Publications

Peer Reviewed Publications: (Ordered from New to Old)

  • Feldmann, M. J., Pincot, D. D., Cole, G. S., & Knapp, S. J. (expected 2024) Genetic Gains Underpinning a Little-Known Strawberry Green Revolution. Nature Communications, in review.
  • Knapp, S.J., Cole, G.S., Pincot, D. D., Dilla-Ermita, C. J., Bjornson, M., Famula, R. A., Gordon, T. R., Harshman, J. M., Henry, P. M., & Feldmann, M. J. (2024) Transgressive Segregation, Hopeful Monsters, and Phenotypic Selection Drove Rapid Genetic Gains and Breakthroughs in Predictive Breeding for Quantitative Resistance to Macrophomina in Strawberry. Horticulture Research, accepted. 
  • Knapp, S. J., Cole, G. S., Pincot, D. D., Lòpez, C. M., Gonzalez-Benitez, O. A., & Famula, R. A. (2023). ‘UC Eclipse’, a Summer Plant-adapted Photoperiod-insensitive Strawberry Cultivar. HortScience, 58(12), 1568-1572. https://doi.org/10.21273/HORTSCI17363-23
  • Feldmann, M. J., Pincot, D. D., Vachev, M. V., Famula, R. A., Cole, G. S., & Knapp, S. J. (2023). Accelerating genetic gains for quantitative resistance to Verticillium wilt through predictive breeding in strawberry. The Plant Genome, e20405. https://doi.org/10.1002/tpg2.20405
  • Hardigan, M. A., Feldmann, M. J., Carling, J., Zhu, A., Kilian, A., Famula, R. A., Cole, G. S., & Knapp, S. J. (2023). A medium‐density genotyping platform for cultivated strawberry using DArTag technology. The Plant Genome, 16(4), e20399. https://doi.org/10.1002/tpg2.20399
  • Feldmann, M. J., Covarrubias-Pazaran, G., & Piepho, H. P. (2023). Complex traits and candidate genes: estimation of genetic variance components across multiple genetic architectures. G3: Genes, Genomes, Genetics, 13(9), jkad148. https://doi.org/10.1093/g3journal/jkad148
  • Pincot, D. D., Feldmann, M. J., Hardigan, M. A., Vachev, M. V., Henry, P. M., Gordon, T. R., Bjornson, M., Rodriguez, A., Cobo, N., Famula, R. A., Cole, G. S., Coaker, G. L., & Knapp, S. J. (2022). Novel Fusarium wilt resistance genes uncovered in natural and cultivated strawberry populations are found on three non-homoeologous chromosomes. Theoretical and Applied Genetics, 135(6), 2121-2145. https://doi.org/10.1007/s00122-022-04102-2
  • Fan, Z., Tieman, D. M., Knapp, S. J., Zerbe, P., Famula, R., Barbey, C. R., Folta, K. M., Amadeu, R. R., Lee, M., Oh, Y., Lee, S., & Whitaker, V. M. (2022). A multi‐omics framework reveals strawberry flavor genes and their regulatory elements. New Phytologist, 236(3), 1089–1107. https://doi.org/10.1111/nph.18416
  • Jiménez, N. P., Feldmann, M. J., Famula, R. A., Pincot, D. D., Bjornson, M., Cole, G. S., & Knapp, S. J. (2022). Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry. The Plant Genome, 16, e20275. https://doi.org/10.1002/tpg2.20275
  • Feldmann, M. J., & Tabb, A. (2022). Cost‐effective, high‐throughput phenotyping system for 3D reconstruction of fruit form. The Plant Phenome Journal, 5, e20029. https://doi.org/10.1002/ppj2.20029
  • Feldmann, M. J., Piepho, H. P., & Knapp, S. J. (2022). Average semivariance directly yields accurate estimates of the genomic variance in complex trait analyses. G3: Genes, Genomes, Genetics, 12(6), jkac080. https://doi.org/10.1093/g3journal/jkac080
  • Petrasch, S., Mesquida-Pesci, S. D., Pincot, D. D., Feldmann, M. J., López, C. M., Famula, R., Hardigan, M. A., Cole, G. S., Knapp, S. J., & Blanco-Ulate, B. (2022). Genomic prediction of strawberry resistance to postharvest fruit decay caused by the fungal pathogen Botrytis cinerea. G3: Genes, Genomes, Genetics, 12(1), jkab378. https://doi.org/10.1093/g3journal/jkab378
  • Qiao, Q., Edger, P. P., Xue, L., Qiong, L., Lu, J., Zhang, Y., Cao, Q., Yocca, A. E., Platts, A. E., Knapp, S. J., Van Montagu, M., Van de Peer, Y., Lei, J., & Zhang, T. (2021). Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.). Proceedings of the National Academy of Sciences, 118(45). https://doi.org/10.1073/pnas.2105431118 
  • Feldmann, M. J., Piepho, H. P., Bridges, W. C., & Knapp, S. J. (2021). Average semivariance yields accurate estimates of the fraction of marker-associated genetic variance and heritability in complex trait analyses. PLoS Genetics, 17(8), e1009762. https://doi.org/10.1371/journal.pgen.1009762
  • Feldmann, M. J., Gage, J. L., Turner‐Hissong, S. D., & Ubbens, J. R. (2021). Images carried before the fire: The power, promise, and responsibility of latent phenotyping in plants. The Plant Phenome Journal, 4, e20023. https://doi.org/10.1002/ppj2.20023
  • Hardigan, M. A., Lorant, A., Pincot, D. D., Feldmann, M. J., Famula, R. A., Acharya, C. B., Lee, S., Verma, S., Whitaker, V. M., Bassil, N., Zurn, J., Cole, G. S., Bird, K., Edger, P. P., & Knapp, S. J. (2021). Unraveling the complex hybrid ancestry and domestication history of cultivated strawberry. Molecular Biology and Evolution, 38(6), 2285-2305. https://doi.org/10.1093/molbev/msab024
  • Henry, P. M., Pincot, D. D., Jenner, B. N., Borrero, C., Aviles, M., Nam, M. H., Epstein, L., Knapp, S. J., & Gordon, T. R. (2021). Horizontal chromosome transfer and independent evolution drive diversification in Fusarium oxysporum f. sp. fragariae. New Phytologist, 230, 327-340. https://doi.org/10.1111/nph.17141
  • Pincot, D. D. A., Ledda, M., Feldmann, M. J., Hardigan, M. A., Poorten, T. J., Runcie, D. E., Heffelfinger, C., Dellaporta, S. L., Cole, G. S., & Knapp, S. J. (2021). Social network analysis of the genealogy of strawberry: retracing the wild roots of heirloom and modern cultivars. G3: Genes, Genomes, Genetics, 11(3), jkab015. https://doi.org/10.1093/g3journal/jkab015
  • Whitaker, V. M., Knapp, S. J., Hardigan, M. A., Edger, P. P., Slovin, J. P., Bassil, N. V., Hytönen, T., Mackenzie, K. K., Lee, S., Jung, S., Main, D., Barbey, C. R., & Verma, S. (2020). A roadmap for research in octoploid strawberry. Horticulture Research, 7, 33. https://doi.org/10.1038/s41438-020-0252-1 
  • Castillejo, C., Waurich, V., Wagner, H., Ramos, R., Oiza, N., Muñoz, P., Triviño, J. C., Caruana, J., Liu, Z., Cobo, N., Hardigan, M. A., Knapp, S. J., Vallarino, J. G., Osorio, S., Martín-Pizarro, C., Posé, D., Toivainen, T., Hytönen, T., Oh, Y., Barbey, C. R., Whitaker, V. M., Lee, S., Olbricht, K., Sánchez-Sevilla, J. F., & Amaya, I. (2020). Allelic variation of MYB10 is the major force controlling natural variation in skin and flesh color in strawberry (Fragaria spp.) fruit. The Plant Cell, 32(12), 3723–3749. https://doi.org/10.1105/tpc.20.00474 
  • Pincot, D. D. A., Hardigan, M. A., Cole, G. S., Famula, R. A., Henry, P. M., Gordon, T. R., & Knapp, S. J. (2020). Accuracy of genomic selection and long‐term genetic gain for resistance to Verticillium wilt in strawberry. The Plant Genome, 13(3), e20054. https://doi.org/10.1002/tpg2.20054
  • Edger, P. P., Poorten, T. J., VanBuren, R., Hardigan, M. A., Colle, M., McKain, M. R., Smith, R. D., Teresi, S. J., Nelson, A. D., Wai, C. M., Alger, E. I., Bird, K. A., Yocca, A. E., Pumplin, N., Ou, S., Ben-Zvi, G., Brodt, A., Baruch, K., Swale, T., Shiue, L., Acharya, C. B., Cole, G. S., Mower, J. P., Childs, K. L., Jiang, N., Lyons, E., Freeling, M., Puzey, J. R., & Knapp, S. J. (2019). Origin and evolution of the octoploid strawberry genome. Nature Genetics, 51(3), 541–547. https://doi.org/10.1038/s41588-019-0356-4 
  • Petrasch, S., Silva, C. J., Mesquida-Pesci, S. D., Gallegos, K., Van Den Abeele, C., Papin, V., Fernandez-Acero, F. J., Knapp, S. J., & Blanco-Ulate, B. (2019). Infection strategies deployed by Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer as a function of tomato fruit ripening stage. Frontiers in Plant Science, 10, 223. https://doi.org/10.3389/fpls.2019.00223
  • Petrasch, S., Knapp, S. J., Van Kan, J. A., & Blanco‐Ulate, B. (2019). Grey mould of strawberry, a devastating disease caused by the ubiquitous necrotrophic fungal pathogen Botrytis cinerea. Molecular Plant Pathology, 20(6), 877-892. https://doi.org/10.1111/mpp.12794
  • Hardigan, M. A., Poorten, T. J., Acharya, C. B., Cole, G. S., Hummer, K. E., Bassil, N., Edger, P. P., & Knapp, S. J. (2018). Domestication of temperate and coastal hybrids with distinct ancestral gene selection in octoploid strawberry. The Plant Genome, 11(3), 180049. https://doi.org/10.3835/plantgenome2018.07.0049
  • 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 Fw1, a dominant gene conferring resistance to Fusarium wilt in strawberry. G3: Genes, Genomes, Genetics, 8(5), 1817-1828. https://doi.org/10.1534/g3.118.200129
  • Edger, P. P., VanBuren, R., Colle, M., Poorten, T. J., Wai, C. M., Niederhuth, C. E., Alger, E. I., Ou, S., Acharya, C. B., Wang, J., Callow, P., McKain, M. R., Shi, J., Collier, C., Xiong, Z., Mower, J. P., Slovin, J. P., Hytönen, T., Jiang, N., Childs, K. L., & Knapp, S. J. (2017). Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity. GigaScience, 7(2), gix124. https://doi.org/10.1093/gigascience/gix124 

 

Related Preprints: (Ordered from New to Old)

Preprints associated with a published, peer-reviewed manuscript are not listed.

  • Hardigan, M. A., Feldmann, M. J., Pincot, D. D., Famula, R. A., Vachev, M. V., Madera, M. A., Zerbe, P., Mars, K., Peluso, P., Rank, D., Ou, S., Saski, C. A., Acharya, C. B., Cole, G. S., Yocca, A. E., Platts, A. E., Edger, P. P., & Knapp, S. J. (2021). Blueprint for phasing and assembling the genomes of heterozygous polyploids: application to the octoploid genome of strawberry. bioRxiv, 2021.11.03.467115.  https://doi.org/10.1101/2021.11.03.467115
  • Hardigan, M. A., Feldmann, M. J., Lorant, A., Famula, R., Acharya, C., Cole, G., Edger, P. P., & Knapp, S. J. (2019). Chromosome evolution of octoploid strawberry. bioRxiv, 861526. https://doi.org/10.1101/861526