Aim 3

Aim 3 Root Synthetic Biology: Tool Development and Applications


Cahoon*, Clemente*, Adamec, Alfano, Helikar, Herr, Moriyama, Schnable, Walia, Yu, Zhang,


  • Root Samples on lab counter
Synthetic biology provides tool sets for next-generation crop improvement to deliver multiple genes to precise locations in the host plant genome for expression in specific cell types. By integrating synthetic biology with systems biology (Aim 1), the effects of genetic alterations on cellular metabolism can be more predictability achieved and iteratively improved. Synthetic biology applications can be guided by findings on the influence of root exudates on the rhizobiome (Aim 2) and the effects of environmental perturbations on the interface between root metabolism and soil microbes (Aim 4).


  1. Development of Synthetic Biology Tools
  2. Application of Synthetic Biology Tools for Improvement of Root Traits

Associated Publications

Chenyong Miao, Jinliang Yang and James C. Schnable. 2018. Optimizing the identification of causal variants across varying genetic architectures in crops. bioRxiv

Cuevas, H.E., C. Zhou, H. Tang, P.P. Khadke, S. Das, Y.R. Lin, Z. Ge, T. Clemente, H.D. Upadhyaya, C.T. Hash, and A.H. Paterson.. 2016. The evolution of photo-insensitive flowering in sorghum, A genomic model for Panicoid grasses. Mol Biol Evol 33:2417-2428
DOI: 10.1093/molbev/msw120

Dou Y, Li S, Yang W, Liu K, Du Q, Ren G, Yu B* and Zhang C .. 2017. Genome-wide Discovery of Circular RNAs in the Leaf and Seedling Tissues of Arabidopsis Thaliana. Current Genomics 18:360-365

Gelli, M., S.E. Mitchell, K. Liu, T.E. Clemente, D.P. Weeks, C. Zhang, D.R. Holding, and I.M. Dweikat.. 2017. Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum. BMC Plant Biol 16:16
DOI: 10.1186/s12870-015-0696-x

Haslam R. P., Sayanova O., Kim H. J., Cahoon E. B., Napier J. A.. 2017. Synthetic redesign of plant lipid metabolism. Plant J. 87: 76-86
DOI: 10.1111/tpj.13172

Haslam RP, Sayanova O, Kim HJ, Cahoon EB, Napier JA. . 2016. Synthetic redesign of plant lipid metabolism. Plant J. 2016 Jul;87(1):76-86.

Jia T, Zhang B, You C, Zhang Y, Zeng L, Li S, Johnson KCM, Yu B, Li, X, and Chen X.. 2017. he Arabidopsis MOS4-associated complex promotes microRNA biogenesis and precursor messenger RNA splicing. Plant Cell 29:2626-2643

Kaur, J., J. Fellers, A. Adholeya, S.L. Velivelli, K. El-Mounadi, N. Nersesian, T. Clemente, and D. Shah.. 2016. Expression of apoplast-targeted plant defensing MtDef4.2 confers resistance to leaf rust pathogen Puccinia triticina but does not affect mycorrhizal symbiosis in transgenic wheat. Transgenic Res. 26: 37-49
DOI: 10.1007/s11248-016-9978-9

Kohler, I.H., U.M. Ruiz-Vera, A. VanLoocke, M.L. Thomey, T. Clemente, S.P. Long, D.R. Ort, and C.J. Bernacchi.. 2017. Expression of cyanobacterial FBP/SBPase in soybean prevents yield depression under future climate conditions. J. Exp. Bot. 68: 715-726
DOI: 10.1093/jxb/erw435

Li S, Liu K, Zhou B, Li M, Zhang S, Zeng L, Zhang C and Yu B*. . 2018. MAC3A and MAC3B, two core subunits of the MOS4-associated complex, positively impact miRNA biogenesis. Plant Cell

Li S and Yu B* . 2017. miRNA limits MAP kinase-mediated immunity: optimization of plant fitness. Journal of Experimental Botany 68:5685-5687

Li, S., Castillo-Gonzalez, C., Yu, B., and Zhang, X.. 2017. The functions of plant small RNAs in development and in stress responses. Plant J.
DOI: 10.1111/tpj.13444

Li, S., Liu, K., Zhang, S., Wang, X., Rogers, K., Ren, G., Zhang, C., and Yu, B.. 2017. STV1, a ribosomal protein, binds primary microRNA transcripts to promote their interaction with the processing complex in Arabidopsis. PNAS114: 1424-1429
DOI: 10.1073/pnas.1613069114

Li, S., Castillo-Gonzalez, C., Yu, B., and Zhang, X.. 2016. The functions of plant small RNAs in development and in stress responses. Plant J.
DOI: 10.1111/tpj.13444

Liang Z, Pandey P, Stoerger V, Xu Y, Qiu Y, Ge Y, Schnable JC.. 2017. Conventional and hyperspectral time-series imaging of maize lines widely used in field trials. GigaScience

Liang Z., Schnable J.C.. 2018. Functional Divergence between Subgenomes and Gene Pairs after Whole Genome Duplications. Molecular Plant, Volume 11, Issue 3, 5 March 2018, Pages 388-397

Liu K, Du Q, Ren G, Yu B and Zhang C.. 2017. Identification of Differential Alternative Splicing Events with an Adjusted Beta-Distribution Model.. IEEE International Conference on Electro Information Technology (EIT)

Malachy T Campbell, Harkamal Walia, Gota Morota. 2018. Utilizing random regression models for genomic prediction of a longitudinal trait derived from high-throughput phenotyping. bioRxiv

Palmer, N.A., A.J. Saathoff, E.D. Scully, C.M. Tobias, P. Twigg, S. Madhavan, M. Schmer, R. Cahoon, S.E. Sattler, S.J. Edme, R.B. Mitchell, & G. Sarath. . 2017. Seasonal below-ground metabolism in switchgrass. The Plant J. 92: 1059-1075.

Park, H., S. Weier, F. Razvi, P.A. Pena, N.A. Sims, J. Lowell, C. Hungate, K. Kissinger, G. Key, P. Fraser, J.A. Napier, E.B. Cahoon, and T.E. Clemente.. 2017. Towards the development of a sustainable soya bean-based feedstock for aquaculture. Plant Biotechnol. J. 15: 227-236
DOI: 10.1111/pbi.12608

Ren G, Wang X, Yu B.. 2017. Analysis of the Uridylation of Both ARGONAUTE-Bound MiRNAs and 5' Cleavage Products of Their Target RNAs in Plants. Methods Mol Biol. 1640:23-37

Scully, E.D., T. Gries, N.A. Palmer, G. Sarath, D.L. Funnell-Harris, L. Baird, P. Twigg, J. Seravelli, T.E. Clemente, & S. Sattler. . 2018. Overexpression of SbMyb60 in Sorghum bicolor impacts both primary and secondary metabolism. New Phytol. 217: 82-104.

Scully, E. D., T. Gries, G. Sarath, N.A. Palmer, L. Baird, M.J. Serapiglia, B.S. Dien, A.A. Boateng, Z. Ge, D.L. Funnell-Harris, P. Twigg, T.E. Clemente, and S.E. Sattler.. 2016. Overexpression of the SbMyb60 impacts phenylpropanoid biosynthesis and alters secondary cell wall composition in Sorghum bicolor. Plant J. 85:378-395
DOI: 10.1111/tpj.13112

Shuxin Zhang, Yongchao Dou, Shengjun Li, Guodong Ren, David Chevalier, Chi Zhang, Bin Yu.. 2018. DAWDLE interacts with DICER-LIKE proteins to mediate small RNA biogenesis. Plant Physiology

Stacey, M.G., R.E. Cahoon, H.T. Nguyen, Y. Cui, S. Sato, C.T., Nguyen, N. Phoka, K.M. Clark, Y. Liang, J. Forrester, J. Batek, P.T. Do, D.A. Sleper, T.E. Clemente, E.B. Cahoon, and G. Stacey.. 2016. Identification of homogentisate dioxygenase as a target for vitamin E biofortification in oilseeds. Plant Physiol. 172: 1506-1518
DOI: 10.1104/pp.16.00941

Wang, H., C. Zhang, Y. Dou, B. Yu, Y. Liu, T. Heng-Moss, G. Lu, M. Wachholz, J. Bradshaw, P. Twigg, E.Scully, N. Palmer, and G. Sarath.. 2017. Insect and plant-derived miRNAs in greenbug (Schizapis graminum) and yellow sugarcane aphid (Sipha flava) revealed by deep sequencing. Gene. 599: 68-77
DOI: 10.1016/j.gene.2016.11.014

Yu, Q., Liu, Y., Li, M., and Yu, B.. 2017. Small RNA biogenesis and degradation RNA technology. In Press

Zhang Y, Ngu DW, Carvalho D, Liang Z, Qiu Y, Roston RL, Schnable JC. 2017. Differentially regulated orthologs in sorghum and the subgenomes of maize. The Plant Cell