Photo of Charles Chen holding up a sample of the AU peanutCharles Y. Chen

Professor — Peanut Breeding, Genetics and Genomics

Department of Crop, Soil and Environmental Sciences


2002 Ph.D., University of Illinois at Urbana-Champaign (Plant Breeding and Genetics)
1990 M.S., The Graduate School of Chinese Academy of Agricultural Sciences
1984 B.S., China Agricultural University (former Beijing Agricultural University)


Aug. 2017-present Professor, Auburn University, Auburn, AL
2012-July 2017 Associate Professor, Auburn University
2007-2011 Research Geneticist and Lead Scientist, USDA-ARS, Dawson, GA
2002-2006 Senior Research Associate, Michigan State University
1997-2001 Graduate Research Assistant, University of Illinois at Urbana-Champaign
1984-1996 Assistant Curator of Chinese Soybean Germplasm Collection, CAAS, Beijing



  • Science & Technology Advancement Award, 3rd Prize, the Ministry of Agriculture of China, 1990.
  • National Science & Technology Advancement Award, 2nd Prize, the State Science-Technology Commission of China, 1993.
  • Member of the Honor Society of Agriculture, Gamma Sigma Delta, October 2000.
  • Science & Technology Advancement Award, 2nd Prize, the People’s Government of Beijing Municipality, 2003.
  • Outstanding Research Award by the International Peanut Genome Initiative for the contributions to ongoing efforts to establish links between genetics and key traits in cultivated peanuts, 2014.



  • 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) since 1997-present.

Research Activities


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. The breeding program is conducted by Auburn University in cooperation with the USDA-ARS National Peanut Research Lab (NPRL) located in Dawson, GA as a part of ARS NP301 Research Project 6604-21000-003-00D entitled ‘Developing strategies to identify useful genes in peanut and breeding high yielding peanut varieties and germplasm’. We use pedigree selection as our primary method of breeding and backcrossing is applied as well. About 2,000 breeding lines from F2 to F7 progenies are maintained in the program for selection in Headland, AL. Each year about 80 F7 lines are advanced the next year in preliminary yield tests in the two locations. Thirty-nine of the best performing lines will be tested in yield trials in four locations at Dawson, GA; Headland, AL; Fairhope, AL and Lucedale, MS for two years. Lines that perform well in these tests are entered into Uniform Peanut Performance Tests (UPPT) for testing in 9 locations of the eight states. After 2 to 3 years of testing in this program, the line that consistently performs superior may be released as a cultivar. A virginia-type peanut cultivar named as ‘AU-1101’ was released in 2011, and a runner-type peanut cultivar ‘AU-NPL 17’ was released in 2017.

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.

Courses Taught


CSES 7160 Genetic Data Analysis / 3.0 Credit hours

CSES 5010/6010

CSES 5016/6016 Analysis of Plant, Soil & Animal Data / 3.0 Credit hours

Analysis of Plant, Soil & Animal Data (Distance Education Course)

Recent Publications

1.       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. (2017) 18:18 DOI 10.1186/s12864-016-3397-4

2.       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.

3.       Wang, M.L., M.A. Grusak, C.Y. Chen, B. Tonnis, N.A. Barkley, S. Evans, D. Pinnow, J. Davis, C.C. Holbrook, and G.A. Pederson. 2016. Seed protein percentage and mineral concentration variability and their correlation with other seed quality traits in the U.S. peanut mini-core collection. Peanut Science. doi:10.3146/PS15-15.1.

4.       Leamy, L.J., C.R. Lee, I. Mujacic, Q. Song, R.L. Nelson, Y. Luo, C.Y. Chen, E. Peregrine, and B.H. Song. 2016. Environmental adaption in wild soybean (Glycine soja) across their native geographic range in northeast Asia. Ecology and Evolution. Doi:10.1002/ece3.2351.

5.       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

6.       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.

7.       Lu, X., H. Zhou, Y.B. Pan, C.Y. Chen, J.R. Zhu, P.H. Chen, Y.R. Li, Q. Cai, and R.K. Chen. 2015. Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids. Genetics and Molecular Research. 14(4):18384-18395.

8.       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.

9.       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.

10.   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.

11.   Nuti, R., C.Y. Chen, P. Dang, and E. Harvey. 2014. Peanut cultivar response to tomato spotted wilt virus over five planting dates. Peanut Science. Vol. 41, No. 1, pp. 32-41. doi: 50%

12.   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.

13.   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.