STRAWBERRY BREEDING PROGRAM

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1010470
• Project Start Date: Oct 1, 2016
• Project End Date: Sep 30, 2021
• Program Code: [(N/A)]- (N/A)

Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671

Performing Department
Plant Sciences

Non Technical Summary
Strawberry production has expanded and fruit yields have increased several-fold in California over the last 60 years. The development and introduction of genetically superior culitvars, utilizing natural genetic variation, has played a vital role in this, along with intensive production practices, especially methyl bromide fumigation (starting in 1961). The latter has enabled growers to dramatically reduce losses caused by soil-borne pathogens and weeds and to continuously plant strawberries in ideal coastal environments without rotating crops. Furthermore, the protection offered by methyl bromide fumigation has enabled breeders to focus on increasing yield without increasing resistance to soil-borne diseases. This is no longer possible. Methyl bromide fumigation was banned in 2005 as part of "The Montreal Protocol on Substances that Deplete the Ozone Layer". While replacements for methyl bromide have been sought, growers are facing inreasingly greater challenges in sustaining yields because of losses caused by soil-borne pathogens, weed, and other pests. The University of California breeding program focuses on developing cultivars with greater resistance to the most important soil-borne pathogens without compromising yield and quality. Our long-term goals are to: (a) increase the profitability and sustainability of strawberry production through the development of cultivars with greater resistance to soil-borne diseases, increased fruit quality, increased marketable fruits yield, and consistent fruit yields over a long production period; (b) advance the understanding of the genetics of economically important characteristics in strawberry; (c) conserve and understand natural genetic diversity needed to apply breeding solutions to production problems; and (d) accelerate the development of outstanding disease resistance cultivars throught the application of genomic-knowledge.

Animal Health Component

50%

Research Effort Categories

Basic

50%

Applied

50%

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1122	1080	50%
201	1122	1081	50%

Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1122 - Strawberry;

Field Of Science
1081 - Breeding; 1080 - Genetics;

Keywords

fragaria

strawberry

heritability

fruit quality

population genetics

high-throughput genotyping

genomic-selection

gentetic mapping

association mapping

genomic-estimated breeding value

phenotyping

single nucleotide

polymorphism

rna and dna seuqencing

Goals / Objectives
The long-term goals of this research program are to:(a) develop and deploy genetically superior short-day and day-neutral cultivars for organic and non-organic strawberry production systems in California and the US;(b) gain a broader and deeper understanding of genetic mechanisms underlying economically important phenotypes in strawberry, with a strong focus on developing genotypic selection platforms for phenotypes caused by large-effect loci;(c) expand and strengthen genomic- and bioinformatic resources for genomic-enabled breeding in strawberry;(d) identify, preserve, and utilize elite, heirloom, and historically important accessions in the UC strawberry germplasm collection.The specific objectives for the 5-year project period are to:(a) complete five cycles of breeding in the short-day and day-neutral breeding programs, including the production of 500-800 crosses, screening of 80,000-120,000 seedlings (unreplicated full-sib individuals), clonal propagation and advanced testing of 800-1,200 selected full-sib individuals, on-farm testing of 20-40 experimental cultivars, and formal release of 2-4 cultivars;(b) complete association mapping and genomic-prediction analyses for 16-20 economically important phenotypes in a training population of 960 genotypes (accessions) held in the University of California and USDA germplasm collections;(c) complete the development and genetic analyses in 10 or more three-generation pedigree mapping populations segregating for 20 or more economically important phenotypes, identify targets for marker-assisted selection (exclusively large-effect loci), develop high-throughput DNA marker genotyping assays for MAS applications in the breeding program, and implement MAS in seedlings for 2-4 large-effect loci;(d) apply genomic-selection to the problems of parent selection and hybrid prediction in the breeding program, quantify the economic efficiency of phenotypic and genomic-selection, and implement genomic-selection in a 20% of the short-day and day-neutral breeding pipelines.

Project Methods
Cultivar Development Pipelines. One hundred to 200 full-sib crosses and segregating populations (full-sib families) will be produced each year for the short-day and day-neutral breeding pipelines. Seedlings (unreplicated) and clones (replicated) in each breeding pipeline will be phenotyped for fruit yield, plant architecture, days to flowering, flowering duration, sugar and acid concentration, fruit number, size, and firmness. Clones (replicated) in each breeding pipeline will be phenotyped for resistant to Fusarium, Verticillium, and Macrophomina, fruit yield, biomass, plant architecture, days to flowering, flowering duration, sugar and acid concentration, fruit number, size, and firmness. Selection will be performed within and among full-sib families. We anticipate screening 12,000 seedlings in the first year, 360-600 cloned full-sib individuals in the second year, 18-30 cloned full-sib individuals in the third year, and 1-2 cloned full-sib individuals in the fourth year of each breeding cycle. Selection intensities may deviate from these numbers depending on results and outcomes. The results from each cycle of selection will be communicated to the industry through annual reports, scientific presentations and publications, field days, and meetings with stakeholders.Genome-Wide Association Mapping (GWAS). GWAS will be applied to a population of 960 germplasm accessions representing extant genetic diversity in the UC and USDA germplasm collections. The GWAS or training population will be genotyped for 38,000 SNPs and phenotyped for resistance to Fusarium, Verticillium, and Macrophomina, fruit yield, days to flowering, flowering duration, sugar and acid concentration, fruit number, size, and firmness. Statistical analyses will be performed using standard methods implemented in PLINK or other open-source software to identify SNP loci in linkage disequilibrium with causative loci. These analyses will be performed as part of the process of estimating genome-estimated breeding values (GEBVs) and building a training population for the application of genomic selection (see next). The results of this research will be incorporated into graduate student and postdoctoral scholar studies and publications, presented at scientific meetings, and published in open-source peer-reviewed scientific publications.Genomic-Selection (GS). Genomic-estimated breeding values (GEBVs) will be estimated in the training population (n = 960) to initiate genomic selection and identify parents for subsequent cycles of selection. We will perform cross-validation analyses and estimate the accuracy of genomic selection for yield, sugar and acid concentration, and resistance to Fusarium, Verticillium, and Macrophomina, and estimate the economic feasibility of supplementing phenotypic selection with GS. The training population will be genotyped with a high-density, genome-wide SNP array (k = 38,000 SNPs). Statistical analyses will be performed using PLINK, R, and other open-source software to estimate genomic-estimated breeding values (GEBVs), predict GEBVs, estimate the accuracy of genomic-selection, heritability and other genetic parameters, and effects of individual loci. The results of this research will be incorporated into graduate student and postdoctoral scholar studies and publications, presented at scientific meetings, and published in open-source peer-reviewed scientific publications.Linkage Disequilibrium Mapping. We anticipate developing and analyzing 20-24 three-generation pedigree segregating populations with 96-192 full-sib individuals per population. This work will primarily focus on sugar and acid concentration, resistance to Fusarium, Verticillium, and Macrophomina, and day-neutrality loci. We will estimate genetic parameters and identify genomic locations of putative causative loci using FLEX-QTL or similar open-source software packages. The results of this research will be incorporated into graduate student and postdoctoral scholar studies and publications, presented at scientific meetings, and published in open-source peer-reviewed scientific publications.

Progress 10/01/16 to 09/30/21

Outputs
Target Audience:The target audiences for this research program are: (a) Strawberry growers, producers, processors, nursery propagators, and other industry stakeholders in the state of California, the US, and abroad. (b) Scientists in academia. (c) Scientists in the private sector, particularly the seed and nursery industry. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project has supported the training and professional development of four postdoctoral researchers, six graduate students, and three staff research associates. How have the results been disseminated to communities of interest?We have presented at least 20 posters or invited talks at scientific meetings. Progress reports and scientific results were presented at field days, cooperative extension meetings, and additional meetings with stakeholders. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? We released three day-neutral cultivars (UCD Royal Royce, Moxie, and Valiant) and two short-day cultivars (UCD Warrior and Victor) in 2019 and two extended day-neutral cultivars (UCD Mojo and UCD Finn) in 2020. We expect these cultivars to have a significant commercial impact. Warrior, Victor, and Moxie provide some of the strongest packages of resistance to soil-borne diseases in the industry, whereas Royal Royce and Valiant have produced record yields in California. The commercial demand for these cultivars has already outstripped supply. We completed three years of commercial testing and selection of extended day-neutral breeding materials and identified two EDN cultivars (EDN15 and 19) for commercial advancement and official release. Both are superior in fruit quality to the current market leader (Portola), which was validated by hedonic and sensory testing. EDN15 and 19 are currently being propagated by Foundation Plant Services (FPS) for commercial release in 2020-21 (pending the submission and approval of cultivar releases). We are working closely with FPS, IA, nurseries, and industry business partners to accelerate their introduction. Similar to the story for the recently released short-day and day-neutral cultivars, the commercial interest in and demand for EDN15 and 19 has already outstripped supply. We developed the first reference genomes for octoploid strawberry (F. × ananassa) and diploid F. iinumae, one of the diploid ancestors of F. × ananassa, in addition to developing a reference genome for diploid woodland strawberry (F. vesca) with chromosome-scale contiguity. The publication of these genomes has included the public release of the annotated genomes, DNA and RNA sequences for several diploid and octoploid Fragaria, and other supporting data at NCBI and DRYAD. The assembly of the octoploid genome was a significant achievement that has had a significant impact on strawberry research worldwide and created the foundation needed to overcome other long-standing technical barriers in the octoploid species complex. Following the assembly of an octoploid reference genome, we developed an innovative strategy for phasing and assembling complex polyploid genomes in outbred species using whole genome shotgun (WGS) genotyping by sequencing (GBS) of segregating populations developed from the reference genome parents. Using this strategy, we recently assembled four phased octoploid reference genomes, two for F. x ananassa (cultivated strawberry) and two for F. chiloensis subsp. lucida (beach strawberry)--the latter is a native of California and one of the octoploid progenitors of cultivated strawberry. This strategy appears to overcome the problem of haplotype collapse or switching during assembly and should be powerful for assembling complex genomes in other highly heterozygous species. Finally, we recently collaborated with investigators at Pacific Biosciences to assemble a chromosome-scale genome for UCD Royal Royce, one of our recently released day-neutral cultivars. We expect these phased octoploid genomes to become important resources for genome-informed studies in strawberry. We developed the first high-density single nucleotide polymorphism (SNP) genotyping platforms for strawberry using DNA variants anchored to the octoploid reference genome. This work included the development and pre-publication release of 50K and 850K SNP genotyping arrays that are being used in laboratories around the world. This work involved the genome-wide identification of sub-genome and copy-specific DNA variants and enabled the complete resolution of the four sub-genomes. We showed that short-read DNA sequences could be unambiguously aligned to an octoploid reference genome, which was essential for accurate DNA variant calling, GBS, and the application of other NGS-reliant approaches. This was an important breakthrough that seems trivial in hindsight; however, these problems had not been previously solved in strawberry, a species that had been described in the literature as "notoriously complex" and an "extreme example of difficulty". We comparatively genetically mapped the genomes of F. × ananassa and five wild octoploid taxa (the progenitors of F. × ananassa) and developed the first sub-genome resolved telomere-to-telomere genetic maps for octoploid strawberry (which yielded 28 contiguous linkage groups). This research established a common language for communicating genetic and physical coordinates and eliminated two decades of confusion surrounding linkage group nomenclature and sub-genome organization and enabled the development of a Rosetta stone for cross-referencing previously published linkage group nomenclatures (five had persisted in the literature). We discovered the first Fusarium wilt resistance (R) gene in strawberry and have since identified three additional R-genes and numerous sources of resistance to California, Australian, and Japanese races of the pathogen. These and other studies in our laboratory have shown that strawberry harbors a diverse arsenal of race-specific R-genes. To support marker-assisted selection, we developed high-throughput sub-genome specific DNA markers that are in linkage disequilibrium with the causative loci and accurately predict resistance phenotypes. Our studies and others have shown that the genetics of resistance to the other three diseases is complex (we have not found any evidence that race-specific R-genes play a role in resistance to these diseases). Using genomic prediction approaches, we have shown that genomic-estimated breeding values for resistance to Verticillium wilt can be accurately predicted, that heirloom cultivars and wild ecotypes harbor favorable alleles for resistance to Verticillium wilt that are not found in modern cultivars, and that genomic selection has significant potential to increase genetic gain and outperform phenotypic selection in strawberry.

Publications

• Type: Journal Articles Status: Published Year Published: 2019 Citation: Zurn JD, Ivors KL, Cole GS, Knapp SJ, Hummer KE, Hancock JF, Finn CE, Bassil NV (2020) Assessing cultivated strawberries and the Fragaria supercore for resistance to soilborne pathogens. J Am Pom Soc 74:18-23
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Whitaker V, Knapp SJ, Hardigan M, Edger P, Slovin J, Bassil N, Hyt�nen T, Mackenzie K, Lee S, Jung S, Main D, Barbey C, Verma S (2020) A roadmap for research in octoploid strawberry. Horticulture Research 7: 33. https://doi.org/10.1038/s41438-020-0252-1
• Type: Journal Articles Status: Submitted Year Published: 2020 Citation: Henry PM, Pincot DDA, Jenner B, Borrero C, Aviles M, Nam M-H, Knapp SJ, Gordon TR (2021) Horizontal chromosome transfer, convergent evolution, and host heterogeneity drive diversification in the global population of Fusarium oxysporum f. sp. fragariae. New Phytologist 230: 327340. https://doi.org/10.1111/nph.17141
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Hon T, Mars K, Young G, Tsai Y-C, Karalius J, Landolin J, Maurer N, Kudrna D, Hardigan MA, Steiner C, Knapp SJ, Ware D, Shapiro B, Peluso P, Rank D (2020) Highly accurate long-read HiFi sequencing data for five complex genomes. Nature Scientific Data 7: 399. https://doi.org/10.1038/s41597-020-00743-4
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Casttillejo C, Waurich V, Wagner H, Ramos R, Oiza N, Munoz P, Trivino JC, Caruana J, Liu Z, Cobo N, Hardigan MA, Knapp SJ, Vallarino JG, Osorio S, Martin-Pizarro C, Pose D, Toivainen T, Hytonen T, Oh Y, Barbey CR, Whitaker VM, Lee S, Olbricht K, Sanchez-Sevilla JF, Amaya I (2020) Allelic variation of MYB10 is the major force controlling natural variation of skin and flesh color in strawberry (Fragaria spp.) fruit. The Plant Cell 32: 3723-3749. https://doi.org/10.1105/tpc.20.00474
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Pincot DDA, Hardigan MA, Cole GS, Famula R, Henry PA, Gorden TR, Knapp SJ (2020) Accuracy of genomic selection and long-term genetic gain for resistance to Verticillium wilt in strawberry. The Plant Genome: e20054. https://doi.org/10.1002/tpg2.20054
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Hardigan MA, Feldmann MJ, Lorant A, Bird KA, Famula R, Acharya C, Cole GS, Edger PP, Knapp SJ (2020) Genome synteny has been conserved among the octoploid progenitors of cultivated strawberry over millions of years of evolution. Frontiers Plant Sci 10:1789. https://doi.org/10.3389/fpls.2019.01789
• Type: Journal Articles Status: Published Year Published: 2021 Citation: Bird K, Hardigan MA, Ragsdale AP, Knapp SJ, VanBuren R, Edger PE (2021) Diversification, spread, and admixture of octoploid strawberry in the Western Hemisphere. Amer. J Bot. 108: 2269-2281. https://doi.org/10.1002/ajb2.1776
• Type: Journal Articles Status: Published Year Published: 2021 Citation: Qiao Q, Edger PE, Qiong L, Lu J, Zhang Y, Cao Q, Yocca AE, Platts AE, Knapp SJ, Montagu MV, de Peer YV, Lei J, Zhang T (2021) Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.). Proceedings National Academy of Science 118: e2105431118. https://doi.org/10.1073/pnas.210543111
• Type: Journal Articles Status: Published Year Published: 2021 Citation: Petrasch S, Mesquida-Pesci SD, Pincot DDA, Feldmann MJ, Lopez CM, Famula R, Hardigan MA, Cole GS, Knapp SJ, Blanco-Ulate B (2021) Genomic prediction of strawberry resistance to postharvest fruit decay caused by the fungal pathogen Botrytis cinerea. G3: Genes|Genomes|Genetics jkab378. https://doi.org/10.1093/g3journal/jkab378
• Type: Journal Articles Status: Published Year Published: 2021 Citation: Feldmann MJ, Piepho HP, Bridges WC, Knapp SJ (2021) Average semivariance yields accurate estimates of the fraction of marker-associated genetic variance and heritability in complex trait analyses. PLOS Genetics 17: e1009762. https://doi.org/10.1371/journal.pgen.1009762
• Type: Journal Articles Status: Published Year Published: 2021 Citation: Hardigan MA, Lorant A, Pincot DDA, Feldmann MJ, Famula R, Acharya C, Lee Seonghee, Bassil NV, Whitaker VM, Cole GS, Knapp SJ (2021) Unraveling the complex hybrid ancestry and domestication history of cultivated strawberry. Molecular Biology & Evolution 38:2285-2305. https://doi.org/10.1093/molbev/msab024
• Type: Journal Articles Status: Published Year Published: 2021 Citation: Pincot, DDA, Ledda M, Feldmann MJ, Hardigan MA, Poorten TP, Heffelfinger C, Dellaporta S, Cole CS, Knapp SJ (2021) Social network analysis of the genealogy of cultivated strawberry: retracing the wild roots of modern cultivars. G3: Genes|Genomes|Genetics 11: jkab015. https://doi.org/10.1093/g3journal/jkab015
• Type: Journal Articles Status: Published Year Published: 2021 Citation: Nelson JR, Verman S, Bassil NV, Finn CE, Hancock JF, Cole CS, Knapp SJ, Whitaker VM (2020) Discovery and validation of three loci increasing resistance to charcoal rot caused by Macrophomina phaseolina in octoploid strawberry. G3: Genes|Genomes|Genetics 11:jkab037. https://doi.org/10.1093/g3journal/jkab037
• Type: Journal Articles Status: Submitted Year Published: 2022 Citation: Feldmann MJ, Piepho H-P, Knapp SJ (2022) Methods for calculating genomic relationship matrices affect the estimation of genomic heritability and genomic selection prediction accuracy. G3: Genes|Genomes|Genetics (submitted)
• Type: Journal Articles Status: Submitted Year Published: 2022 Citation: Pincot DDA, Feldmann MJ, Hardigan MA, Vachev MV, Henry PM, Gordon TR, Rodriguez A, Cobo N, Cole GS, Coaker GL, Knapp SJ (2022) Novel Fusarium wilt resistance genes uncovered in the wild progenitors and heirloom cultivars of strawberry. Theor. Appl. Genet.

Progress 10/01/19 to 09/30/20

Outputs
Target Audience:The target audiences for this research program are: (a) Strawberry growers, producers, processors, nursery propagators, and other industry stakeholders in the state of California, the US, and abroad; (b) Scientists in academia; (c) Scientists in the private sector, particularly the seed and nursery industry. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project has supported the training and professional development of four postdoctoral researchers, six graduate students, and five staff research associates. How have the results been disseminated to communities of interest?Our results have been disseminated through field days, virutal extension meetings, virtual scientific meetings, several UC, public, and non-profit websites, scientific journals, and the deposit of all of the scientific data in open source repositories. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? We released three day-neutral cultivars (UCD Royal Royce, Moxie, and Valiant) and two short-day cultivars (UCD Warrior and Victor) in 2019 (US Plant Patent applications are pending). We expect these cultivars to have a significant commercial impact. Warrior, Victor, and Moxie provide some of the strongest packages of resistance to soil-borne diseases in the industry, whereas Royal Royce and Valiant have produced record yields in California. The commercial demand for these cultivars has already outstripped supply. We completed three years of commercial testing and selection of extended day-neutral breeding materials and identified two EDN cultivars (EDN15 and 19) for commercial advancement and official release. Both are superior in fruit quality to the current market leader (Portola), which was validated by hedonic and sensory testing. EDN15 and 19 are currently being propagated by Foundation Plant Services (FPS) for commercial release in 2020-21 (pending the submission and approval of cultivar releases). We are working closely with FPS, IA, nurseries, and industry business partners to accelerate their introduction. Similar to the story for the recently released short-day and day-neutral cultivars, the commercial interest in and demand for EDN15 and 19 has already outstripped supply. We developed the first reference genomes for octoploid strawberry (F. × ananassa) and diploid F. iinumae, one of the diploid ancestors of F. × ananassa, in addition to developing a reference genome for diploid woodland strawberry (F. vesca) with chromosome-scale contiguity. The publication of these genomes has included the public release of the annotated genomes, DNA and RNA sequences for several diploid and octoploid Fragaria, and other supporting data at NCBI and DRYAD. The assembly of the octoploid genome was a significant achievement that has had a significant impact on strawberry research worldwide and created the foundation needed to overcome other long-standing technical barriers in the octoploid species complex. Following the assembly of an octoploid reference genome, we developed an innovative strategy for phasing and assembling complex polyploid genomes in outbred species using whole genome shotgun (WGS) genotyping by sequencing (GBS) of segregating populations developed from the reference genome parents. Using this strategy, we recently assembled four phased octoploid reference genomes, two for F. x ananassa (cultivated strawberry) and two for F. chiloensis subsp. lucida (beach strawberry)--the latter is a native of California and one of the octoploid progenitors of cultivated strawberry. This strategy appears to overcome the problem of haplotype collapse or switching during assembly and should be powerful for assembling complex genomes in other highly heterozygous species. Finally, we recently collaborated with investigators at Pacific Biosciences to assemble a chromosome-scale genome for UCD Royal Royce, one of our recently released dayneutral cultivars. We expect these phased octoploid genomes to become important resources for genome-informed studies in strawberry. We developed the first high-density single nucleotide polymorphism (SNP) genotyping platforms for strawberry using DNA variants anchored to the octoploid reference genome. This work included the development and pre-publication release of 50K and 850K SNP genotyping arrays that are being used in laboratories around the world. This work involved the genome-wide identification of sub-genome and copy-specific DNA variants and enabled the complete resolution of the four sub-genomes. We showed that short-read DNA sequences could be unambiguously aligned to an octoploid reference genome, which was essential for accurate DNA variant calling, GBS, and the application of other NGS-reliant approaches. This was an important breakthrough that seems trivial in hindsight; however, these problems had not been previously solved in strawberry, a species that had been described in the literature as "notoriously complex" and an "extreme example of difficulty". We comparatively genetically mapped the genomes of F. × ananassa and five wild octoploid taxa (the progenitors of F. × ananassa) and developed the first sub-genome resolved telomere-to-telomere genetic maps for octoploid strawberry (which yielded 28 contiguous linkage groups). This research established a common language for communicating genetic and physical coordinates and eliminated two decades of confusion surrounding linkage group nomenclature and sub-genome organization and enabled the development of a Rosetta stone for cross-referencing previously published linkage group nomenclatures (five had persisted in the literature). We discovered the first Fusarium wilt resistance (R) gene in strawberry and have since identified three additional R-genes and numerous sources of resistance to California, Australian, and Japanese races of the pathogen. These and other studies in our laboratory have shown that strawberry harbors a diverse arsenal of race-specific R-genes. To support marker-assisted selection, we developed high-throughput sub-genome specific DNA markers that are in linkage disequilibrium with the causative loci and accurately predict resistance phenotypes. Our studies and others have shown that the genetics of resistance to the other three diseases is complex (we have not found any evidence that race-specific R-genes play a role in resistance to these diseases). Using genomic prediction approaches, we have shown that genomic-estimated breedingvalues for resistance to Verticillium wilt can be accurately predicted, that heirloom cultivars and wild ecotypes harbor favorable alleles for resistance to Verticillium wilt that are not found in modern cultivars, and that genomic selection has significant potential to increase genetic gain and outperform phenotypic selection in strawberry.

Publications

• Type: Journal Articles Status: Published Year Published: 2021 Citation: Hardigan MA, Lorant A, Pincot DDA, Feldmann MJ, Famula R, Acharya C, Lee Seonghee, Bassil NV, Whitaker VM, Cole GS, Knapp SJ (2021) Unraveling the complex hybrid ancestry and domestication history of cultivated strawberry. Molecular Biology & Evolution (in press). https://doi.org/10.1093/molbev/msab024
• Type: Journal Articles Status: Published Year Published: 2021 Citation: Pincot, DDA, Ledda M, Feldmann MJ, Hardigan MA, Poorten TP, Heffelfinger C, Dellaporta S, Cole CS, Knapp SJ (2021) Social network analysis of the genealogy of cultivated strawberry: retracing the wild roots of modern cultivars. G3: Genes|Genomes|Genetics (in press). https://doi.org/10.1093/g3journal/jkab015
• Type: Journal Articles Status: Published Year Published: 2021 Citation: Henry PM, Pincot DDA, Jenner B, Borrero C, Aviles M, Nam M-H, Knapp SJ, Gordon TR (2021) Horizontal chromosome transfer, convergent evolution, and host heterogeneity drive diversification in the global population of Fusarium oxysporum f. sp. fragariae. New Phytologist (in press) https://doi.org/10.1111/nph.17141
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Hon T, Mars K, Young G, Tsai Y-C, Karalius J, Landolin J, Maurer N, Kudrna D, Hardigan MA, Steiner C, Knapp SJ, Ware D, Shapiro B, Peluso P, Rank D (2020) Highly accurate long-read HiFi sequencing data for five complex genomes. Nature Scientific Data 7: 399. https://doi.org/10.1038/s41597-020-00743-4
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Casttillejo C, Waurich V, Wagner H, Ramos R, Oiza N, Munoz P, Trivino JC, Caruana J, Liu Z, Cobo N, Hardigan MA, Knapp SJ, Vallarino JG, Osorio S, Martin-Pizarro C, Pose D, Toivainen T, Hytonen T, Oh Y, Barbey CR, Whitaker VM, Lee S, Olbricht K, Sanchez-Sevilla JF, Amaya I (2020) Allelic variation of MYB10 is the major force controlling natural variation of skin and flesh color in strawberry (Fragaria spp.) fruit. The Plant Cell 32: 3723-3749. DOI: 10.1105/tpc.20.00474.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Pincot DDA, Hardigan MA, Cole GS, Famula R, Henry PA, Gorden TR, Knapp SJ (2020) Accuracy of genomic selection and long-term genetic gain for resistance to Verticillium wilt in strawberry. The Plant Genome: e20054. https://doi.org/10.1002/tpg2.20054.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Feldmann MJ, Hardigan MA, Famula RA, L�pez CM, Tabb A, Cole GS, Knapp SJ (2020) Multi-dimensional machine learning approaches for fruit shape recognition and phenotyping in strawberry. GigaScience 9. https://doi.org/10.1093/gigascience/giaa030
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Whitaker V, Knapp SJ, Hardigan M, Edger P, Slovin J, Bassil N, Hyt�nen T, Mackenzie K, Lee S, Jung S, Main D, Barbey C, Verma S (2020) A roadmap for research in octoploid strawberry. Horticulture Research 7: 33. https://doi.org/10.1038/s41438-020-0252-1
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Hardigan MA, Feldmann MJ, Lorant A, Bird KA, Famula R, Acharya C, Cole GS, Edger PP, Knapp SJ (2020) Genome synteny has been conserved among the octoploid progenitors of cultivated strawberry over millions of years of evolution. Frontiers Plant Sci 10:1789. https://doi.org/10.3389/fpls.2019.01789
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Edger PP, McKain MR, Yocca AE, Knapp SJ, Qiao Q, Zhang T (2020) Reply to: Revisiting the origin of octoploid strawberry. Nat Genet 52:57. https://doi.org/10.1038/s41588-019-0544-2
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Zurn JD, Ivors KL, Cole GS, Knapp SJ, Hummer KE, Hancock JF, Finn CE, Bassil NV (2020) Assessing cultivated strawberries and the Fragaria supercore for resistance to soilborne pathogens. J Am Pom Soc 74:18-23
• Type: Theses/Dissertations Status: Published Year Published: 2020 Citation: Feldmann MJ (2020) A Quantitative Analysis of Complex, Agronomic Traits in Garden Strawberry (Fragaria � ananassa). Ph.D. Dissertation, University of California, Davis.
• Type: Theses/Dissertations Status: Published Year Published: 2020 Citation: Pincot DDA (2020) The Genealogy of Strawberry and Host Resistance in Strawberry-Vascular Wilt Pathosystems. Ph.D. Dissertation, University of California, Davis.
• Type: Theses/Dissertations Status: Published Year Published: 2020 Citation: Petrasch S (2020) Genetics of Strawberry Postharvest Fruit Quality and Resistance to Necrotrophic Fungi. Ph.D. Dissertation, University of California, Davis.
• Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Nelson JR, Verman S, Bassil NV, Finn CE, Hancock JF, Cole CS, Knapp SJ, Whitaker VM (2020) Discovery and validation of three loci increasing resistance to charcoal rot caused by Macrophomina phaseolina in octoploid strawberry. G3: Genes|Genomes|Genetics (in press).
• Type: Journal Articles Status: Submitted Year Published: 2021 Citation: Feldmann MJ, Piepho HP, Bridges WC, Knapp SJ (2021) Accurate estimation of marker-associated genetic variance and heritability in complex trait analysis. Theoretical and Applied Genetics (submitted).

Progress 10/01/18 to 09/30/19

Outputs
Target Audience:The target audiences for this research program are: (a) Strawberry growers, producers, processors, nursery propagators, and other industry stakeholders in the state of California, the US, and abroad. (b) Scientists in academia. (c) Scientists in the private sector, particularly the seed and nursery industry. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project has supported the training and professional development of four postdoctoral researchers, six graduate students, and three staff research associates. How have the results been disseminated to communities of interest?We have presented at least 20 posters or invited talks at scientific meetings. Progress reports and scientific results were presented at field days, cooperative extension meetings, and additional meetings with stakeholders. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? We released three day-neutral cultivars (UCD Royal Royce, Moxie, and Valiant) and two short-day cultivars (UCD Warrior and Victor) in 2019 (US Plant Patent applications are pending). We expect these cultivars to have a significant commercial impact. Warrior, Victor, and Moxie provide some of the strongest packages of resistance to soil-borne diseases in the industry, whereas Royal Royce and Valiant have produced record yields in California. The commercial demand for these cultivars has already outstripped supply. We completed three years of commercial testing and selection of extended day-neutral breeding materials and identified two EDN cultivars (EDN15 and 19) for commercial advancement and official release. Both are superior in fruit quality to the current market leader (Portola), which was validated by hedonic and sensory testing. EDN15 and 19 are currently being propagated by Foundation Plant Services (FPS) for commercial release in 2020-21 (pending the submission and approval of cultivar releases). We are working closely with FPS, IA, nurseries, and industry business partners to accelerate their introduction. Similar to the story for the recently released short-day and day-neutral cultivars, the commercial interest in and demand for EDN15 and 19 has already outstripped supply. We developed the first reference genomes for octoploid strawberry (F. × ananassa) and diploid F. iinumae, one of the diploid ancestors of F. × ananassa, in addition to developing a reference genome for diploid woodland strawberry (F. vesca) with chromosome-scale contiguity. The publication of these genomes has included the public release of the annotated genomes, DNA and RNA sequences for several diploid and octoploid Fragaria, and other supporting data at NCBI and DRYAD. The assembly of the octoploid genome was a significant achievement that has had a significant impact on strawberry research worldwide and created the foundation needed to overcome other long-standing technical barriers in the octoploid species complex. Following the assembly of an octoploid reference genome, we developed an innovative strategy for phasing and assembling complex polyploid genomes in outbred species using whole genome shotgun (WGS) genotyping by sequencing (GBS) of segregating populations developed from the reference genome parents. Using this strategy, we recently assembled four phased octoploid reference genomes, two for F. x ananassa (cultivated strawberry) and two for F. chiloensis subsp. lucida (beach strawberry)--the latter is a native of California and one of the octoploid progenitors of cultivated strawberry. This strategy appears to overcome the problem of haplotype collapse or switching during assembly and should be powerful for assembling complex genomes in other highly heterozygous species. Finally, we recently collaborated with investigators at Pacific Biosciences to assemble a chromosome-scale genome for UCD Royal Royce, one of our recently released day-neutral cultivars. We expect these phased octoploid genomes to become important resources for genome-informed studies in strawberry. We developed the first high-density single nucleotide polymorphism (SNP) genotyping platforms for strawberry using DNA variants anchored to the octoploid reference genome. This work included the development and pre-publication release of 50K and 850K SNP genotyping arrays that are being used in laboratories around the world. This work involved the genome-wide identification of sub-genome and copy-specific DNA variants and enabled the complete resolution of the four sub-genomes. We showed that short-read DNA sequences could be unambiguously aligned to an octoploid reference genome, which was essential for accurate DNA variant calling, GBS, and the application of other NGS-reliant approaches. This was an important breakthrough that seems trivial in hindsight; however, these problems had not been previously solved in strawberry, a species that had been described in the literature as "notoriously complex" and an "extreme example of difficulty". We comparatively genetically mapped the genomes of F. × ananassa and five wild octoploid taxa (the progenitors of F. × ananassa) and developed the first sub-genome resolved telomere-to-telomere genetic maps for octoploid strawberry (which yielded 28 contiguous linkage groups). This research established a common language for communicating genetic and physical coordinates and eliminated two decades of confusion surrounding linkage group nomenclature and sub-genome organization and enabled the development of a Rosetta stone for cross-referencing previously published linkage group nomenclatures (five had persisted in the literature). We discovered the first Fusarium wilt resistance (R) gene in strawberry and have since identified three additional R-genes and numerous sources of resistance to California, Australian, and Japanese races of the pathogen. These and other studies in our laboratory have shown that strawberry harbors a diverse arsenal of race-specific R-genes. To support marker-assisted selection, we developed high-throughput sub-genome specific DNA markers that are in linkage disequilibrium with the causative loci and accurately predict resistance phenotypes. Our studies and others have shown that the genetics of resistance to the other three diseases is complex (we have not found any evidence that race-specific R-genes play a role in resistance to these diseases). Using genomic prediction approaches, we have shown that genomic-estimated breeding values for resistance to Verticillium wilt can be accurately predicted, that heirloom cultivars and wild ecotypes harbor favorable alleles for resistance to Verticillium wilt that are not found in modern cultivars, and that genomic selection has significant potential to increase genetic gain and outperform phenotypic selection in strawberry.

Publications

• Type: Journal Articles Status: Accepted Year Published: 2020 Citation: Feldmann MJ, Hardigan MA, Famula RA, L�pez CM, Tabb A, Cole GS, and Knapp SJ. (2020) Multi-dimensional machine learning approaches for fruit shape recognition and phenotyping in strawberry. GigaScience (in press).
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Hardigan MA, Feldmann MJ, Lorant A, Bird KA, Famula R, Acharya C, Cole GS, Edger PP, Knapp SJ (2020) Genome synteny has been conserved among the octoploid progenitors of cultivated strawberry over millions of years of evolution. Frontiers Plant Sci 10:1789. https://doi.org/10.3389/fpls.2019.01789
• Type: Journal Articles Status: Submitted Year Published: 2020 Citation: Pincot DDA, Hardigan MA, Cole GS, Famula R, Henry PA, Gorden TR, Knapp SJ (2020) Accuracy of genomic selection and long-term genetic gain for resistance to Verticillium wilt in a genetically diverse population of strawberry. The Plant Genome (submitted).
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Whitaker V, Knapp SJ, Hardigan M, Edger P, Slovin J, Bassil N, Hyt�nen T, Mackenzie K, Lee S, Jung S, Main D, Barbey C, Verma S (2020) A roadmap for research in octoploid strawberry. Horticulture Research (in press).
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Barbey C, Lee S, Verma S, Bird KA, Yocca AE, Edger PP, Knapp SJ, Whitaker VM, Folta K (2019) Disease resistance genetics and genomics in octoploid strawberry. G3: Genetics Genomes Genes (accepted). https://doi.org/10.1101/646000
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Edger PP, McKain MR, Yocca AE, Knapp SJ, Qiao Q, Zhang T (2020) Reply to: Revisiting the origin of octoploid strawberry. Nat Genet 52:57. https://doi.org/10.1038/s41588-019-0544-2
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Zurn JD, Ivors KL, Cole GS, Knapp SJ, Hummer KE, Hancock JF, Finn CE, Bassil NV (2020) Assessing cultivated strawberries and the Fragaria supercore for resistance to soilborne pathogens. J Am Pom Soc 74:18-23
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Petrasch S, Knapp SJ, van Kan JAL, Blanco-Ulate B (2019) Grey mould of strawberry, a devastating disease caused by the ubiquitous necrotrophic fungal pathogen Botrytis cinerea. Mol. Plant Path. 20: 877-892.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Petrasch S, Silva CJ Mesquida-Pesci SD, Gallegos K, van den Abeele C, Papin V, Fernandez-Acero FJ, Knapp SJ, Blanco-Ulate B (2019) Infection strategies deployed by Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer as a function of tomato fruit ripening stage. Front. Plant Sci. 10: 1-17.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi S, Nelson ADL, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, Ben- Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Acharya CB, Cole GS, Mower JP, Childs KL, Jiang N, Lyons E, Freeling M, Puzey JR, Knapp SJ (2019) Origin and evolution of the octoploid strawberry genome. Nature Genetics 51: 541547. doi: 10.1038/ s41588-019-0356-4.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Noh Y-H, Oh Y, Mangandi J, Verma S, Zurn JD, Lu Y-T, Fan Z, Bassil N, Peres N, Cole GS, Acharya C, Famula R, Knapp SJ, Whitaker VM, Lee S (2018) High-throughput marker assays for FaRPc2-mediated resistance to Phytopthora crown rot in octoploid strawberry. Molecular Breeding 38: 104. https://doi.org/10.1007/ s11032-018-0861-7
• Type: Journal Articles Status: Submitted Year Published: 2020 Citation: Henry PM, Pincot DD, Anchieta A, Jenner B, Brinker S, Borrero C, Aviles M, Nam MH, Klosterman SJ, Knapp SJ, Gordon TR (2020) Horizontal chromosome transfer, convergent evolution, and host heterogeneity drive diversification in the global population of Fusarium oxysporum f. sp. fragariae. Proc Nat Acad Sci (submitted)

Progress 10/01/17 to 09/30/18

Outputs
Target Audience:The target audiences for this research program are: (a) strawberry growers, producers, processors, nursery propagators, and other industry stakeholders in the state of California, the US, and abroad; (b) scientists in academia; and (c) scientists in the private sector, particularly the seed and nursery industry. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project has provided training and professional development opportunities for at least 12 people, including graduate students, staff research associates, and postdoctoral researchers. How have the results been disseminated to communities of interest?Yes, through field days, presentations at stakeholder and scientific meetings, written and verbal reports to funding agencies, and scientific publications. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; Helvetica Neue'; -webkit-text-stroke: #000000} p.p2 {margin: 0.0px 0.0px 0.0px 0.0px; Helvetica Neue'; -webkit-text-stroke: #000000; min-height: 12.0px} span.s1 {font-kerning: none} Several important milestones were achieved in 2018, including the identification of several promising cultivars for day-neutral, short-day, and summer-plant production systems, the development of genomic tools and resources that are transforming breeding and genomic-enabled research in strawberry.

Publications

• Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi S, Nelson ADL, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Acharya CB, Cole GS, Mower JP, Childs KL, Jiang N, Lyons E, Freeling M, Puzey JR, Knapp SJ (2018) Origin and evolution of the octoploid strawberry genome. Nature Genetics
• Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Petrasch S, Knapp SJ, va Kan JAL, Blanco-Ulate B (2018) Gray mold of strawberry, a devastating disease caused by the ubiquitous necrotrophic fungal pathogen Botrytis cinerea. Mol. Plant Path.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Hardigan MA, Poorten TJ, Acharya C, Cole GS, Hummer K, Bassil N, Edger PP, Knapp SJ (2018) Domestication of temperate and coastal hybrids selected different ancestral genomes in octoploid strawberry. The Plant Genome
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Noh Y-H, Oh Y, Mangandi J, Verma S, Zurn JD, Lu Y-T, Fan Z, Bassil N, Peres N, Cole GS, Acharya C, Famula R, Knapp SJ, Whitaker VM, Lee S (2018) High-throughput marker assays for FaRPc2-mediated resistance to Phytopthora crown rot in octoploid strawberry. Molecular Breeding
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Pincot DD, Poorten TJ, Hardigan MA, Harshman JM, Acharya CB, Cole GS, Gordon TR, Stueven M, Edger PP, Knapp SJ (2018) Genome-wide association mapping uncovers Fw1, a dominant gene conferring resistance to Fusarium wilt in strawberry. G3: Genetics|Genomes|Genes 8: 1817-1828.

Progress 10/01/16 to 09/30/17

Outputs
Target Audience:The target audiences for this research program are: (a) Strawberry growers, producers, processors, nursery propagators, and other industry stakeholders in the state of California, the US, and abroad. (b) Scientists in academia. (c) Scientists in the private sector, particularly the seed and nursery industry. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project has provided training for four graduate students, three postdoctoral scholars, and five research associates. How have the results been disseminated to communities of interest?Progress reports and scientific results were presented at three industry field days, three cooperative extension meetings, and four meetings with stakeholders and university faculty. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Two day-neutral and two short-day experimental cultivars were identified for commercial advancement. These were submitted to Foundation Plant Services for the development of disease-free nursery stock, multipled in high-elevation nurseries (to produce planting stock for commercial testing), and are currently in commercial testing. We identified a gene conferring resistance to Fusarium wilt and multiple novel sources of resistance to Fusarium wilt, currently most important disease problem in California and many other parts of the world. We discovered several sources of resistance to Macrophomina and that the genetics of resistance to Macrophomina is complex. Similarly, we discovered several sources of resistance to Verticillium wilt, that the genetics of resistance to Verticillium wilt is complex, and that UCD strawberry breeding program has some of the strongest sources of resistance to Verticillium wilt.

Publications

• Type: Journal Articles Status: Published Year Published: 2017 Citation: Edger P, VanBuren R, Colle M, Poorten T, Man Wai C, Niederhuth C, Alger EI, Ou Shujun, Acharya C, Wang Jie, Callow P, McKain M, Shi J, Collier C, Xiong Z, Mower J, Slovin J, Hyt�nen T, Jiang N, Childs K, Knapp SJ (2017) Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity. Gigascience, doi.org/10.1093/gigascience/gix124
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Verma, S., Bassil, N.V., van de Weg, E., Harrison, R.J., Monfort, A., Hidalgo, J.M., Amaya, I., Denoyes, B., Mahoney, L., Davis, T.M., Fan, Z., Knapp, S. and Whitaker, V.M. (2017). Development and evaluation of the Axiom�IStraw35 384HT array for the allo-octoploid cultivated strawberry Fragaria�ananassa. Acta Hortic. 1156, 75-82
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Badouin H, Gouzy, J, Grassa CJ, Carrere S, Baptiste Mayjonade B, Legrand L, Gill N, Kane NC, Bowers JE, Hubner S, Bellec A, Berard A, Berges H, Blanchet N, Boniface MC, Dominique B, Catrice O, Chaidir N, Claudel C, Donnadieu C, Faraut T, Fievet G, Helmstetter N, King M, Knapp SJ, Lai Z, Paslier MC, Lippi Y, Lorenzon L, Mandel J, Marage G, Marchand G, Marquand E, Mestries E, Morien E, Nambeesan S, Nguyen T, Pegot-Espagnet P, Pouilly N, Raftis F, Sallet E, Schiex T, Thomas J, Vandecasteele C, Vares D, Vear F, Vautrin S, Crespi M, Mangin B, Burke JM, Salse J, Munos S, Vincourt P, Rieseberg LH, Langlade NB (2017) The sunflower genome illuminates the evolutionary history of the Asterids and provides new insights into oil metabolism and flowering time. Nature 546: 148-161, doi:10.1038/nature22380
• Type: Journal Articles Status: Submitted Year Published: 2018 Citation: Pincot D.D.A., Poorten T.J., Hardigan M.A., Harshman J.M., Acharya C.B., Cole G.S., Gordon T.R., Stueven M., Edger P.P., Knapp S.J. (2018) Genome-wide association mapping uncovers FoR2C-1, a dominant gene conferring resistance to Fusarium wilt in strawberry. G3: Genes, Genomes, Genetics
• Type: Journal Articles Status: Submitted Year Published: 2018 Citation: Hardigan MA, Poorten TJ, Acharya CA, Cole GS, Hummer KE, Bassil N, Edger P, Knapp SJ (2018) Domestication history of strawberry: selection and genetic bottlenecks shaping the octoploid hybrid complex. Proc. Natl. Acad. Sci.