/13/2022. https://www.polyploids.org/sites/default/files/2022-02/Ira%20H.poster.mp4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Beatriz Tome Gouveia, Brian Schwartz, Yangi Wu, Kevin Kenworthy, Ambika Chandra, Paul Raymer, Marta Pudzianowska, Esdras Carbajal, Manual Chavarria Sanchez, Jing Zhang, Bradley Battershell, Pamela Rowe, Meghyn Meeks, Tianyi Wang, Chase McKeithen, Susan Milla-Lewis. Improving zoysiagrass (Zoysia Wild. Species) for drought tolerance across the Southern US. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. https://www.polyploids.org/sites/default/files/2022-02/Beatriz%20G.poster.mp4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Sanjeev Gautam, Maria Isabel Vales. Genome-Wide Association Study on Potato Tuber Defects Under Heat Stress. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. https://www.polyploids.org/sites/default/files/2022-02/Sanjeev.poster.mp4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Christopher Benson, David Huff, Shaun Bushman, Peter Maughan, Rick Jeelen, Matthew Robbins. Sequenced Genomes of Allotetraploid Poa annua and its Diploid Progenitors, Poa infirma and Poa supina, Provide Insight into the Evolution and Breeding of Versatile Polyploid. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. https://www.polyploids.org/sites/default/files/2022-02/Chris%20B.poster.mp4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Tessa Hochhaus, Cris Taniguti, Jeekin Lau, Patricia Klein, David Byrne, Oscar Riera-Lizarazu. Development of a Genotyping by Sequencing Pipeline in Tetraploid Roses (Rosa sp.) Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. https://www.polyploids.org/sites/default/files/2022-02/Tessa.poster.mp4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Jeekin Lau, Cris Taniguti, David Byrne, Oscar Riera-Lizarazu. Identifying a Rose Germplasm Panel to Attain Optimal SNP Array Genotype Calling of Small Samples of Genotyped Individuals. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. https://www.polyploids.org/sites/default/files/2022-02/Jeekin.poster.mp4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Michael Miller, Laura Shannon. Predicting Length to Width Ratio, Roundness, and Compactness in Potatoes. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. https://www.polyploids.org/sites/default/files/2022-02/Michael%20Miller.poster.mp4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Lindsay Clark, Joyce Njuguna, Alexander Lipka, Erik Sacks. Multiploidy support in polyRAD. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. https://www.polyploids.org/sites/default/files/2022-02/Lindsay.poster.mp4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Cesar Medina, Harpreet Kaur, Ian Ray, Long-Xi Yu. Increasing the Prediction Accuracy in Genomic Selection of Complex Traits using WGBlup. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. https://www.polyploids.org/sites/default/files/2022-02/Cesar%20M.poster.mp4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Felipe Bitencourt Martins, Aline Moraes, Alexandre Aono, Rebecca Ferreira, Lucimara Chiari, Rosangela Simeao, Sanzio Barrios, Mateus Santos, Liana Jank, Cacilda Borges do Valle, Bianca Vigna, Anete Pereira de Souza. A Semi-Automated SNP-Based Approach for Contaminant Identification in Biparental Polyploid Populations of Tropical Forage Grasses. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. https://www.polyploids.org/sites/default/files/2022-02/Felipe.poster.mp4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Neil Anderson, Liesl Bower-Jernigan, Rajmund Eperjesi, Robert Suryani, Steven Gullickson, Albert Radloff. Unusual dalliances within the polyploid Chrysanthemum species complex. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. https://www.polyploids.org/sites/default/files/2022-02/Neil.A.Bower_.poster.mp4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Haramrit Gill, Jeekin Lau, Qiuyi Fu, Natalie Anderson, David Byrne, Oscar Riera-Lizarazu. Quantitative Trait Loci Associated with Flower Color Transition Phenotype in Tetraploid Roses. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. https://www.polyploids.org/sites/default/files/2022-02/Haramrit.poster.mp4
  • Type: Other Status: Published Year Published: 2022 Citation: Huff D.R. 2022. Coming soon: Poa annua seed for greens and fairways. Pennsylvania Turfgrass 11 (3):12-14. Cover Story.
  • Type: Journal Articles Status: Submitted Year Published: 2022 Citation: Robbins, Matthew D., Scott E. Warnke, P. Jeff Maughan, David R. Huff, Christopher W. Benson, Eric N. Jellen, Paul G. Johnson, and B. Shaun Bushman. 2022. Chromosome level genome assembly and annotation of the allotetraploid annual bluegrass (Poa annua L.). Submitted to: Genome Biology and Evolution.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Taniguti, C.H., G. Gesteira, J. Lau, G. Pereira, Z.-B. Zeng, D. Byrne, O. Riera-Lizarazu, and M. Mollinari. 2022. VIEWpoly: a visualization tool to integrate and explore results of polyploid genetic analysis. J. Open Source Softw. 7(74): 4242, doi: 10.21105/joss.04242
  • Type: Journal Articles Status: Accepted Year Published: 2022 Citation: Rawandoozi, Z.J., E.L. Young, M. Yan, S. Noyan, Q. Fu, T. Hochhaus, M.Y. Rawandoozi, P.E. Klein, D.H. Byrne, and O. Riera-Lizarazu. 2022. QTL mapping and characterization of black spot disease resistance using two multi-parental diploid rose populations. Hort. Res. (accepted)
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Lau, J., E.L. Young, S. Collins, M.T. Windham, P.E. Klein, D.H. Byrne, and O. Riera-Lizarazu. 2022. Rose rosette disease resistance loci detected in two interconnected tetraploid garden rose populations. Front. Plant Sci. 13:916231, doi: 10.3389/fpls.2022.916231
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Young, E.L., J. Lau, N.B. Bentley, Z. Rawandoozi, S. Collins, M.T. Windham, P.E. Klein, D.H. Byrne, and O. Riera-Lizarazu. 2022. Identification of QTLs for reduced susceptibility to rose rosette disease in diploid roses. Pathogens 11:660, doi: 10.3390/pathogens11060660
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Pandey, J, D.C. Scheuring, J.W. Koym, and M.I. Vales. 2022. Genomic regions associated with tuber traits in tetraploid potatoes and identification of superior clones for breeding purposes. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2022.952263.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Caraza-Harter MV, Endelman JB (2022) The genetic architectures of vine and skin maturity in tetraploid potato. Theor Applied Genet, https://doi.org/10.1007/s00122-022-04159-z
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Chizk, T.M., M. Worthington, R. Threlfall, H. Ashrafi, R. Aryal, J.R. Clark. 2021. Genome wide association study (GWAS) in tetraploid blackberry for improvement of fruit morphological and shipping characteristics. 2021 ASHS Annual Meeting. Denver, CO. Aug. 5-9, 2021. HortScience 56(9) Supplement - P. S163.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Godwin, C., M. Worthington, R. Aryal, H. Ashrafi, R. Threlfall, J.R. Clark. Genetic control of sweetness and acidity in blackberry. 2021 ASHS Annual Meeting. Denver, CO. Aug. 5-9, 2021. HortScience 56(9) Supplement - P. S226.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Johns, C., M. Worthington, and J.R. Clark. 2021. Genetic control of internode length in blackberry. 2021 ASHS Annual Meeting. Denver, CO. Aug. 5-9, 2021. HortScience 56(9) Supplement - P. S65.
  • 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. 2021 ASHS Annual Meeting. Denver, CO. Aug. 5-9, 2021. HortScience 56(9) Supplement - P. S177.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Mollinari et al (2022), Computational Tools for Genomic Analysis in Polyploids. Oral presentation at American Society for Horticultural Science Conference 2022 https://ashs.confex.com/ashs/2022/meetingapp.cgi/Paper/38640
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Gill, H., Lau, J., Zhen, S., Byrne, D., & Riera-Lizarazu, O. 2022. QTL and Pigment Analysis of the Flower Color Transition Phenotype in Autotetraploid Rose Populations. Annual Conference of the American Society for Horticultural Science, July 29- August 03, Chicago, IL.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Hochhaus, T., C.H. Taniguti, J. Lau, P.E. Klein, D.H. Byrne and O. Riera-Lizarazu. 2022. Optimization of a reduced representation sequencing pipeline for polyploid roses (Rosa sp.). In: Abstracts of Presentations from the Annual Conference of the American Society for Horticultural Science, July 30-August 3, Chicago, IL.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Pandey, J., D.C. Scheuring, J.W. Koym, and M.I. Vales. 2022. Genomic prediction of chipping quality in tetraploid potato. Plant and Animal Genome Conference XXIX. January 8-12. Online. Digital poster.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Gautam S., J. Pandey, D. C. Scheuring, J.W. Koym, and M.I. Vales. 2022. Genome-wide association study on potato tuber defects under heat stress. Plant and Animal Genome Conference XXIX. January 8-12. Online. Digital poster.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Jiao, A., S. Gautam, J. Pandey, D.C. Scheuring, J. Koym, M.I. Vales. 2022. Investigating the genetic background of potato tuber dormancy. Plant and Animal Genome Conference XXIX. January 8-12. Online. Digital poster.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Chris Benson, Shaun Bushman, Peter Maughan, Rick Jellen, Matthew Robbins, and David Huff. Sequenced Genomes of Allotetraploid Poa annua and its Diploid Progenitors, Poa infirma and Poa supina, Provide Insight into the Evolution and Breeding of Versatile Polyploid, Plants and Animal Genome Conference (Virtual: Jan 2022)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Taniguti, C.H., G.S. Gesteira, J. Lau, G.S. Pereira, Z.-B. Zeng, D.H. Byrne, O. Riera-Lizarazu and Marcelo Mollinari. 2022. VIEWpoly: An Interactive Tool to Visualize, Explore and Integrate Genetic Maps and QTL Analysis with Genomic Information. In: Abstracts of Plant & Animal Genome XXIX (virtual), January 8-12, San Diego, CA. PE0086, Linkage and Deletion Mapping Workshop.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Endelman, JB. Fully efficient, two-stage analysis for genomic selection and GWAS. Plant and Animal Genome XXIX, Jan. 8, 2022
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Jiao, A., S. Gautam, J. Pandey, D.C. Scheuring, J. Koym, M.I. Vales. 2022. Genome-wide association studies for tuber dormancy in tetraploid potatoes. American Society for Horticultural Sciences. 2022 Annual Conference. Chicago, IL, July 30 - August 3, 2022. Poster.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Fu, Q, N. Anderson, H. Gill, D.H. Byrne, and O. Riera-Lizarazu. 2022. Identification of Rose Germplasm Carrying the Black Spot Resistance Gene, Rdr1. In: Abstracts of Plant & Animal Genome XXIX (virtual), January 8-12, San Diego, CA. PO0387
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Gill, H., J. Lau, Q. Fu, N. Anderson, D.H. Byrne, and O. Riera-Lizarazu. 2022. Quantitative Trait Loci Associated with the Flower Color Transition Phenotype in Tetraploid Roses. In: Abstracts of Plant & Animal Genome XXIX (virtual), January 8-12, San Diego, CA. PE0388
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Hochhaus, T., C.H. Taniguti, J. Lau, P.E. Klein, D.H. Byrne and O. Riera-Lizarazu. 2022. Development of a Genotyping by Sequencing Pipeline in Tetraploid Roses (Rosa sp.). In: Abstracts of Plant & Animal Genome XXIX (virtual), January 8-12, San Diego, CA. PE0042
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Lau, J., C.H. Taniguti, D.H. Byrne and O. Riera-Lizarazu. 2022. Identifying a Rose Germplasm Panel to Attain Optimal SNP Array Genotype Calling of Small Samples of Genotyped Individuals. In: Abstracts of Plant & Animal Genome XXIX (virtual), January 8-12, San Diego, CA. PE0046
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Taniguti, C.H., L.M. Taniguti, G.S. Gesteira, T.P. Oliveira, G.C. Ferreira, R. Amadeu, J. Lau, D.H. Byrne, O. Riera-Lizarazu, G.S. Pereira, M. Mollinari and A.A. F. Garcia. 2022. Reads2Map: Practical and Reproducible Workflows to Build Linkage Maps from Sequencing Data. In: Abstracts of Plant & Animal Genome XXIX (virtual), January 8-12, San Diego, CA. PO0089
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Endelman, JB. Genomic selection in potato. International Potato e-Conference. ICAR-Central Potato Research Institute, Shimla, India. November 23, 2021.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Riera-Lizarazu, O. 2022. Exploring Genomics-Aided Breeding in Roses. Texas A&M Plant Breeding Symposium: Hybrid Horizons, 18 February, Texas A&M University, College Station, TX.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Mollinari M, Gesteira G, Taniguti CH (Aug 25-26, 2022) Genetic data analysis in polyploids. From allelic dosage to QTL mapping. University of S�o Paulo, Brazil (in Portuguese) https://tinyurl.com/4vbjfx6c.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Taniguti, C.H.; Gesteira, G.S.; Lau, J.; Amadeu, R.R.; Byrne, D.; Riera-Lizarazu, O.; Pereira, G.S.; Mollinari, M. & Garcia, A.A.F. 2022. Genetic data analysis in polyploids: from allelic dosage to QTL mapping. August, Workshop at University of S�o Paulo, Brazil (virtual).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Taniguti, C.H.; Taniguti, L.M.; Gesteira, G.S.; Oliveira, T.P.; Lau, J.; Ferreira, G.C.; Amadeu, R. R.; Byrne, D.; Riera-Lizarazu, O.; Pereira, G.S.; Mollinari, M. & Garcia, A.A.F. 2022. Building linkage maps with OneMap 3.0: new approaches using workflows. August, University of S�o Paulo, Brazil (virtual).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Jiao, A., S. Gautam, J. Pandey, D.C. Scheuring, J. Koym, M.I. Vales. 2022. Phenotypic evaluation of potato tuber dormancy and genome-wide association studies. Texas A&M Plant Breeding Symposium. College Station, TX. February 17, 2022. Poster.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Vales, M.I., J. Pandey, S. Toinga-Villafuerte, S. Gautam, A. Jiao, A.M. Ifeduba, D.C. Scheuring, J.W. Koym, and USA Breeding Programs. 2022. Potato breeding practices in the USA. International Seed Potato Symposium. July 25, 2022, Denver, CO.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Vales, M.I., S. Gautam, J. Pandey, D.C. Scheuring, and J.W. Koym. 2021. Heat tolerance in potatoes -Texas A&M Potato Breeding Program- NCCC215 Breeding and Genetic Technical Committee Meeting, Chicago, IL, December 7, 2021.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Vales, M.I., S. Gautam, J. Pandey, J. Da Silva, K. Mandadi, D. Kurouski, S. Toinga-Villafuerte, A. Jiao, D.C. Scheuring, and J.W. Koym. 2021. Development of climate-change-ready potato varieties to overcome heat stress. Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens. October 21, 2021.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Hochhaus, T., C.H. Taniguti, J. Lau, P.E. Klein, D.H. Byrne and O. Riera-Lizarazu. 2022. Development of genomic-based tools for disease resistance and ornamental trait improvement in tetraploid roses (Rosa sp.), February 4, Plant Breeding and Genetics Circle, Texas A&M University, College Station, TX.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Taniguti, C.H., L.M. Taniguti, G.S. Gesteira, T.P. Oliveira, J. Lau, G.C. Ferreira, R. Amadeu, D.H. Byrne, O. Riera-Lizarazu, G.S. Pereira, M. Mollinari and A.A. F. Garcia. 2022. Comparing genotype calling software performance in Genotyping-by-Sequencing data of F1 outcrossing based on genetics maps quality. In: Abstracts of the 30th Conference on Intelligent Systems for Molecular Biology, July 10-14, Madison, WI. O-016
  • Type: Other Status: Published Year Published: 2022 Citation: Cris Taniguti, Jeekin Lau, Gabriel Gesteira, Maria Caraza-Harter. Computational Support Session: Genotype calling.. Tools for Genomics-Assisted Breeding in Polyploids Computational Support Session 12/14/2021. 31 views. https://www.youtube.com/watch?v=4bwJ_1qAlPU&t=1s
  • Type: Other Status: Published Year Published: 2022 Citation: Jeekin Lau, Cris Taniguti, Gabriel Gesteira, Maria Caraza-Harter. Computational Support Session: Linkage analysis. Tools for Genomics-Assisted Breeding in Polyploids Computational Support Session 12/21/2021. 46 views. https://www.youtube.com/watch?v=dXnDwvUNCfg
  • Type: Other Status: Published Year Published: 2022 Citation: Gabriel Gesteira, Jeekin Lau, Cris Taniguti, Maria Caraza-Harter. Computational Support Session: QTL analysis Tools for Genomics-Assisted Breeding in Polyploids Computational Support Session 1/10/2022. 47 views. https://www.youtube.com/watch?v=xtTi2unTXp8
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: David Byrne. Workshop Introduction. Workshop on Tools for Genomics-Assisted Breeding in Polyploids 1/13/2022. 24 views. https://www.youtube.com/watch?v=vozSOwMD52g


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: 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: 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: 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