Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)


Environmental Engineering and Earth Sciences

Committee Member

Paula Agudelo, Co-Chair

Committee Member

Christina Wells, Co-Chair

Committee Member

Julia Frugoli

Committee Member

Patrick Gerard


The semi-endoparastic reniform nematode (Rotylenchulus reniformis) infects over 300 plant species. Females penetrate host roots and induce formation of complex, multinucleate feeding sites called syncytia. While anatomical changes associated with syncytia morphology are well documented, little is known about their molecular basis or the local impact on root development. Using a soybean (Glycine max) split-root system across a twelve-day time course, we identified over 6,000 genes that were differentially expressed between inoculated and control roots (FDR = 0.01, |log2FC| ≥ 1) and 507 gene sets that were significantly enriched or depleted in inoculated roots (FDR = 0.05). Numerous genes up-regulated during syncytium formation had previously been associated with rhizobia nodulation. These included the nodule-initiating transcription factors CYCLOPS, NSP1, NSP2, and NIN, as well as multiple nodulins associated with the plant-derived peribacteroid membrane. Nodulation-related NIP aquaporins and SWEET sugar transporters, CLAVATA3/ESR-related (CLE) signaling proteins, and cell cycle regulators such as CCS52A and E2F were induced. Greenhouse growth studies showed that the roots of young soybean plants produced more new lateral roots per unit length when infected with reniform nematode. A pre-selected set of 440 genes with documented roles in lateral root formation were examined, and 131were differentially expressed in response to parasitism on at least one sampling date. These included genes for auxin biosynthetic proteins and transporters, as well as transcription factors such as LATERAL ROOT PRIMORDIUM 1, LATERAL ORGAN BOUNDARIES, SOMBRERO, SHORT-ROOT, RPT2a, and several MADS-box genes. Finally, RNAseq data from infected soybean and cotton (Gossypium hirsutum) roots were used to assemble reniform nematode transcriptomes and identify putative nematode effectors based on sequence homology. A total of 3,485 and 4,852 reniform nematode protein-coding genes were assembled from infected soybean and cotton roots, respectively. One hundred and two of these genes shared homology to published plant parasitic nematode effectors, including CLEs, CTLs, FARs, VAPs, cell wall modifying enzymes, and putative secretory proteins of unknown function. The nematode and host genes identified here offer insight into reniform nematode parasitism and provide numerous avenues for further exploration.