GDCB Seminar - David Holding, Univ. of NE

Tuesday, January 31, 2017 - 4:10am
Event Type: 

David Holding
University of Nebraska, Lincoln
Department of Agronomy and Horticulture

Functional genomics investiations of maize and sorghum seed development and protein quality

Abstract: Although the hard kernel Quality Protein Maize version of the high lysine opaque-2 mutant has been in use for decades, the nature of the modifier genes has remained ambiguous.  To dissect QPM QTLs we used a deletion mutageneisis approach which confirmed the 27-kDa gamma zein as the major chromosome 7 QTL. BSR-seq mapping of QPM recombinant inbred lines has identified a starch biosynthesis-related candidate behind the other major QTL on chromosome 9. For more general seed and whole plant functional genomics, we have extended the deletion mutagenesis approach to the B73 maize reference background and have developed a substantial population of novel seed and vegetative mutants. I will use several mutants to exemplify the BSR-seq and exon-seq tools we have been using to map these mutants and identify causal mutations and to demonstrate that a useful proportion of deletions affect single genes. Finally, I will describe our efforts to generate and characterize reduced kafirin sorghum lines for improved grain digestibility and protein quality.

Refreshments in the MBB atrium at 3:45 pm. before the seminar.

Host: Tom Peterson (


Associate Professor

B.S., Biochemistry, University of Sussex, UK, 1991
PH.D., Plant Molecular Genetics, Kings College London, UK, 1997

Area of Focus

Plant Molecular Genetics

Research Interests

The endosperm constitutes the major seed storage tissue in cereals and aside from its role in supporting seed germination and early growth, it is vital as a food source in humans and livestock and has many industrial applications. Research in my laboratory focuses on understanding the essential trait of endosperm hardening during kernel maturation and its relationship to protein quality in maize. Maize is an incomplete protein source since its storage proteins are deficient in the essential amino acids, lysine and tryptophan. Maize mutants such as opaque2 reduce storage protein accumulation and their seeds can be used as a complete protein source.

However, these mutants have soft, chalky kernels conferring undesirable harvest, storage and processing traits. 'Quality Protein Maize' was developed by selecting for genetic modifiers that restore the desirable hard endosperm texture in opaque2 whilst maintaining its high levels of lysine and tryptophan. My research seeks to determine the nature and mode of action of these modifier genes in order to simplify the further development and utilization of maize with improved protein quality. Also by characterizing a series of opaque endosperm mutants, we are generating a more complete understanding of the process of endosperm hardening during kernel maturation. Furthermore, we have developed a new platform for functional genomics analysis of maize and sorghum kernel maturation and protein quality.

Major Research Activities

  • Investigating the nature, mode of action and potential applications of opaque2 modifier genes. We use transcriptional, proteomic and metabolic profiling as well as biotechnological approaches to study these genes. We are also mining maize diversity and conducting a mutagenesis approach to identify QPM genes.
  • Studying vitreous endosperm formation by cloning transposon tagged, opaque endosperm mutants and functionally characterizing the gene products
  • Seed and whole plant functional genomics of maize and sorghum
  • Breeding of Quality Protein Popcorn



  • Shangang Jia, Aixia Li, Kyla Morton, Penny Avoles-Kianian, Shahryar F. Kianian, Chi Zhang, and David Holding (2016) G3: Genes, Genomes and Genetics, A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize G3 g3.116.030528; Early Online June 3, 2016, doi:10.1534/g3.116.030528
  • Gelli, M., Mitchell, S.E., Liu, K., Clemente, T.E., Weeks, D.P., Zhang, C., Holding, D.R., Dweikat, I.M. (2016) Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum. BMC Plant Biology. doi: 10.1186/s12870-015-0696-x
  • Morton, K., Jia, S., Zhang, C., Holding, D.R. (2015) Proteomic profiling of maize opaque endosperm mutants reveals selective accumulation of lysine-enriched proteins. Journal of Experimental Botany. doi: 10.1093/jxb/erv532
  • Dou, Y., Guo, X., Yuan, L., Holding, D.R., Zhang, C. (2015) Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local Normalization. BioMed Research International Article ID 789516, doi:10.1155/2015/789516
  • Holding DR (2014) Recent advances in the study of prolamin storage protein organization and function. Front. Plant Sci. 5:276. doi: 10.3389/fpls.2014.00276
  • Malleswari Gelli, Yongchao Duo, Anji Reddy Konda, Chi Zhang, David Holding and Ismail Dweikat (2014) Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling. Gelli et al. BMC Genomics 2014, 15:179.
  • Lingling Yuan, Yongchao Dou, Shahryar Kianian, Chi Zhang and David R. Holding (2014) Deletion mutagenesis identifies a haploinsufficient role for gamma-zein in opaque-2 endosperm modification. Plant Physiology, January 2014, Vol. 164, pp. 119-130.
  • Holding, D.R., and Messing, J. (2013) Evolution, Structure, and Function of Prolamin Storage Proteins, in: P. Becraft (Ed.), Seed Genomics, John Wiley & Sons, New York. pp. 139-158.
  • Wu, Y., .Yuan, L, Guo, X, Holding, D.R. and Messing, J. (2013). Mutation in the seed storage protein kafirin creates a high-value food trait in sorghum. Nature Communications, Volume 4, Published 8-16-2013.
  • Guo, X., Yuan, L., Chen, H., Sato, S.J., Clemente, T.E, and Holding, D.R. (2013). Nonredundant Function of Zeins and Their Correct Stoichiometric Ratio Drive Protein Body Formation in Maize Endosperm. Plant Physiol. 162: 1359-1369.
  • Guo, X , Ronhovde, K, Yuan, L, Yao, B, Soundararajan, M, Elthon, T, Zhang, C and Holding, D (2012) Pyrophosphate dependent fructose-6-phosphate 1-phosphotransferase induction and attenuation of Hsp gene expression during endosperm modification in Quality Protein Maize, Plant Physiology, 158: 917-929.
  • Holding, D.R., Hunter, B.G., Klingler, J.P., Wu, S., Guo, X., Gibbon, B.C., Wu, R., Schulze, J., Jung, R., and Larkins, B.A. (2011) Characterization of opaque2 modifier QTLs and candidate genes in recombinant inbred lines derived from the K0326Y Quality Protein Maize inbred. Theoretical and Applied Genetics 122, 783-794.
  • Reyes, F.C., Chung, T., Holding, D., Jung, R., Vierstra, R., and Otegui, M.S. (2011) Delivery of Prolamins to the Protein Storage Vacuole in Maize Aleurone Cells, The Plant Cell 23, 769-784.
  • Holding, D.R., Meeley, R.B., Hazebroek, J., Selinger, D, Jung, R. and Larkins, B.A. (2010) Identification and characterization of the maize arogenate dehydrogenase gene family, Journal of Experimental Botany 61: 3663-3673
  • Wu, R., Holding, D.R., and Messing, J. (2010) Gamma zeins are essential for endosperm modification in Quality Protein Maize. Proceedings of the National Academy of Sciences, USA. 107: 12,810-12,815
  • Holding, D.R. and Larkins, B. A. (2009) Zein storage proteins, Chapter V: Molecular Biology and Physical Studies, in Molecular Genetic Approaches to Maize Improvement, (A.L. Kriz and B.A. Larkins eds.) pp 269-286. Springer-Verlag Publishers, Heidelberg, Germany./li>
  • Holding, D.R., Hunter, B.G., Chung, T., Gibbon, B.C., Ford, C.F., Bharti, A.K., Messing, J., Hamaker, B.R. and Larkins, B.A. (2008) Genetic Analysis of opaque2 Modifier Loci in Quality Protein Maize. Theoretical and applied genetics 117: 157-170.
  • Holding, D.R. and Larkins, B.A. (2008) Genetic Modification of Seed Storage Proteins. in "Advances in Plant Biochemistry and Molecular Biology" (Lewis, N.G., Ed.-in-chief) Vol. 1, Bioengineering and Molecular Biology of Plant Pathways (Bohnert, H.J. and Nguyen, H.T, eds.), pp. 107-133. Elsevier Publishers, Oxford, UK.
  • Holding, D.R, Otegui, M.S., Li, B., Meeley, R.B.,  Hunter, B.G., Jung. R. and Larkins, B.A. (2007) The maize Floury1 gene encodes a novel ER protein involved in zein protein-body formation. Plant Cell 19:2569-2582.
  • Settles, M.,  Holding, D., Tan, B.C. Latshaw, S., Susuki, M, O'Brien, B., Fajardo, D., Wroclwaska, E., Lai, J., Hunter, C., Avigne, W., Peacock, S., Baier, J., Lonon, D., Messing, J., Hannah, L.C., Koch, K., Becraft, P., Larkins, B., and McCarty, D. (2007) Maize Sequence Indexed Knockouts using the UniformMu Transposon Tagging Population. (2007) BMC Genomics, 8:116.
  • Holding, D.R. and Larkins, B.A. (2006) The development and importance of zein protein bodies in maize endosperm. Maydica 51 (2): 243-254.
  • Lopez-Valenzuela, J.A., Gibbon, B.C., Holding, D.R., and Larkins, B.A. (2004) Cytoskeletal proteins are coordinately increased in maize genotypes with high levels of eEF1A. Plant Physiology 135: 1784-1797.
  • Holding, D.R. and Springer, P.S. (2002) The VASCULAR PREPATTERN enhancer trap marks early vascular development in Arabidopsis. Genesis 33 (4): 155-159 2002.
  • Holding, D.R. and Springer, P.S. (2002) The Arabidopsis gene PROLIFERA is expressed at all stages of reproductive development and is required for cytokinesis. Planta, 214 373-382.
  • Springer, P.S., Holding. D.R., Groover, A., Yordan, C. and Martienssen, R.A. (2000) The essential Mcm7 protein PROLIFERA is localized to the nucleus of dividing cells during the G1 phase and is required maternally for early Arabidopsis development. Development 127, 1815-1822.
  • Holding, D.R., Springer, P.S. and Coomber, S.A. (2000) The chloroplast and leaf developmental mutant, pale cress, exhibits light-conditional severity and symptoms characteristic of its ABA deficiency. Annals of Botany. 86, 953-962.
  • Holding, D.R., McKenzie, R.J. and Coomber, S.A. (1994) Genetic and Structural analysis of five mutants with abnormal root morphology generated by the seed transformation method. Annals of Botany 74, 193-204.