Dr. Jonathan Fresnedo Ramirez

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Assistant Professor

fresnedoramirez.1@osu.edu

330-263-3822

Office:

204A Williams Hall - Wooster Campus

Lab 217A Williams Hall - Wooster Campus

Professional Information

Degrees & Credentials:

2000-2007 B.S. Agronomy and Plant Production, Universidad Autónoma Chapingo, Mexico

2009-2014 Ph.D. Horticulture & Agronomy, University of California – Davis, USA

2014-2016 Post-doctoral associate. Institute of Biotechnology, Cornell University, USA

Research Area(s):

Plant domestication and breeding

Genetic improvement for biomaterials production

Quantitative genetics of outcrossing crops

Applied bioinformatics

Plant genomics

Biomaterials

Fruits and nuts

Germplasm improvement of outcrossing species

Plant genetic resources

Biography:

Jonathan Fresnedo Ramirez, Ph.D. earned his B.S. in Agronomy and Plant Production from Universidad Autónoma Chapingo in Mexico. Subsequently, he earned his Ph.D. at the University of California at Davis working on the implementation of genomics and Bayesian statistics in the genetic improvement of perennial fruits such as peach and almond. In the Institute of Biotechnology at Cornell University, he was a Postdoctoral Associate working with genomics and breeding of grapevine and related species in the genus Vitis. In August 2016, Jonathan joined the Department of Horticulture and Crop Science at The Ohio State University, established at the Ohio Agricultural and Development Center (OARDC) on the Wooster campus.

Classes Taught:

HCS 7806: Introduction to concepts of Bayesian statistics (Autumn 2017, Spring 2020)

HCS 7806: Fundamentals of molecular population genetics (Summer 2020)

HCS 7194: Genome Analytics (Autumn 2018, Autumn 2019)

HCS 7004: Genome Analytics (Autumn 2020)

HCS 7625: Plant Breeding and Biotechnology (Autumn 2020)

Other academic affiliations

Core Faculty member of the Sustainability Institute (https://si.osu.edu/)

Member of Center for Applied Plant Sciences (https://caps.osu.edu/)

The Fresnedo lab:

Jonathan is interested in the use and implementation of genomics for efficient germplasm improvement of outcrossing species and domestication of new crops. Trait targets include the production of biomaterials. The research pursued by graduate students, visiting researchers and staff in Jonathan’s lab is expected to deliver results and technologies relevant for outbreeding species considering translational and applied perspectives. The outcomes from this research will also be developed in a perspective of a sustainable and resilient economy.

Major Projects

Genomic characterization of aging and its effect in perennial crops with emphasis in almond
Domestication and characterization of Taraxacum kok-saghyz as a novel source of natural rubber
Integration of genomics and metabolomics for the improvement of apple (collaboration with the Cooperstone lab: https://phytochemicals.osu.edu and Dr. Diane Miller: https://hcs.osu.edu/our-people/dr-diane-miller)

Current graduate advisees

Daniel Williams – joined the lab in 2019, his project address issues on the domestication and genetic characterization of Taraxacum kok-saghyz. Ph.D. expected in 2023.
Camila Gutierrez Manriquez – joined the lab in 2021, her project aims the development of molecular markers for self-compatibility in Taraxacum kok-saghyz. M. Sc. expected in 2023.

Former graduate advises

Matthew Willman – 2017-2019, earned a M. Sc. working on the genetic characterization of black raspberry (Rubus occidentalis) to enhance its breeding.
Katherine D’Amico –2017-2020, earned a Ph.D. addressing the role of epigenetics in the ageing outcrossing perennial crops using almond and the bud-failure disorder as a model. Katie received an USDA NIFA AFRI Predoctoral Fellowship in 2018.

Works

Journal articles

^§Graduate Advisee ^¶Undergraduate advisee ^‡Committee member advisee ^†Visiting scholar

D’Amico-Willman K.M.^§, Niederhuth C., Anderson, E.S.^¶, Gradziel T.M., Fresnedo-Ramírez, J. (2021). Integrated analysis of the methylome and transcriptome of twin almonds (Prunus dulcis [Mill.] D.A.Webb) reveals genomic features associated with non-infectious bud failure, Pre-print: https://doi.org/10.1101/2020.09.25.294074
Bilbrey, E.A.^‡, Williamson K., Hatzakis, E., Miller D.D., Fresnedo-Ramírez, J., Cooperstone J.L. (2021). Integrating genomics and multi-platform metabolomics enables metabolite QTL detection in breeding-relevant apple germplasm. Pre-print: https://doi.org/10.1101/2021.02.18.431481
D’Amico-Willman K.M.^§, Niederhuth C., Gradziel T.M., Ouma W.Z., Meulia T., Fresnedo-Ramírez, J. (2020). Integrated analysis of the methylome and transcriptome of twin almonds (Prunus dulcis [Mill.] D.A.Webb) reveals genomic features associated with non-infectious bud failure, Pre-print: https://doi.org/10.1101/2020.09.25.294074
D’Amico-Willman, K.M.^§; Anderson, E.S.^¶; Fresnedo-Ramírez, J. (2020). Relative telomere length and Telomerase Reverse Transcriptase (TERT) expression are associated with age in almond (Prunus dulcis [Mill.] D.A.Webb)., Plants 10(2) 189 https://doi.org/10.3390/plants10020189
Vargas-Canales, J.M.; Carbajal-Flores, G. Bustamante-Lara, T.I. Camacho-Vera, J.H.; Fresnedo-Ramírez, J.; Palacios-Rangel, M.I. (2020). Impact of the Market on the Specialization and Competitiveness of Avocado Production in Mexico. International Journal of Fruit Science 20 S1942-S1958 https://doi.org/10.1080/15538362.2020.1837711
Schuchovski, C.^†, Meulia, T., Sant’Anna-Santos, B.F., Fresnedo-Ramírez J. (2020) Inflorescence ontogeny and floral organogenesis in Taraxacum kok-saghyz. Plants 9(10) 1258. https://doi.org/10.3390/plants9101258
Gradziel, T.M.; Fresnedo-Ramírez, J. (2019). Noninfectious Bud-failure As a Model For Studying Age Related Genetic Disorders in Long-Lived Perennial Plants. Journal of the American Pomological Society, 73 (4), 240-253. Retrieved from: http://www.pubhort.org/aps/73/v73_n4_a5.htm
Vargas-Canales, J.M.; Camacho-Vera, J.H.; Pineda-Pineda, J.; Mendoza-Castillo, V.M.; Fresnedo-Ramírez, J.; Lopez-Garcia, S.M.; Andrade-Saavedra, Z.X. (2019). Specialization and competitiveness of natural rubber (Hevea brasiliensis [Willd. ex A. Juss.] Mull. Arg.) production in Mexico. Revista Chapingo Serie Ciencias Forestales Y Del Ambiente, 25 (3), 425-439. https://doi.org/10.5154/r.rchscfa.2018.12.092
Fresnedo-Ramírez J., Yang S., Sun Q., Karn A., Reisch B.I. and Cadle-Davidson L. (2019) Computational analysis of AmpSeq data for targeted, high-throughput genotyping of amplicons. Front. Plant Sci. 10:599. https://www.doi.org/10.3389/fpls.2019.00599
Guzmán F.A., Segura, S., Fresnedo-Ramírez J. (2018) Morphological variation in black cherry (Prunus serotina Ehrh.) associated with environmental conditions in Mexico and the United States. Genetic Resources and Crop Evolution 65(8):2151-2168 https://doi.org/10.1007/s10722-018-0681-y.
Luo Z., Iaffaldano B.J., Zhuang X., Fresnedo-Ramírez J., Cornish K (2018). Variance, inter-trait correlation, heritability and marker-trait association of rubber yield related characteristics in Taraxacum kok-saghyz. Plant Molecular Biology Reporter 36(4):576-587 https://doi.org/10.1007/s11105-018-1097-8
Segura S. Fresnedo-Ramírez J., Mathuriau C., Segura O., Andrés, J, Muratalla A. The edible fruit species in Mexico (2018). Genetic Resources and Crop Evolution 65(6):1767-1793 https://doi.org/10.1007/s10722-018-0652-3
Stansell Z.J., Hyma K.E., Fresnedo-Ramírez J., Sun Q., Mitchell S., Björkman T., Hua J. (2018) Genotyping-by-sequencing of B. oleracea vegetables reveals unique phylogenetic patterns, population structure and domestication footprints. Horticulture Research 5:38 https://doi.org/10.1038/s41438-018-0040-3
Fresnedo-Ramírez J., Yang S., Sun Q., Cote L.M., Schweister P.A., Reisch B.I., Ledbetter C.A., Luby J.J., Clark M.D., Londo J.P., Gadoury D.M., Cadle-Davidson L., (2017) An integrative AmpSeq platform for highly multiplexed marker-assisted pyramiding of grapevine powdery mildew resistance loci. Molecular Breeding 37:145 https://doi.org/10.1007/s11032-017-0739-0
Luo Z., Iaffaldano B.J., Zhuang X., Fresnedo-Ramírez J., Cornish K. (2017) Analysis of the first Taraxacum kok-saghyz transcriptome reveals potential rubber yield related SNPs Scientific Reports 7 https://doi.org/10.1038/s41598-017-09034-2.
Fresnedo-Ramírez J., Chan H.M., Crisosto C.H., Parfitt D.E., Gradziel T.M. (2017) Genome-wide DNA-(de)methylation is associated with Noninfectious Bud-failure exhibition in Almond [Prunus dulcis (Mill.) D.A.Webb] Scientific Reports 7 https://doi.org/10.1038/srep42686
Fresnedo-Ramírez J., Famula T.R., Gradziel T.M. (2017) Application of a Bayesian ordinal animal model for the estimation of breeding values for the resistance to Monilinia fruticola (G.Winter) Honey in progenies of peach [Prunus persica (L.) Batsch]. Breeding Science https://doi.org/10.1270/jsbbs.16027
Teh S.L., Fresnedo-Ramírez J., Clark M.D., Sun Q., Cadle-Davidson L., Luby J.J. (2017) Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps. Molecular Breeding 37:1 https://doi.org/10.1007/s11032-016-0586-4
Fresnedo-Ramírez J., Sun Q., Hwang C-F., Ledbetter C.A., Ramming D.W., Fennell A.Y., Walker M.A., Luby J.J., Clark M.D., Londo J.P., Cadle-Davidson L., Zhong G-Y., Reisch B.I. (2016) Towards the elucidation of cytoplasmic diversity in North American grape breeding programs. Molecular Breeding 36:116-126 https://doi.org/doi:10.1007/s11032-016-0538-z
Cadle-Davidson L., Gadoury D., Fresnedo-Ramírez J., Yang S., Barba P., Sun Q., Demmings E.M., Seem R., Schaub M., Nowogrodzki A., Kasinathan H., Ledbetter C.A., Reisch B.I. (2016) Lessons from a phenotyping center revealed by the genome-guided mapping of powdery mildew resistance loci. Phytopathology https://doi.org/10.1094/PHYTO-02-16-0080-FI
Fresnedo-Ramírez J., Frett T.J., Sandefur P.J., Salgado-Rojas A., Clark J.R., Gasic K., Peace C.P., Anderson N., Hartmann T.P., Byrne D.H., Bink M.C.A.M., van de Weg E., Crisosto C.H., Gradziel T.M. (2016) QTL mapping and breeding value estimation through pedigree-based analysis of fruit size and weight in four diverse peach breeding programs. Tree Genetics & Genomes 12:1-18 https://doi.org/10.1007/s11295-016-0985-z
Yang S., Fresnedo-Ramírez J., Sun Q., Manns D.C., Sacks G.L., Mansfield A.K., Luby J.J., Londo J.P., Reisch B.I., Cadle-Davidson L.E., Fennell A.Y. (2016) Next-generation mapping of enological traits in an F₂ interspecific grapevine hybrid family. PLoS ONE 11:e0149560 https://doi.org/10.1371/journal.pone.0149560
Yang S., Fresnedo-Ramírez J., Wang M., Cote L., Schweitzer P., Barba P., Takacs E.M., Clark M.D., Luby J.J., Manns D.C., Sacks G.L., Mansfield A.K., Londo J.P., Fennell A.Y., Gadoury D., Reisch B.I., Cadle-Davidson L., Sun Q. (2016) A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine. Horticulture Research 3:16002 https://doi.org/10.1038/hortres.2016.2
Fresnedo-Ramírez J., Bink M.C.A.M., Van de Weg E., Famula T.R., Crisosto C.H., Frett T.J., Gasic K., Peace C.P., Gradziel T.M. (2015) QTL mapping of pomological traits in peach and related species breeding germplasm. Molecular Breeding 35:166. https://doi.org/10.1007/s11032-015-0357-7
Martínez-García P., Parfitt D., Bostock R.M., Fresnedo-Ramírez J., Vazquez-Lobo A., Ogundiwin E.A., Gradziel T., Crisosto C. (2013) Application of genomic and quantitative genetic tools to identify candidate resistance genes for brown rot resistance in peach. PLoS ONE 8(11): e78634. https://doi.org/10.1371/journal.pone.0078634
Fresnedo-Ramírez J., Martínez-García P., Parfitt D., Crisosto C. Gradziel T.M. (2013) Heterogeneity in the entire genome for three genotypes of Peach [Prunus persica (L.) Batsch] as distinguished from sequence analysis of genomic variants. BMC Genomics: 2013, 14:750. https://doi.org/10.1186/1471-2164-14-750
Fresnedo-Ramírez J. (2013) The floral biology of Jatropha curcas L.— a review. Tropical Plant Biology: 1-15. https://doi.org/10.1007/s12042-012-9113-x
Fresnedo-Ramírez J. and Orozco-Ramírez Q., (2013) Diversity and distribution Jatropha in Mexico. Genetic Resources and Crop Evolution: 60(3): 1080-1104, https://doi.org/10.1007/s10722-012-9906-7
Martínez-García P., Fresnedo-Ramírez J., Parfitt D., Gradziel T., Crisosto C. (2013) Effect prediction of identified SNPs linked to fruit quality and chilling injury in peach [Prunus persica (L.) Batsch]. Plant Molecular Biology: 81:161–174. https://doi.org/10.1007/s11103-012-9989-8
Martínez-García P., Peace C., Parfitt D., Ogundiwin E., Fresnedo-Ramírez J., Dandekar A., Gradziel T., Crisosto C. (2012) Influence of year and genetic factors on chilling injury susceptibility in peach (Prunus persica (L.) Batsch). Euphytica: 185:267-280. https://doi.org/10.1007/s10681-011-0572-1
Fresnedo-Ramírez J., Segura S., Muratalla-Lúa A. (2010) Morphovariability of capulín (Prunus serotina Ehrh.) in the central-western region of Mexico from a plant genetic resources perspective. Genetic Resources and Crop Evolution: 58(4): 481-495. https://doi.org/10.1007/s10722-010-9592-2

Editor-Reviewed Articles

^§Graduate Advisee ^¶Undergraduate advisee ^‡Committee member advisee ^†Visiting scholar

Willman M.R.^§, Bushakra J.M., Bassil N., Finn C.E., Dossett M., Perkins-Veazie P., Bradish C.M., Fernandez G.E., Weber C., Scheerens J.C., Dunlap L. and Fresnedo-Ramírez J. 2020 Genetic analysis of drupelet count in black raspberry (Rubus occidentalis). Acta Horticulturae 1277:65-72. https://doi.org/10.17660/ActaHortic.2020.1277.9
Fresnedo-Ramírez J., Lee S.A., Ledbetter C.A. 2019. The genetic dissection of Natural Dry-on-Vine (NDOV) trait in grapevine. Acta Horticulturae 1248:409-415. https://www.doi.org/10.17660/ActaHortic.2019.1248.58
Gradziel T.M., Fresnedo-Ramírez J. 2018. Epigenetic selection in almond breeding. Acta Horticulturae 1219:13-18. https://www.doi.org/10.17660/ActaHortic.2018.1219.3
Demmings E.M., Cadle-Davidson L., Sacks G., Gadoury D.M., Sun Q., Schweitzer P., Londo J., Ledbetter C., Clark M., Luby J., Teh S.L., Mansfield A.K., Manss D., Springer L., Chitwood D., Barba P., Hwang C-F., Sapkota D., Fresnedo-Ramírez J., Yang S., Reisch B.I. 2017. VitisGen discoveries in local and centralized trait evaluation. Acta Horticulturae 1188:323-328. https://www.doi.org/10.17660/ActaHortic.2017.1188.43
Fresnedo-Ramírez J., Famula T.R., Crisosto C.H., Gradziel T.M. 2013. Pedigree correction and estimation of breeding values for peach genetic improvement. Acta Horticulturae 1084:249-256. https://doi.org/10.17660/ActaHortic.2015.1084.35
Segura S., Andrés J., Fresnedo J., Zavala F., Marroquín L., Vidal E., Nicolás M., Vidal L., Bolívar N., Castañeda A., González A., Barrios S., Carmona A. 2012. Where do we go with Annona in Mexico? Acta Horticulturae 948:79-89. https://doi.org/10.17660/ActaHortic.2012.948.8

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Dr. Jonathan Fresnedo Ramirez

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