David L. Hyten

Associate Department Head, Haskins Professor in Plant Genetics and Associate Professor, Soybean Genetics/Genomics, Center for Plant Science Innovation, Nebraska Food for Health Center

Area of Expertise: Plant Breeding and Genetics

B.A., Microbiology, Southern Illinois University, 1999

M.S., Plant Breeding and Genetics, 2002

Ph.D. Crop Genetics, 2005

Area of Focus

Soybean Genetics and Genomics

Research Interests

My lab is focused on taking basic genetic and genomic discoveries in soybean and translating those discoveries into applied methods that can be used for the real-world improvement of soybean varieties. The program focuses specifically on improving agronomically important traits such as drought tolerance and response to water abundance. As we experience climate change, making cultivars able to withstand drought and highly responsive to water abundance will be key to feeding the world. My lab is working towards understanding the underlying genetic diversity that leads to drought tolerance so that we can link genetic diversity to this agronomically important phenotype and understand how genetic diversity interacts across the diverse environments encountered across Nebraska and the rest of the United States. To help translate that understanding into applied breeding methods, my lab also focuses on developing better methods, tools and genomic breeding strategies for utilizing that knowledge within soybean public and private breeding programs. A specific area of interest is understanding genetic recombination hotspots and coldspots and the genetic mechanisms responsible for recombination in soybean. The goal of this research will be to develop new techniques that allow breeders to manipulate recombination to incorporate essential genetic diversity into new breeding varieties while maintaining yield gains needed to meet future demands from population growth. Through this work my research program has the goal of accelerating the rate of genetic gain within soybean to meet the long-term challenges of feeding the world, and in combating the negative effects of climate change on soybean production.


Book Chapters

  • Hyten, D.L. 2012. Advances in genome sequencing and genotyping technology for soybean diversity analysis. In: R.F. Wilson (Ed.) Designing Soybeans for 21st Century Markets, AOCS Press, Urbana, IL. pp. 45-52.

Research Articles

  • Song, Q., Hyten, D.L., Jia, G., Quigley, C.V., Fickus, E.W., Nelson, R.L., and Cregan, P.B. 2015. Fingerprinting soybean germplasm and its utility in genomic research. G3. Early Online, DOI 10.1534/g3.115.019000.
  • Fallen, B.D., Allen, F.L., Kopsell, D.A., Saxton, A.M., McHale, L., Shannon, J.G., Kantartzi, S.K., Cardinal, A.J., Cregan, P.B., Hyten, D.L., and Pantalone, V.R. 2015. Selective genotyping for marker assisted selection strategies for soybean yield improvement. Plant Genetics, Genomics, and Biotechnology. 2:95-119.
  • Warrington, C.V., Abdel-Haleem, H., Hyten, D.L., Cregan, P.B., Orf, J.H., Killam, A.S., Bajjalieh, N., Li, L., and Boerma, H.R. 2015. QTL for seed protein and amino acids in the Benning x Danbaekkong soybean population. Theor. Appl. Genet. 128:839-850.
  • Schmutz, … Hyten, D.L. (24 of 41 authors), and Jackson, S.A. 2014. A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics. 46:707-713.
  • Wang, X., Jiang, G. L., Green, M., Scott, R.A., Song, Q., Hyten, D.L., and Cregan, P.B. 2014. Identification and validation of quantitative trait loci for seed yield, oil and protein contents in two recombinant inbred line populations of soybean. Molecular Genetics and Genomics 33:281-296.
  • Bolon, Y.T., Hyten, D.L., Orf, J.H., Vance, C.P., and Muehlbauer, G.J. 2014. eQTL networks reveal complex genetic architecture in the immature soybean seed. Plant Genome 7:1.
  • Abdelmajid, K.M., Ramos, L., Hyten, D., Bond, J., Bendahmane, A., Arelli, P.R., Njiti, V.N., Cianzio, S., Kantartzi, S.K., and Meksem, K. 2014. Quantitative trait loci (QTL) that underlie SCN resistance in soybean [Glycine max (L.) Merr.] PI438489B by ‘Hamilton’ recombinatnt inbred line (RIL) population. Atlas J. of Plant Bio. 3:29-38.
  • Zhang, Z., Hao, J., Yuan, J., Song, Q., Hyten, D.L., Cregan, P.B., Zhang, G., Gu, C., Li, M., Wang, D. 2014. Phytophthora root rot resistance in soybean E00003. Crop Sci. 54:492-499.
  • Wang, X., Jiang, G.-L., Green, M., Scott, R.A., Hyten, D.L., Cregan, P.B. 2014. Quantitative trait locus analysis of unsaturated fatty acids in a recombinant inbred population of soybean. Mol. Breeding 33:281-296.
  • Hwang, E.-Y., Song, Q., Jia, G., Specht, J.E., Hyten, D.L., Costa, J., Cregan, P.B. 2014. A genome-wide association study of seed protein and oil content in soybean. BMC Genomics 15:1.
  • Cardinal, A., Whetten, R., Wang, S., Auclari, J., Hyten, D., Cregan, P., Bachlava, E., Gillman, J., Ramirez, M., Dewey, R., Upchurch, G., Miranda, L., Burton, J. 2014. Mapping the low palmitate fap1 mutation and validation of its effects in soybean oil and agronomic traits in three soybean populations. Theor. Appl. Genet. 127:97-111.
  • Smallwood, C.J., Nyinyi, C.N., Kopsell, D.A., Sams, C.E., West, D.R., Chen, P., Kantartzi, S.K., Cregan, P.B., Hyten, D.L., and Pantalone, V.R. 2014. Detection and confirmation of quantitative trait loci for soybean seed isoflavones. Crop Sci. 54:595-606.
  • Bales, C., Zhang, G., Liu, M., Mensah, C., Gu, C., Song, Q., Hyten, D., Cregan, P., and Wang, D. 2013. Mapping soybean aphid resistance genes in PI 567598B. Theor. Appl. Genet. 126:2081-2091.
  • Song, Q., Hyten, D.L., Jia, G., Quigley, C.V., Fickus, E.W., Nelson, R.L., and Cregan, P.B. 2013. Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLOS One 8:e54985.
  • Fallen, B.D., Hatcher, C.N., Allen, F.L., Kopsell, D.A., Saxton, A.M., Chen, P., Kantartzi, S.K., Cregan, P.B., Hyten, D.L., and Pantalone, V.R. 2013. Soybean seed amino acid content QTL detected using the Universal Soy Linkage Panel 1.0 with 1,536 SNPs. J. of Plant Genome Sciences. 1:68-79.
  • Pathan, S.M., Vuong, T., Clark, K., Lee, J-D., Shannon, J.G., Roberts, C.A., Ellersieck, M.R., Burton, J.W., Cregan, P.B., Hyten, D.L., Nguyen, H.T., and Sleper, D.A. 2013. Genetic mapping and confirmation of quantitative trait loci (QTL) for seed protein and oil contents and seed weight in soybean. Crop Sci. 53:765-774.
  • Kim, K.-S., Diers, B.W., Hyten, D.L., Rouf Mian, M.A., Shannon, J.G., Nelson, R.L. 2012. Identification of positive yield QTL alleles from exotic soybean germplasm in two backcross populations. Theor. Appl. Genet. 125:1353-1369.
  • Abdelmajid, K.M., Ramos, L., Leandro, L., Mbofung, G., Hyten, D.L., Kantartzi, S.K., Grier, R.L., Njiti, V.N., Cianzio, S., and Meksem, K. 2012. The ‘PI 438489B’ by ‘Hamilton’ SNP-based genetic linkage map of soybean [Glycine max (L.) Merr.] identified quantitative trait loci that underlie seedling SDS resistance. J. of Plant Gen. Sci. 1:18-30.
  • McHale, L.K., Haun, W.J., Xu, W.W., Bhaskar, P.B., Anderson, J.E., Hyten, D.L., Gerhardt, D.J., Jeddeloh, J.A., Stupar, R.M. 2012. Structural variants in the soybean genome localize to clusters of biotic stress-response genes. Plant Physiol. 159:1295-1308.
  • Wang, X., Jiang, G.-L., Green, M., Scott, R.A., Hyten, D.L., Cregan, P.B. 2012. Quantitative trait locus analysis of saturated fatty acids in a population of recombinant inbred lines of soybean. Molecular Breeding 30:1163-1179.
  • Kim, K.-S., Unfried, J.R., Hyten, D.L., Frederick, R.D., Hartman, G.L., Nelson, R.L., Song, Q., Diers, B.W. 2012. Molecular mapping of soybean rust resistance in soybean accession PI 561356 and SNP haplotype analysis of the Rpp1 region in diverse germplasm. Theor. Appl. Genet. 125:1339-1352.
  • Mamidi, S., Chikara, S., Goos, R.J., Hyten, D.L., Annam, D., Moghaddam, S.M., Lee, R.K., Cregan, P.B., and McClean, P.E. 2011. Genome-wide association analysis identifies candidate genes associated with iron deficiency chlorosis in soybean. The Plant Genome 4:154-164.
  • Polacco, J.C., Hyten, D.L., Medeiros-Silva, M., Sleper, D.A., Bilyeu, K.D. 2011. Mutational analysis of the major soybean UreF paralogue involved in urease activation. J. of Experimental Botany 62:3599-3608.
  • Kendrick, M.D., Harris, D.K., Ha, B.-K., Hyten, D.L., Cregan, P.B., Frederick, R.D., Boerma, H.R., Pedley, K.F. 2011. Identification of a second Asian soybean rust resistance gene in Hyuuga soybean. Phytopathology 101:535-543.
  • Kim, M., Hyten, D.L., Niblack, T.L., Diers, B.W. 2011. Stacking resistance alleles from wild and domestic soybean sources improves soybean cyst nematode resistance. Crop Sci. 51:934-943.
  • Haun, W.J., Hyten, D.L., Xu, W.W., Gerhardt, D.J., Albert, T.J., Richmond, T., Jeddeloh, J.A., Jia, G., Springer, N.M., Vance, C.P., Stupar, R.M. 2011. The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82. Plant Physiol. 155:645-655.
  • Hyten, D.L., Q. Song, E.W. Fickus, C.V. Quigley, J-S. Lim, I-Y. Choi, E-Y Hwang, M. Pastor-Corrales, and P.B. Cregan. 2010. High-throughput SNP discovery and assay development in common bean. BMC Genomics 11:475.
  • Lin, Y-Y., Stupar, R.M., Hans, C., Hyten, D.L., and Jackson, S. 2010. Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to Phaseolus vulgaris. Plant Cell. 22:2545-2561.
  • Severin, A.J., Peiffer, G., Xu, W.W., Hyten, D.L., Bucciarelli, B., O'Rourke, J.A., Bolon, Y-T., Grant, D., Farmer, A.D., May, G.D., Vance, C.P., Shoemaker, R.C., and Stupar, R.M. 2010. An integrative approach to genomic introgression mapping. Plant Physiol. 154:3-12.
  • Song, Q., Jia, G., Zhu, Y., Hwang, E-Y., Hyten, D.L., and Cregan P.B. 2010. Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in soybean. Crop Sci. 50:1950-1960.
  • Kim, K. S., Hill, C. B., Hartman, G. L., Hyten, D. L., Hudson, M. E., Diers, B. W. 2010. Fine mapping of the soybean aphid-resistance gene Rag2 in soybean PI 200538. Theor. Appl. Genet.121:599-610.
  • 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. 50:960-968.
  • Hyten, D.L., S.B. Cannon, Q. Song, N. Weeks, E.W. Fickus, R.C. Shoemaker, J.E. Specht, A.D. Farmer, G.D. May, and P.B. Cregan. 2010. High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11:38.
  • Schmutz, J., S. Cannon, J. Schlueter, J. Ma, T. Mitros, W. Nelson, D.L. Hyten, Q. Song, J. Thelen, J. Cheng, D. Xu, U. Hellsten, G. May, Y. Yu, T. Sakurai, T. Umezawa, M. Bhattacharyya, D. Sandhu, B. Valliyodan, E. Lindquist, M. Peto, D. Grant, S. Shu, D. Goodstein, K. Barry, M. Futrell-Griggs, J. Du, Z. Tian, L. Zhu, N. Gill, T. Joshi, M. Libault, A. Sethuraman, X.-C. Zhang, K. Shinozaki, H. Nguyen, R. Wing, P. Cregan, J. Specht, J. Grimwood, D. Rokhsar, G. Stacey, R. Shoemaker, and S. Jackson. 2010. Genome seqeunce of the paleopolyploid soybean. Nature 463:178-183.
  • Kim, K-S., Bellendir, S., Hudson, K., Hill, C., Hartman, G., Hyten, D.L., Hudson, M., and Diers, B. 2010. Fine mapping the soybean aphid resistance gene Rag1 in soybean. Theor. Appl. Genet. 120:1063-1071.
  • Chakraborty, N., Curley, J., Frederick, R.D., Hyten, D.L., Nelson, R.L., Hartman, G.L., and Diers, B.W. 2009. Mapping and confirmation of a new allele at Rpp1 from soybean PI 594538A conferring RB lesion type resistance to soybean rust. Crop Sci. 49: 783-790. 
  • Hyten, D.L., J.R. Smith, R.D. Frederick, M.L. Tucker, Q. Song, and P.B. Cregan. 2009. Bulked segregant analysis using the GoldenGate assay to locate the Rpp3 locus that confers resistance to Phakopsora pachyrhizi (soybean rust) in soybean. Crop Sci. 49: 265-271.
  • Hyten, D.L., Song, Q., Choi, I-Y., Yoon, M-S., Specht, J.E., Matukumalli, L.K., Nelson, R.L., Shoemaker, R.C., Young, N.D., and Cregan, P.B. 2008. High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theor. Appl. Genet. 116:945-952.
  • Choi, I.-Y., Hyten, D.L., Matukumalli, L.K., Song, Q., Chaky, J.M., Quigley, C.V., Chase, K., Lark, K.G., Reiter, R.S., Yoon, M-S., Hwang, E-Y., Yi, S-In., Young, N.D., Shoemaker, R.C., Van Tassell, C.P., Specht, J.E., and Cregan, P.B. 2007. A soybean transcript map: gene distribution, haplotype and SNP analysis. Genetics 176:685-696.
  • Hyten, D.L., Choi, I-Y., Song, Q., Shoemaker, R.C., Nelson, R.L., Costa, J.M., Specht, J.E., and Cregan, P.B. 2007. Highly variable patterns of linkage disequilibrium in multiple soybean populations. Genetics 175:1937-1944.
  • Hyten D., Hartman G., Nelson R., Frederick R., Concibido V., and Cregan P. 2007. Map Location of the Rpp1 locus that confers resistance to Phakopsora pachyrhizi (Soybean Rust) in soybean. Crop Sci. 47:835-838.
  • Yoon M-S., Song Q., Choi I-Y., Specht J., Hyten D., and Cregan P. 2007. BARCSoySNP23: A panel of 23 selected SNPs for soybean cultivar identification. Theor. Appl. Genet. 114:885-899.
  • Hyten D., Song Q., Zhu Y., Choi I-Y., Nelson R., Costa J., Specht J., Shoemaker R., and Cregan P. 2006. Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl. Acad. Sci. U.S.A. 103:16666-16671. 
  • Matukumalli, L., Grefenstette J., Hyten D., Choi, I-Y., Cregan P., and Van Tassell C. 2006. SNP-PHAGE – High throughput SNP discovery pipeline. BMC Bioinformatics 7:468.
  • Matukumalli, L., Grefenstette J., Hyten D., Choi, I-Y., Cregan P., and Van Tassell C. 2006. SNP-PHAGE-ML: Application of machine learning in SNP discovery. BMC Bioinformatics 7:4.
  • Stefaniak T., Hyten D., Pantalone V., Klarer A., and Pfeiffer T. 2006. Soybean cultivars resulted from more recombination events than unselected lines in the same population. Crop Sci. 46:43-51.
  • Hyten D., Pantalone V., Saxton A., Schmidt M., and Sams C. 2004. Molecular mapping and identification of soybean fatty acid modifier quantitative trait loci. J. Am. Oil Chem. Soc. 81:1115-1118.
  • Hyten D., Pantalone V., Sams C., Saxton A., Landau-Ellis D., Stefaniak T., Schmidt M. 2004. Seed quality QTL in a prominent soybean population. Theor. Appl. Genet. 109: 552-561.
  • Zhu Y., Song Q., Hyten D., Van Tassell C., Matukumalli L., Grimm D., Hyatt S., Fickus E., Young N., and Cregan P. 2003. Single-nucleotide polymorphisms in soybean. Genetics 163:1123-1134.
  • Spencer M., Pantalone V., Meyer E., Landau-Ellis D., Hyten D. 2003. Mapping the Fas locus controlling stearic acid content in soybean. Theor. Appl. Genet. 106:615-619.
  • Meksem K., Ruben E., Hyten D., Triwitayakorn K., Lightfoot D. A. 2001. Conversion of AFLP bands to high-throughput DNA markers. Mol. Genet. Genomics 265:207-214.
  • Meksem K., Ruben E., Hyten D., Lightfoot D. 2001. Highthroughput genotyping for the detection of polymorphism physically linked soybean cyst nematode resistance gene Rhg4 using Taqman Probes. Mol. Breeding 77:63-71.
  • Meksem K., Pantazopoulos P., Njiti V., Hyten D., Arelli P., Lightfoot D. 2001. “Forrest” resistance to the soybean cyst nematode is bigenic: saturation mapping of the Rhg1 and Rhg4 loci. Theor. Appl. Genet. 103:710-717.
  • Meksem K., Njiti V., Banz W., Iqbal M., Kassem M., Hyten D., Yuang J., Winters T., and Lightfoot D. 2001. Genomic regions that underlie soybean seed isoflavone content. J. Biomed. Biotechnol. 1:35-42.
  • Meksem K., Zobrist K., Ruben E., Hyten D., Quanzhou T., Zhang H-B., Lightfoot D. 2000. Two large-insert soybean genomic libraries constructed in a binary vector: applications in chromosome walking and genome wide physical mapping. Theor. Appl. Genet. 101:747-755.