Charles Y. Chen

Professor (Peanut Breeding & Genetics)

Crop, Soil & Environmental Sciences

(334) 844-3974 


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258 Funchess Hall
Auburn Univ, AL 36849



  • Ph.D. Plant Breeding and Genetics, The University of Illinois at Urbana-Champaign
  • M. S. Crop Science, The Graduate School of Chinese Academy of Agricultural Sciences
  • B. S. Agronomy, China Agricultural University, Beijing, China


  • Professor, Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, Alabama (2017-present)
  • Associate Professor, Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, Alabama (2012-2017)
  • Research Geneticist/Lead Scientist, USDA/ARS National Peanut Research Lab, Dawson, Georgia (2007-2012)
  • Senior Research Associate, Michigan State University, East Lansing, Michigan (2002-2007)
  • Ph.D. Graduate Research Assistant, The University of Illinois at Urbana-Champaign (1997-2002)


  • Auburn University College of Agriculture Dean’s Grantsmanship Award (2020)
  • Auburn University College of Agriculture Dean’s Grantsmanship Award (2018)
  • Outstanding Research Award by the International Peanut Genome Initiative for contributions to ongoing efforts to establish links between genetics and key traits in cultivated peanuts. (2014)
  • Member of the Honor Society of Agriculture, Gamma Sigma Delta (2000)


  • The Secretary/President-elect/President for The Association of Chinese Soil & Plant Scientists in North America (ACSPSNA) under ASA-CSSA-SSSA (2017-2019)
  • University faculty senator (2016-2018)
  • Alabama representative to the S-009 Multistate Committee “Plant Genetic Resources Conservation and Utilization” (2016-present)
  • Program 3+2 faculty liaison: for the College of Agriculture and the Dept. of Crop, Soil, and Environmental Sciences (2013-present)
  • Bailey Award Committee Chair, APRES (2015-2017)
  • Peanut Germplasm Committee Member, APRES (2007-present)
  • Associate editor for Journal of Plant Registration (2015-2017)
  • Associate editor for The Journal of the American Oil Chemists’ Society (JAOCS) (2015-2017)
  • Senior associate editor for Agronomy Journal (2008-2011)
  • Member, Gamma Sigma Delta (2000 -present)
  • Member, Crop Science Society of America (CSSA) (1997-present)


  • Crop Science Society of America since 1997
  • American Society of Agronomy since 1997
  • Gamma Sigma Delta – The Honor Society of Agriculture since 2000
  • American Peanut Research and Education Society since 2007
  • National Association of Plant Breeders (NAPB) since 2013



Primary research responsibilities are in peanut breeding, genetics, and genomics. The major objectives of the research are to develop cultivars with desirable improved traits adapted to all U.S. peanut producing regions; and enhance elite peanut germplasm through conventional and genomic approaches. The targeted traits are high yield, resistance to tomato spotted wilt virus and leaf spot, maturity, seed characteristics (size, split, and taste etc.), high oil content, high oleic and low linoleic fatty acids, and drought tolerance.

In addition to the breeding effort, second focus of my research program is to understand the genetic principles of important agronomic traits in peanut; to map quantitative trait loci (QTLs) underlying the desired traits in peanuts; to explore genetic potential for peanut improvement, and to discover new genes related to desirable agronomic and seed quality traits. Ongoing projects include the research to identify drought-induced genes and to associate and map the genes or alleles that control leaf spot disease resistance in peanuts. In order to discover alleles/genes contributing to the leaf spot resistance in Arachis germplasm for cultivated peanut improvement, several recombinant inbred line (RIL) populations were constructed. A great effort of phenotyping the US peanut mini-core collection has achieved significant progress on identifying QTLs underlying TSWV (tomato spotted wilt virus) resistance, leaf spot resistance, peanut favor characters and chemistry. We also investigated the effects of drought stress on symbiotic nitrogen fixation in peanut. A runner-type peanut cultivar ‘AU-NPL 17’ was released in 2017 and a Virginia-type peanut cultivar named as ‘AU14-34’ was released in 2021.



  • CSES 7160: Genetic Data Analysis / 3.0 Credit hoursThe goal of this course is to teach the graduate students the principles of statistical analysis of quantitative traits using genetic markers. Learning is reinforced through hands-on training with computer software for the analysis of quantitative traits. Class hours are equally divided between lectures on the principles of statistical analysis of quantitative traits and hands-on training of students on genetic data analysis with software including SAS, Mapmaker, JoinMap, QTL-Cartographer, etc.
  • CSES 7170: Advanced Plant Breeding (Quantitative Genetics in Plant) / 3.0 Credit hoursMost economically important traits in crops are quantitative rather than qualitative. It is therefore fitting that we study how quantitative genetics applies to plant breeding. The goals of this course are to: 1. Understand fundamental concepts of population and quantitative genetics; 2. Explore how quantitative genetics principles can help a plant breeder design and implement a breeding program; and 3. Appreciate the theory, experimental approaches, and evidence that form the basis for these concepts and breeding strategies.



Note: Selected refereed journal articles from 75 published papers. The asterisk sign ‘*’ indicates as a corresponding author.

  • Wang, X., X. Yang, Y. Feng, P. Dang, W. Wang, R. Graze, J. Clevenger, Y. Chu, P. Ozias-Akins, C. Holbrook , and C. Chen*. 2021. Transcriptome profile reveals drought induced genes preferentially expressed in response to water deficit in cultivated peanut (Arachis hypogaea L.). Frontiers in Plant Science: (in press)
  • Dang, P.M., M.C. Lamb, and C.Y. Chen, 2021. Association of differentially expressed R‑gene candidates with leaf spot resistance in peanut (Arachis hypogaea L.). Molecular Biology Reports.
  • Zhang, H., M.L. Wang, P. Dang, T. Jiang, S. Zhao, M. Lamb, and C. Chen*. 2020. Identification of potential QTLs and genes associated with seed composition traits in peanut (Arachis hypogaea L.) using GWAS and RNA-Seq analysis. Gene.
  • Zhang, H., Y. Chu, P. Dang, Y. Tang, T. Jiang, J. Clevenger, P. Ozias-Akins, C. Holbrook, M.L. Wang, H. Campbell, A. Hagan, and C.Y. Chen*. 2020. Identification of QTLs for resistance to leaf spots in cultivated peanut (Arachis hypogaea L.) through GWAS analysis. dio: 10.1007/s00122-020-03576-2.
  • Yin, D. Yin, C. Ji, Q. Song, W. Zhang, X. Zhang, K. Zhao, C.Y. Chen, C. Wang, G. He, Z. Liang, X. Ma, Z. Li, Y. Tang, Y. Wang, K. Li, L. Ning, H., K. Zhao, X. Li, H. Yu, Y. Lei, M. Wang, L. Ma, H. Zheng, Y. Zhang, J. Zhang, W. Hu, and Z. J. Chen. 2020. Comparison of Arachis monticola with diploid and cultivated tetraploid genomes reveals asymmetric subgenome evolution and improvement of peanut. Adv. Sci. 2020, 7, 1901672.
  • Zhang H., M.L. Wang, R. Schaefer, P. Dang, T. Jiang, and C. Chen*. 2019. GWAS and coexpression network reveal ionomic variation in cultivated peanut. J. Agric. Food Chem. 67, 12026-12036. DOI: 10.1021/acs.jafc.9b04939.
  • Li, L., X. Yang, S. Cui, G. Mu, M. Hou, M. He, H. Zhang, L. Liu, and C.Y. Chen*. 2019. Construction of high-density genetic map and mapping quantitative trait loci for growth habit related traits of peanut (Arachis hypogaea L.). Frontiers in Plant Science: DOI: 10.3389/fpls.2019.00745.
  • Yuan, M., J. Zhu, L. Gong, L. He, C. Lee, S. Han, C. Chen, and G. He. 2019. Mutagenesis of FAD2 genes in peanut with CRISPR/Cas9 based gene editing. BMC Biotechnology 19:24.
  • Dang, P.M., M.C. Lamb, K.L. Bowen, and C.Y. Chen. 2019. Identification of expressed R-genes associated with leaf spot diseases in cultivated peanut. Molecular Biology Reports (2019) 46:225–239.
  • Li, J., Y. Tang, A. Jacobson, P. Dang, X. Li, M.L. Wang, A. Hagan, and C. Chen*. 2018. Population structure and association mapping to detect QTL controlling tomato spotted wilt virus resistance in cultivated peanuts. The Crop Journal.
  • Han, S., M. Yuan, J. Clevenger, C. Li, A. Hagan, X. Zhang, C. Chen*, and G. He. 2018. A SNP-based linkage map revealed QTLs for resistance to early and late leaf spot diseases in peanut (Arachis hypogaea L.). Frontiers in Plant Science: 9:1021. Doi: 10.3389/fpls.2018.01012.
  • Wang, M.L., C.Y. Chen, B. Tonnis, D. Pinnow, J. Davis, Y.Q. C. An, and P. Dang. 2018. Changes of seed weight, fatty acid composition, and oil and protein contents from different peanut FAD2 genotypes at different seed developmental and maturation stages. J. Agric. Food Chem. DOI: 10.1021/acs.jafc.8b01238.
  • Leamy, L.J., H. Zhang, C. Li, C.Y. Chen*, and B.H. Song. 2017. A genome-wide association study of seed composition traits in wild soybean (Glycine soja). BMC Genomics.18:18. DOI 10.1186/s12864-016-33974.
  • Meng, S., X. Yang, P.M. Dang, S. Cui, G. Mu, L. Liu, and C.Y Chen*. 2016. Evaluation of genetic diversity with Insertion-Deletion marker and marker-trait association analysis in cultivated peanut (Arachis hypogaea L.). Genetics and Molecular Research. doi: 10.4238/gmr.15028207.
  • Liu, L. P. Dang, and C.Y. Chen*. 2015. Development and utilization of InDel markers to identify peanut (Arachis hypogaea) disease resistance. Frontiers in Plant Science. 6:988. doi: 10.3389/fpls.2015.00988.
  • Chen, C.Y.*, N.A. Barkley, M.L. Wang, C.C. Holbrook, and P.M. Dang. 2014. Registration of purified accessions for the U.S. peanut mini-core germplasm collection. Journal of Plant Registrations. 8(1):77-85.
  • Chen, C.Y.*, R. Nuti, D. Rowland, W. Faircloth, M. Lamb, and E. Harvey. 2013. Heritability and genetic relationships for drought-related traits in peanut. Crop Sci. 53(4): 1392-1402.
  • Chen, C.Y.*, J.E. Harvey, M. Lamb, and J. Touchton. 2013. Registration of ‘AU-1101’ peanut. Journal of Plant Registrations. 7:18-21.
  • Wang, M.L., C.Y. Chen, B. Tonnis, N.A. Barkley, D.L. Pinnow, R.N. Pittman, J.Davis, C. C. Holbrook, H.T. Stalker, and G.A. Pederson. 2013. Oil, fatty acid, flavonoid, and resveratrol content variability in the U.S. peanut mini-core collection. Journal of Agricultural and Food Chemistry. 61:2875−2882.
  • Dang, P., C.Y. Chen, and C.C. Holbrook. 2013. Evaluation of five peanut (Arachis hypogaea) genotypes to identify drought responsive mechanisms utilizing candidate-gene approach. Functional Plant Biology.
  • Dang, P.M. and C.Y. Chen. 2013. Modified method for combined RNA and DNA isolation from peanut and other oil seeds. Mol. Biol. Rep. 40(2): 1563-1568.
  • Wang, M. L., C.Y. Chen, D. L. Pinnow, N. A. Barkley, R. N. Pittman, M. Lamb, and G. A. Pederson. 2012. Variability in seed dormancy within the U.S. peanut mini-core collection. Plant Genetic Resources. DOI: 10.3923/rjss.2012.
  • Dang, P. C.Y. Chen, and C.C. Holbrook. 2012. Identification of genes encoding drought-induced transcription factors in peanut (Arachis hypogaea L.). Journal of Molecular Biochemistry. (2012) 1:196-205.
  • Chen, C.Y., C. Gu, C. Mensah, R.L. Nelson, and D. Wang. 2007. SSR Marker diversity of soybean aphid resistance sources in North America. Genome 50:1104- 1111.
  • Chen, Y., D. Wang, P. Arelli, M. Ebrahimi, and R.L. Nelson. 2006. Molecular marker diversity of SCN resistant sources in soybean. Genome. 49:938-949.
  • Chen, Y., and R.L. Nelson. 2006. Variation in early plant height in wild soybean. Crop Science. 46:865-869.
  • Chen, Y., and R.L. Nelson. 2005. Relationship between origin and genetic diversity in Chinese soybean germplasm. Crop Science. 45:1645-1652.
  • Chen, Y., and D. Wang. 2005. Two convenient methods to evaluate soybean for resistance to Sclerotinia sclerotiorum. Plant Disease. 89:1268-1272.
  • Chen, Y., and R.L. Nelson. 2004. Genetic variation and relationships among cultivated, wild, and semi-wild soybean. Crop Science. 44:316-326.
  • Chen, Y., and R.L. Nelson. 2004. Identification and evaluation of a white- flowered wild soybean plant. Crop Science. 44:339-343.
  • Chen, Y., and R.L. Nelson. 2004. Evaluation on leaflet shape and size in wild soybean. Crop Science. 44:671-677.


  • Yuan, M., J. Zhu, L. Gong, L. He, C. Lee, S. Han, C. Chen, and G. He. 2020. Mutagenesis of FAD2 genes in peanut with CRISPR/Cas9 based gene editing. In: Prime Archives in Biotechnology. Hyderabad, India: Vide Leaf.
  • Grey, T.L., C.Y. Chen, Russell Nuti, W.S. Monfort, and G. Cutts. 2017. Characterization of genotype by planting date effects on runner-type peanut seed germination and vigor response to temperature. in Advance in Seed Biology.
  • Holbrook, C.C., M.D. Burow, C.Y. Chen, M.K. Pandey, L. Liu, J.C. Chagoya, Y. Chu, P. Ozias-Akins. 2016. Recent advances in peanut breeding and genetics. in Peanuts: Genetics, Processing and Utilization. ELSEVIER. ISBN 978-16-306-7038-2.
  • Chen, C.Y., C. Butts, P. Dang, and M.L. Wang. 2015. Advances in phenotyping of functional traits, in Phenomics of crop plants: trends, options and limitations. Springer. pp. 163-180. ISBN 978-81-322-2225-5.
  • Chen, C.Y., P.M. Dang, and M.C. Lamb. 2014. Genetic improvement of drought tolerance for productivity and food safety. Auburn Speaks: On Food Systems. Auburn University. P.162-167. ISBN 978-0-615-97504-7.

Honors & Awards by Graduate Students

  • Oluwamosope Adeniji. 2018-2021 Auburn University Presidential Scholarship.
  • Boipelo Nthupisang. 2016-2018 Fulbright Foreign Student Scholarship, The U.S. Department of State, Bureaus of Educational and Cultural Affairs.
  • Jing Li. 2016 Outstanding International Graduate Student Award, Auburn University.
  • Shandrea Stallworth. 2014 Dow AgroSciences R&D Internship.
  • Joshua Carter. 2013 The J. Fielding Reed Scholarship from the American Society of Agronomy, 2013 ASA-CSSA-SSSA Annual Meeting, November 11 – 14, 2013. Tampa, FL.
  • Joshua Carter. 2013 The Hubert J. Byrd Sr. Scholarship from the Soil Science Society of America. 2013 ASA-CSSA-SSSA Annual Meeting, November 11 – 14, 2013. Tampa, FL.
  • Shandrea Stallworth. 2013-2015 NSF Bridge to Doctorate Fellowship.