Education

B.S., Agronomy, University of Nebraska, 1967

M.S., Agronomy, University of Illinois, 1971

Ph.D., Genetics, University of Nebraska, 1974

Research Interests

Plant genetics/genetics and plant physiology and crop production, and the interphase between these two have been my long-term research interests. I am a member of a national research team that developed the first soybean genetic map of 20 linkage groups (Cregan et al., 1999). That genetic map has now been upgraded to 1845 markers plus 150 classical markers (Song et al., 2004). Later on, I was a member of the research team the sequenced the soybean Genome. In terms of the physiology of soybean yield response to a gradient of water supply ranging from water abundance to water scarcity, I discovered that this response was exceptionally linear, and that there were genotypic differentials in the linear regression coefficient from shallow to steep that delineated those genotypes into slow water users and high water users. The former were suitable for production environments that were prone to protracted droughts or soils of low water-holding capacity.  In contrast, the latter were more suitable for high rainfall or irrigated environments. Some more recent accomplishments have involved the use of genomics to search for genes that govern soybean seed protein & oil content. Finally, I was a lead PI with respect to developing the national Nested Associated Mapping (NAM) Populations that will serve as an exceptionally valuable resource for the Soybean Genetics and Physiology Research Community for many years hence.   

Courses Taught

• AGRO 896A (even-numbered years) Linkage Mapping and QTL Analysis.
• AGRO 896B (odd-numbered years) Plant and Crop Response to Abiotic Stress.

Extension Interests

I had no extension appointment before retirement, but did and continue to serve as a scientific expert and liaison for Nebraska soybean producers, and their State level organizations (Nebraska Soybean Board; Nebraska Soybean Association), and at the National level organizations (United Soybean Board; American Soybean Association).

Honors and Awards

• Outstanding Achievement Award, Highest Recognition Award Bestowed by the United (States) Soybean Board, March 4, 2016
• Louise Pound-George Howard Distinguished Career Service Award, University of Nebraska–Lincoln, April 12, 2015
• Special Meritorious Service Award, American Soybean Association, Feb. 23, 2015
• Inducted as a Member, Nebraska Hall of Agricultural Achievement, March 23, 2012
• Soybean Promoter Award, Nebraska Soybean Association, Dec. 20, 2007
• Crop Science Research Award, Crop Science Society of America, Nov. 5, 1996
• Sigma Xi Research Award, Sigma Xi, University of Nebraska Chapter, April 10, 1996
• Production Research Award, American Soybean Association, Feb. 26, 1996
• Agronomic Achievement Award - Crops,  American Society of Agronomy, Nov. 16, 1994
• Fellow, Crop Science Society of America, Oct. 17, 1989
• Fellow, American Society of Agronomy, Nov. 30, 1988 
• Fellow, American Association for the Advancement of Science, Feb. 18, 1987
• Research Award of Merit,  Gamma Sigma Delta, Nebraska Chapter, Nov. 24, 1985
• Research Recognition Award,  American Soybean Association, August 1, 1981
• Sigma Xi Research Honorary, One of 12 University of Nebraska–Lincoln seniors so selected, May 1, 1967
• Gamma Sigma Delta, A national honor society of agriculture, May 16, 1967

Publications

Recent (2014-2016), plus pre-2014 publications but only if cited *150+ times* in Google Scholar

• Jarquin, D., J. Specht, and A. Lorenz. 2016. Prospects of genomic prediction in the USDA Soybean Germplasm Collection: Historical data creates robust models for enhancing selection of accessions. G3: Genes Genomes Genetics. Early online May 31, 2016 doi: 10.1534/G3.116.031443.
• Piyaporn, P., W. Soonsuwon, D.L. Hyten, Q. Song, P.B. Cregan, G.L. Graef, and J.E. Specht. 2016. Selective Genotyping to Identify Soybean (Glycine max (L.) Merr.) Seed Protein QTLs in Multiple F2 Populations. G3 Genes|Genomes|Genetics 6:1635-1648.  
• Grassini P, J.A. Torrion, H.S. Yang, J. Rees, D. Andersen, K.G. Cassman, and J.E. Specht.  2015. Soybean yield gaps and water productivity in the western U.S. Corn Belt. Field Crops Res. 179:150-163.
• Bandillo, N., D. Jarquin, Q. Song, R. Nelson, P. Cregan, J. Specht, and A. Lorenz. 2015. A population structure and genome-wide association analysis on the USDA soybean germplasm collection. The Plant Genome 8:1-13.
• Manavalan, L.P., S.P. Prince, T.A. Musket1, J. Chaky, R. Deshmukh, T.D. Vuong, L. Song, P.B. Cregan, J.C. Nelson, J.G. Shannon, J.E. Specht, and H.T. Nguyen. 2015. Identification of novel QTL governing root architectural traits in an interspecific soybean population. PLoS ONE 10(3): e0120490.
• Mourtzinis, S., J.E. Specht, L.E. Lindsay, W.J. Wiebold, J. Ross, E.D. Nafziger, H.J. Kandell, N. Mueller, P.L. Devillez, F.J. Arriaga, and S.P. Conley. 2015. Climate-reduced in US-wide soybean yields underpinned by region- and in-season specific responses. Nature Plants 1: Article 140216.  
• Torrion, J.A., T.D. Setiyono, G. L. Graef, K.G. Cassman, S. Irmak, and J.E. Specht. 2014. Soybean irrigation management: Agronomic impacts of deferred, deficit, and full-season strategies. Crop Sci. 54:2782-2795.
• Ping, J., Y. Liu, L. Sun, M. Zhao, Y. Li, M. Shea, Y. Suia, F. Lin, X. Liu, Z. Tang, H. Nguyen, Z. Tian, L. Qiu, R.L. Nelson, T.E. Clemente, J.E. Specht, and J. Ma. 2014. Dt2 Is a gain-of-function MADS-domain factor gene that specifies semideterminacy in soybean. Plant Cell 26:2831-2842.
• Posadas, L.G., K.M. Eskridge, J.E. Specht, and G.L. Graef. 2014. Elite performance for grain yield from unadapted exotic soybean germplasm in three cycles of a recurrent selection experiment. Crop Sci. 54:2536-2546.
• Rincker, K., R. Nelson, J. Specht, D. Sleper, T. Cary, S.R. Cianzio, S. Casteel, S. Conley, P. Chen, V. Davis, C.N Fox, G. Graef, C. Godsey, D. Holshouser, G.-L. Jiang, S.K. Kantartzi, W. Kenworthy, C. Lee, R. Mian, L. McHale, S. Naeve, J. Orf, V. Poysa, W. Schapaugh, G. Shannon, R. Uniatowski, D. Wang, and B. Diers. 2014. Genetic improvement of US soybean in maturity groups II, III, and I. Crop Sci. 54:1-14.
• Irmak, Suat, J.E. Specht, L.O. Odhiambo, J.M. Rees, and K.G. Cassman. 2014. Soybean yield, water productivity, evapotranspiration and soil water extraction response to subsurface drip irrigation. Trans. ASABE. 57(3):729-748.
• Weidenbenner, N.H., S.C. Rowntree, E.W. Wilson, J.J. Suhre, S. P. Conley, S.N. Casteel, V.M. Davis, B.W. Diers, P.D. Esker, J.E. Specht, and S.L. Naeve. 2014. Fungicide management does not affect the rate of genetic gain in soybean. Agron. J. 106:2043-2054.
• Suhre, J.J., N.H. Weidenbenner, S.C. Rowntree, E.W. Wilson, S. L. Naeve, S.P. Conley, S.N. Casteel, .W. Diers, P.D. Esker, J.E. Specht, and V. M. Davis. 2014. Soybean yield partitioning changes revealed by genetic gain and seeding rate interactions. Agron. J. 100:971-976.
• Mourtzinis, S., S.C. Rowntree, J.J. Suhre, N.H. Weidenbenner, E.W. Wilson, V. M. Davis, S.L. Naeve, S.N. Casteel, B.W. Diers, P.D. Esker, J.E. Specht, and S.P. Conley. 2014. The Use of reflectance data for in-season soybean yield prediction. Agron. J. 106:1159-1168.
• Grassini P, J.A. Torrion, K.G. Cassman, H.S. Yang, and J.E. Specht. 2014. Drivers of spatial and temporal variation in soybean yield and irrigation requirements in the western US Corn Belt. Field Crops Res.163:32-46.
• Anderson, J.E., M.B. Kantar, T.Y. Kono, F. Fu, A.O. Stec, Q. Song, P.B. Cregan, J.E. Specht, B.W. Diers, S.B. Cannon, L.K. McHale, R.M. Stupar. 2014. A roadmap for functional structural variants in the soybean genome. G3 Genes Genomics Genetics 4:1307-1318.
• King, C., L. Purcell, A. Bolton, and J. Specht. 2014. A possible relationship between shoot N concentration and the sensitivity of N2 fixation to drought in soybean. Crop Sci. 54:746-756.
• Hwang, E.-Y., Q. Song, G. Jia, J. E. Specht, D.L. Hyten, J. Costa, P.B. Cregan. 2014. A genome-wide association study for seed protein and oil content in soybean. BMC Genomics 15:1.
• Wilson, E.W., S.C. Rowntree, J.J. Suhre, N.H. Weidenbenner, S.P. Conley, V.M. Davis, B.W. Diers, P.D. Esker, S.L. Naeve, J.E. Specht, and S.N. Casteel. 2014. Genetic gain x management interactions in soybean: II. Nitrogen utilization. Crop Sci. 54:340:348.
• Severin, A.J., J. L. Woody, Y-T. Bolon, B. Joseph, B.W. Diers, A.D. Farmer, G.J. Muehlbauer, R.T. Nelson, D. Grant, J.E. Specht, M.A. Graham, S.B. Cannon, G.D. May, C.P. Vance, and R.C. Shoemaker. 2010. RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome. BMC Plant Biology 2010, 10:160 (pp. 1-16).
• Hyten, D,L., I.-Y. Choi, Q. Song, J.E. Specht, T.E. Carter, Jr., R.C. Shoemaker, E.-Y. Hwang, L.K. Matukumallif, and P.B. Cregan. 2010. A high density integrated genetic linkage map of soybean and the development of a 1536 universal soy linkage panel for quantitative trait locus mapping. Crop Sci. 50:960-968.
• Tian, Z., X. Wang, R. Lee, Y. Lee, J.E. Specht, R.L. Nelson, P.E. McClean, L. Qui, and J. Ma. 2010. Artificial selection for determinate stem growth habit in soybean. Proc. Natl. Acad. Sci. USA 107:8563-8568.
• Hyten, D.L., S.B. Cannon, Q. Song, N. Weeks, E.W. Fickus, R.C. Shoemaker, J.E. Specht, G. May, and P.B. Cregan. 2010. High-Throughput SNP Discovery via Deep Resequencing of a Reduced Representation Library to Anchor and Orient Scaffolds in the Whole Soybean Genome Sequence. BMC Genomics 11:38 (pp. 1-8).
• Hyten, D.L., I.-Y. Choi, Q. Song, J.E. Specht, T.E. Carter, R.C. Shoemaker, E.-Y. Hwang, L.K. Matukumalli, and P.B. Cregan. 2010. A high density integrated genetic linkage map of soybean and the development of a 1,536 Universal Soy Linkage Panel for QTL mapping. Crop Sci. 960-968.
• Schmutz, J., S.B. Cannon, J. Schlueter, J. Ma, D. Hyten, Q. Song, T. Mitros, W. Nelson, G. D. May, N. Gill, M. Peto, D. Goodstein, J.J. Thelen, J. Cheng, T. Sakurai, T. Umezawa, J. Du, M. Bhattacharyya, D. Sandhu, D. Grant, T. Joshi, M. Libault, X.-C. Zhang, D. Xu, M. Futrell-Griggs, B. Abernathy, U. Hellsten, K. Berry, J. Grimwood, R.A. Wing, P.B. Cregan, G. Stacey, J. Specht, D. Rokhsar, R.C. Shoemaker, S.A. Jackson. 2009. Genome sequence of the paleopolyploid soybean (Glycine max (L.) Merr.). Nature 463:178-183.
• Hyten, D.L., Q. Song, I.-Y. Choi1, M.-S. Yoon, J.E. Specht, L.K. Matukumalli, R.L. Nelson, R.C. Shoemaker, N.D. Young, and P.B. Cregan. 2008. High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theor. Appl. Genet. 116:945-952.
• Salvagiotti, F., K.G. Cassman, J.E. Specht, D.T. Walters, A. Weiss, and A. Dobermann. 2008. Nitrogen uptake, fixation and response to fertilizer N in soybeans: A review. Field Crop Res. 108:1-13.
• Choi, I.-Y., D.L. Hyten, L.K. Matukumalli, Q. Song, J.M. Chaky, C.V. Quigley, K. Chase, K.G. Lark, R.S. Reiter, M.-S. Yoon, E.-Y. Hwang, S.-I. Yi, N.D. Young, R.C. Shoemaker, C.P. van Tassell, J.E. Specht, and P.B. Cregan. 2007. A soybean transcript map: Gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176:685-696.
• Hyten, D.L., I.-Y. Choi, Q. Song, R.C. Shoemaker, R.L. Nelson, J.M. Costa, J.E. Specht, and P.B. Cregan. 2007. Highly Variable Patterns of Linkage Disequilibrium in Multiple Soybean Populations. Genetics 175:1937-1944.
• Hyten, D.L., Q. Song, Y. Zhu, I.-Y. Choi, R.L. Nelson, J.M. Costa, J.E. Specht, R.C. Shoemaker, and P.B. Cregan. 2006. Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl. Acad. Sci. USA 103: 16666–16671.
• Song, Q. J., L.F. Marek, R.C. Shoemaker, K.G. Lark, V.C. Concibido, X. Delannay, J.E. Specht, and P.B. Cregan. 2004. A new genetic linkage map for soybean. Theor. Appl. Genet. 109:122-128.
• Chung, J., H.L. Babka, G.L. Graef, P.E. Staswick, D.J. Lee, P.B. Cregan, R.C. Shoemaker, and J.E. Specht. 2003. The Seed Protein, Oil, and Yield QTL on Soybean Linkage Group I. Crop Sci. 43:1053-1067.
• Specht, J.E., K. Chase, M. Macrander, G.L. Graef, J. Chung, J.P. Markwell, M. Germann, J.H. Orf, and K.G. Lark. 2001. Soybean response to water: A QTL analysis of drought tolerance. Crop Sci. 41:493-509.
• Arahana, V.A., G.L. Graef, J.E. Specht, J.R. Steadman, and K.M. Eskridge. 2001. Identification of QTLs for resistance to Sclerotinia sclerotiorum in soybean. Crop Sci. 41:180-188.
• Specht, J.E., D.J. Hume, and S.V. Kumudini. 1999. Soybean yield potential - A genetic and physiological perspective. Crop Sci. 39:1560-1570.
• Cregan, P.B., T. Jarvik, A.L. Bush, R.C. Shoemaker, K.G. Lark, A.L. Kahler, N. Kaya, T.T. VanToai, D.G. Lohnes, J. Chung, and J.E. Specht. 1999. An integrated genetic linkage map of the soybean. Crop Sci. 39:1464-1490.
• Shoemaker, R.C., K. Polzin, J. Labate, J. Specht, E.C. Brummer, T. Olson, N. Young, V. Concibido, J. Wilcox, J.P. Tamulonis, G. Kochert, and H.R. Boerma. 1996. Genome duplication in soybean (Glycine subgenus soja). Genetics 144:329-339.
• Akkaya, M.S., R.C. Shoemaker, J.E. Specht, A.A. Bhagwat, and P.B. Cregan. 1995. Integration of simple sequence repeat (SSR) DNA markers into a soybean linkage map. Crop Sci. 35:1439-1445.
• Shoemaker, R.C. and J.E. Specht. 1995. Integration of the soybean molecular and classical genetic linkage groups. Crop Sci. 35:436-446. *118* Muehlbauer, G.J., J.E. Specht, M.A. Thomas-Compton, P.E. Staswick, and R.L. Bernard. 1988. Near-isogenic lines - A potential resource in the integration of conventional and molecular marker linkage maps. Crop Sci. 28:729-735.
• Specht, J.E. and J.H. Williams. 1984. Chapter 3. Contribution of Genetic Technology to Soybean Productivity - Retrospect and Prospect. In  W.R. Fehr (ed.) Genetic Contribution to Yield Gains of Five Major Crop Plants. CSSA Special Publication No. 7. American Society of Agronomy. Madison, Wisc. p. 49-74.
• Martineau, J.R., J.E. Specht, J.H. Williams, and C.Y. Sullivan. 1979. Temperature tolerance in soybeans. I. Evaluation of a technique for assessing cellular membrane thermostability. Crop Sci. 19:75-78.