Area of Expertise: Plant Breeding and Genetics

Area of Focus: Plant Molecular Genetics

Education

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

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

Publications

Google Scholar publication list

• Hurst, J.P., Sato, S., Ferris, T., Yobi, A., Zhou. Y., Angelovici, R., Clemente, T.E., Holding, D.R. (2023). Editing the 19 kDa alpha-zein gene family generates non-opaque2-based quality protein maize. https://doi.org/10.1111/pbi.14237
• Hurst, J.P. , Yobi, A., Li, A., Sato, S., Clemente, T., Angelovici, R. and Holding, D.R. (2023) Large and stable genome edits at the sorghum alpha kafirin locus result in changes in chromatin accessibility and globally increased expression of genes encoding lysine enrichment. Frontiers in Plant Science Biotechnology. 14, 762
• Ozturk, O.K., Salgado, A.M., Holding, D.R., Campanella, O.H., Hamaker, B.R. (2022). Dispersion of zein into pea protein with alkaline agents imparts cohesive and viscoelastic properties for plant-based food analogues. Food Hydrocolloids 134, 108044
• N Korth, L Parsons, MJ Van Haute, Q Yang, P Hurst, JC Schnable, D.R. Holding and A.K. Benson (2022) The unique seed protein composition of quality protein popcorn promotes growth of beneficial bacteria from the human gut microbiome Frontiers in microbiology 13
• R Rui Song, Ziyao Wang, Hui Wang, Han Zhang, Xuemeng Wang, Hanh Nguyen, David Holding, Bin Yu, Tom Clemente, Shangang Jia, Chi Zhang BMC genomics 22 (1), 1-7 (2021). InMut-Finder: a software tool for insertion identification in mutagenesis using Nanopore or PacBio long reads. BMC genomics
• Parsons, L., Ren, Y., Yobi, A., Angelovici, R., Rodriguez, O., and Holding, D.R. 2021. Final selection of quality protein popcorn hybrids. Frontiers in plant science 12
• Hurst, P, Schnable, J.C., and Holding, D.R. 2021. Tandem duplicate expression patterns are conserved between maize haplotypes of the α‐zein gene family. Plant Direct 5 (9), e346
• Parsons, L., Rodriguez, O., and Holding, D.R. 2021. Improved taste and texture in novel popcorn varieties compared to conventional lines. Journal of Sensory Studies, e12687
• Jia, S., Yobi, A, Naldrett, M.J., Alvarez, S, Angelovici, R, Zhang, C, and Holding, D.R. 2020. Deletion of maize RDM4 suggests a global role in endosperm maturation as well as vegetative and stress-responsive growth. Journal of Experimental Botany doi.org/10.1093/jxb/eraa325
• Parsons, L., Ren, Y, Yobi, A., Hurst, P, Angelovici, R., Rodriguez, O., and Holding, D.R. 2020 Production and Selection of Quality Protein Popcorn Hybrids using a novel Ranking System and Combining Ability Estimates. Frontiers in Plant Science. 11, doi: 10.3389/fpls.2020.00698.
• Li. A, and Holding, D.R 2020. Genome editing of sorghum. Ch 21, In ‘Gene editing for precision crop breeding’ editor Matthew Willmann, Burleigh Dodds Science Publishing. pp377-402
• Hongjun Liu, Yongcai Huang, Xiaohan Li, Haihai Wang, Yahui Ding, Congbin Kang, Mingfei Sun, Fangyuan Li, Jiechen Wang, Yiting Deng, Xuerong Yang, Xing Huang, Xiaoyan Gao, Lingling Yuan, Dong An, Wenqin Wang, David R. Holding and Yongrui Wu. (2019) High frequency DNA rearrangement at qγ27 creates a novel allele for Quality Protein Maize breeding. Commun Biol 2, 460  doi:10.1038/s42003-019-0711-0
• S Jia, K Morton, C Zhang, D Holding. (2019) An Exome-seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion Mutants. Genomics Proteomics Bioinformatics. 16(6):439-450. doi: 10.1016/j.gpb.2018.02.003.  
• Shengjun Li, Shangang Jia, Lili Hou, Hanh Nguyen, Shirley Sato, David Holding, Edgar Cahoon, Chi Zhang, Tom Clemente, Bin Yu. (2019) Mapping of transgenic alleles in soybean using a Nanopore-based sequencing strategy. J Exp Bot. doi.org/10.1093/jxb/erz202.
• P Gulati, S Jia, A Li, DR Holding, D Santra, DJ Rose (2018) In Vitro Pepsin Digestibility of Cooked Proso Millet (Panicum miliaceum L.) and Related Species from Around the World. J Agric Food Chem. Jul 11;66(27):7156-7164. doi: 10.1021/acs.jafc.8b02315.
•  Ying Ren, Abou Yobi, Leandra Marshall, Ruthie Angelovici, Oscar Rodriguez, and David R. Holding (2018) Generation and evaluation of modified opaque-2 popcorn suggests a route to Quality Protein Popcorn. Front Plant Sci. 9, 1803.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6291453/
• S Jia, A Li, C Zhang, D. Holding (2018) Deletion Mutagenesis and Identification of Causative Mutations in Maize. Methods Mol Biol. 1676:97-108. doi: 10.1007/978-1-4939-7315-6_5.
• Aixia Li, Shangang Jia, Abou Yobi, Zhengxiang Ge, Shirley J. Sato, Chi Zhang, Ruthie Angelovici, Thomas E. Clemente, David R. Holding (2018) Editing of an Alpha-Kafirin gene family increases, digestibility and protein quality in sorghum. Plant physiology 177 (4), 1425-1438. DOI:doi.org/10.1104/pp.18.00200.
• P Gulati, A Li, D Holding, D Santra, Y Zhang, DJ Rose (2017) Heating reduces proso millet protein digestibility via formation of hydrophobic aggregates. J Agric Food Chem. Mar 8;65(9):1952-1959. doi: 10.1021/acs.jafc.6b05574.
• M Gelli, AR Konda, K Liu, C Zhang, TE Clemente, DR Holding, IM Dweikat (2017) Validation of QTL mapping and transcriptome profiling for identification of candidate genes associated with nitrogen stress tolerance in sorghum. BMC Plant Biology 17 (1), 123. doi.org/10.1186/s12870-017-1064-9 
• Shangang Jia, David Holding, Chi Zhang (2017) A mapping-by-sequencing tool for searching causative genes in mutants. IEEE International Conference on Electro Information Technology (EIT),Lincoln, NE, 338-340. DOI: 10.1109/EIT.2017.8053381.
• 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 A. M Streich (2013) Plant Growth Processes: Transpiration, Photosynthesis, and Respiration. Extension Circular 1268.
• 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.