Progress 10/01/17 to 09/30/21
Outputs
Target Audience:The primary audience has been other plant breeders, which have learned about the methods developed in this project through presentations at scientific meetings and through the publication of a software package. The concept of genomic selection has also been communicated to stakeholders in the potato industry. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project supported the training of one MS and one PhD student in both field and molecular plant breeding methods, as well as research experience for several undergraduate students. How have the results been disseminated to communities of interest?PI Endelman has givenmany presentations about this project, and theuse of genomic selection more broadly, to both scientific audiences and potato industry stakeholders (growers and agronomists). The list of scientific meetings includes those organized by thePlant and Animal Genome, the National Association of Plant Breeders, the Potato Association of America, the European Association of Potato Research,the University of Sao Paulo (Brazil), and the ICAR-Central Potato Research Institute (India). What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Impact Statement We achievedthe overarching goal of the proposal, which was to integrate genomic selection into the University of Wisconsin potato chip breeding program. Genomic selection combines historical data with genome-wide markers to predict the breeding value of new germplasm more quickly, which enables reducing the time to parent selection. This reduction is generally considered the most effective way to accelerate genetic improvement for crops and livestock. Genomic prediction models for total yield, vine maturity, specific gravity, and chip color, based on data from 6 years and over 900 genotypes, were made publicly available through the R software package StageWise. These data and models were used to shorten the University of Wisconsin breeding cycle, from the traditional 6-8 years down to 4 years. Based on our dissemination of these results and methods, other US potato breeding programs (including Texas, Minnesota, Maine, and New York) have begun restructuring their programs to reap similar benefits. Outreach to the wider breeding community has contributed to improved knowledge about using genomic selection for many different crops. Objective 1. Develop 129 field-year 3 (FY3) potato chip breeding lines per year for three years (2017-2019) and genotype them with the potato Infinium SNP array. Over 400 FY3 breeding lines were developed in this project and genotyped with over 10,000 markers on the potato SNP array. High quality estimates of allele dosage were made with a normal mixture model, using R packages fitPoly and polyBreedR. When combined with the genotyped breeding lines from two previous years, as well as entries in the National Chip Processing Trial, the size of the training population for genomic selection was 944 clones. Objective 2. For each FY3 cohort, measure total yield, size distribution, specific gravity, internal defects, and chip color at the Hancock Research Station. Field trials were planted in April of each year and harvested in September. Total yield and tuber size were measured using the AgRay Vision system, which is a conveyor system to estimate tuber weight and geometry by X-ray (with a calibrated model). Specific gravity and internal defects were measured on a 10-15 tuber sample within 1 week of harvest. Fry color was measured after 6 months of cold storage. In each year, the plot-based heritability for the traits was estimated from the variance components of a random effects model. For total yield, the heritability ranged from 0.70 to 0.83. The results forspecific gravity weresimilar, while fry color wasmuch lower in one year, ranging from0.25 to 0.74. Objective 3. Determine the genomic prediction accuracy for FY3 breeding lines. Prediction models were developed for four traits--total yield, vine maturity, specific gravity, and fry color--using a two-stage, BLUP methodology. In Stage 1, the genotypic value of each clone was estimated as a fixed effect, within each year separately. In Stage 2, the genomic breeding value across all years was predicted. The additive relationship matrix based on markers (G) was blended with that estimated from pedigree (A) to optimize the prediction model. The optimal blend varied across traits, from zero pedigree contribution for specific gravity to a 50:50 contribution for yield. The accuracy of predictions for the 2020 FY3 breeding lines was estimated by the square-root of the reliability, which is based on the prediction error variance. The results for total yield ranged from 0.77 to 0.84, which was similar to specific gravity at 0.80 to 0.89. The range for fry color was larger: 0.64 to 0.96. Objective 4. Implement genomic selection for the 2020 FY3 cohort. Based on the high expected accuracies, we felt confident implementing genomic selection using a multi-trait index. Equal economic weights were given to yield, specific gravity, and fry color. Seven breeding lines from the 2020 FY3 cohort were selected as potential parents, in addition to more advanced lines with an established history of crossing. Although most potato clones can be used as female parents, our experience is that fewer than 20% can be effectively used as male parents due to low pollen shed or sterility. As a result, good male parents from the previous cohort are retained to ensure success. All 7 clones selected by the genomic prediction model were successfully used as female parents to produce true seeds. Greenhouse minitubers for nearly 1300 offspring from this group of parents were grown in the summer of 2021, at the conclusion of the project.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Endelman JB. 2022. Fully efficient, two-stage analysis for genomic selection and GWAS. Plant and Animal Genome XXIX (Virtual), Jan. 8-11, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Endelman JB. 2021. R/StageWise: Two-stage analysis of multi-environment trials for genomic selection. Annual Meeting of the Potato Association of America (Virtual), July 26-28, 2021.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Endelman JB. 2021. Genomic selection in potato. International Potato e-Conference. ICAR-Central Potato Research Institute, Shimla, India. November 23, 2021.
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Progress 10/01/19 to 09/30/20
Outputs
Target Audience:A wide audience of plant breeders were reached during this period. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project has supported the training of an MSstudent in both field and molecular breeding methods. How have the results been disseminated to communities of interest?On April 24, 2020, Endelman presented results from this project as an invited speaker at an international, virtual symposium on plant breeding, which was sponsored by Corteva Agriscienceand organized by plant breeding graduate students across the US. Several hundredpeople attended the symposium. What do you plan to do during the next reporting period to accomplish the goals?1. The 2020 FY3 cohort will be genotyped, phenotyped, and added to the prediction model. 2. New methods for the genomic prediction of specific combining ability will be completed and added to the polyBreedR software. 3. Parental lines will be selected based on the genomic prediction model, crossed in winter 2021, and used to start the next breeding cycle.
Impacts
What was accomplished under these goals?
Genomic selection uses historical data and genome-wide DNA markers to predict complex traits affected by many genes. Thegoal of this project is to develop this capacity in the potato chip breeding program at UW-Madison, and to share our experiences with others. A major impact during this period was the formation of a national coalition of potato breeders to implement the methods pioneered in this project on a wider scale. Our proposal to theUSDA Specialty Crop Research Initiative was selected for funding (2020-51181-32156). Objective 1.57 clones from the 2019 FY3 cohort were genotyped with version 3 of the potato SNP array. Of the 21,000 markers on the array, 11,043 were used for analysis based on our ability to reliably estimate allele dosage. Ten clones from the 2017-18 FY3 cohorts were entered in the 2020 National Chip Processing Trial, which provides the opportunity to study their performance in 9 states across the US. Objective 2. Data for total yield, size distribution, and specific gravity were compiled in early October. Clones were stored at 45oF until March and then fried to measure chip lightness using a Hunter colorimeter. Objective 3.Genomic predictions were made using the G-BLUP method, and the accuracy of the predictions was estimated from the prediction error variance (using the inverse coefficient matrix from the mixed model equations). The average prediction accuracy for the 2019 FY3 cohort was 0.73 for total yield, 0.82 for specific gravity, and 0.77 for chip color. These accuracies are 0.1-0.2 higher than the 2018 FY3 cohort. Objective 4. Genomic-estimated breeding values for yield, specific gravity, and chip color were combined with other information, such as the presence of R genes for disease resistance and phenotypic data for other traits, to select 15 parents for the winter 2020 crossing block. Male fertility was assessed based on pollen shed and fruit formation upon selfing. This identified three clones as good male parents, and the remainder were used as potential female parents. Cross-pollination was successful for 15 different parental combinations, leading to the production of over 19,000 true potato seeds to begin the next breeding cycle.
Publications
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2020
Citation:
Song, L. 2020. Evaluations of F1, F2, and F3 Generations of Diploid Potato Populations. MS Thesis. University of Wisconsin-Madison.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2020
Citation:
Endelman, J. 2020. Genomic selection in potato. Plant Sciences Symposia Series. Virtual Symposium, April 24, 2020.
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Progress 10/01/18 to 09/30/19
Outputs
Target Audience: Audiences are: potato researchers, growers, and processors, as well as plant breeders working with other crops. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project has supported the training of a PhD student in both field and molecular breeding methods. How have the results been disseminated to communities of interest?Project Director Endelman has given several invited presentations about this research: -Genomics-assisted breeding in potato. 2019 National Association of Plant Breeders Annual Meeting, Pine Mountain, GA. Aug. 28, 2019. -Current trends in potato breeding and variety development.UW Extension and WPVGA Grower Education Conference, Stevens Point, WI. Feb. 7, 2019. -Current trends in potato breeding and variety development.Mid-Atlantic Fruit & Vegetable Convention, Hershey, PA. Jan. 31, 2019. -Genomic selection in tetraploid potato. 19th Joint Meeting of the European Association of Potato Research and EUCARPIA, Rostock, Germany. Dec. 6, 2018. -Genomics-assisted breeding for autotetraploid potato. 2nd International Meeting on Plant Breeding, University of São Paulo, Piracicaba, Brazil. Oct. 4, 2018. What do you plan to do during the next reporting period to accomplish the goals?The 2019FY3 cohort from the UW-Madison program will be genotyped with the potato SNP array and phenotyped for yield, tuber size, specific gravity, and fry color. These data will be added to the prediction model and used to implement selection on genomic-estimated breeding values for the 2020crossing block.
Impacts
What was accomplished under these goals?
Genomic selection uses historical data and genome-wide DNA markers to predict complex traits affected by many genes. The goal of this project is to develop this capacity in the potato chip breeding program at UW-Madison, and to share our experiences with others. Goal 1. Develop 129 field-year 3 (FY3) potato chip breeding lines per year for three years (2017-2019) and genotype them with the potato Infinium SNP array. Accomplishment: 125 clones from the 2018 FY3 cohort were genotyped with version 3 of the potato SNP array. Of the 21,000 markers on the array, 12,448 were used for analysis based on our ability to reliably estimate allele dosage. Goal 2. For each FY3 cohort, measure total yield, size distribution, specific gravity, internal defects, and chip color at the Hancock Research Station. Accomplishment: Data for total yield, median tuber weight, and specific gravity were compiled in early October. Clones were stored at 45oF until March and then fried to measure chip lightness using a Hunter colorimeter. Goal 3. Determine the genomic prediction accuracy for FY3 breeding lines. Accomplishment: Genomic predictions were made using the G-BLUP method, and the accuracy of the predictions was estimated from the prediction error variance (using the inverse coefficient matrix from the mixed model equations). The average prediction accuracy for the 2018 FY3 cohort was 0.61 for total yield, 0.57 for median tuber weight, 0.56 for specific gravity, and 0.62 for chip color. Goal 4. Implement genomic selection for the 2020 FY3 cohort. Accomplishment: Genomic-estimated breeding values for yield, size, specific gravity, and chip color were combined with other information, such as the presence of R genes for disease resistance and phenotypic data for other traits, to select 10 parents for the winter 2019 crossing block. Male fertility was assessed based on pollen shed and fruit formation upon selfing. This identified two clones as good male parents, and the remainder were used as female parents. Cross-pollination was successful for 13 different parental combinations, leading to the production of over 10,000 true potato seeds to begin the next breeding cycle.
Publications
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Progress 10/01/17 to 09/30/18
Outputs
Target Audience: The target audiences are: Potato researchers, growers, and processors, as well as plant breeders working with other crops. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Project Director Endelman mentored a PhD studentto usestatistical ("mixed") models to analyze data from multi-environment trials, which is a critical skill for plant breeders. Thestudentsuccessfully defended her dissertation in Spring 2018 and was awarded a PhD. How have the results been disseminated to communities of interest?Project Director Endelman delivered a presentation about the results from this projectto other professional geneticists and breeders at the Plant and Animal Genome Conference in January 2018. He has also presented on this topic to potato growers and agronomists at several industry-oriented meetings, including the December 2017 meeting of the Potatoes USA National Chip Program and the February 2018 meeting of the Wisconsin Potato and Vegetable Growers Association. What do you plan to do during the next reporting period to accomplish the goals?The 2018 FY3 cohort from the UW-Madison program will be genotyped with the potato SNP array and phenotyped for yield, size, specific gravity, and fry color. These data will be added to the prediction model and used to implement selection on genomic-estimated breeding values for the 2019 crossing block.
Impacts
What was accomplished under these goals?
Genomic selection uses historical data and genome-wide DNA markers to predict complex traits affected by many genes. Research in other crops and animals has shown that genomic selection can improve the efficiency of breeding, but it has yet to be implemented in potato breeding programs. 1. The 2017 FY3 cohort from the potato chip breeding program at UW-Madison was genotyped with the potato Infinium SNP array. 2. Phenotype data for the 2017 FY3 cohort for total yield, tuber size, specific gravity, and fry color after 6 months of cold storage was curated and added to the historicaldataset. 3. Many studies use random cross-validation to assess the accuracy of genome-wide prediction. However, in the context of a pedigreed breeding population, this approach leads to training set individuals that are descendants of individuals in the validation set, which is unrepresentative of how genomic selection will be used in practice and may produce unrealistically high accuracies. To avoid this pitfall, pedigree depth was used to partition the population into a set of 168 candidates for selection and a set of 403 clones ancestral to this groupas the training set. The selection candidates were further narrowed by excluding clones with insufficiently reliable data for validation, leaving 54 clones for yield, 132 clones for specific gravity, and 49 clones for fry color (with mean reliability in the range 0.71-0.72 for all traits). Prediction accuracy using pedigree informationwas just over 0.5 for total yield vs. 0.4 for specific gravity and fry color. When genome-wide markers were used, the accuracy for yield increased by 0.03 and fry color by 0.06, but the accuracy for specific gravity decreased by 0.07.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Schmitz Carley CA, Coombs JJ, Clough ME, De Jong WS, Douches, Haynes KG, Higgins CR, Holm DG, Miller Jr. JC, Navarro FM, Novy RG, Palta JP, Parish DL, Porter GA, Sathuvalli VR, Thompson AL, Yencho GC, Zotarelli L, Endelman JB (2018) Genetic Covariance of Environments in the Potato National Chip Processing Trial. Crop Science, published online ahead of print, Nov. 8, 2018. doi: 10.2135/cropsci2018.05.0314
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Endelman, JB. 2018. Genome-wide prediction in tetraploid potato using pedigree and marker information. Plant and Animal Genome XXVI, San Diego, CA. Jan. 14, 2018.
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