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

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

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

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., 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

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

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

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