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

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.

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
Domestication and characterization of Taraxacum kok-saghyzas a novel source of natural rubber
Germplasm development and genetic characterization of traits in outcrossing crops.

Current graduate advisees

Katherine D’Amico – joined the lab in 2017, 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. Ph.D. expected in 2020.
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.

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.

Works

Journal articles

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 serotinaEhrh.) 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):1767-1793https://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-saghyztranscriptome 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 F₂interspecific 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 curcasL.— 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 serotinaEhrh.) 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

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
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 Annonain Mexico? Acta Horticulturae 948:79-89. https://doi.org/10.17660/ActaHortic.2012.948

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Dr. Jonathan Fresnedo Ramirez

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Dr. Jonathan Fresnedo Ramirez

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Journal articles

Editor-Reviewed Articles