Transcriptome profiling and RNA-Seq SNP analysis of reniform nematode (Rotylenchulus reniformis) resistant cotton (Gossypium hirsutum) identifies activated defense pathways and candidate resistance genes

Authors: Wubben, Martin; KHANAL, SAMEER - University Of Georgia; Gaudin, Amanda; CALLAHAN, FRANKLIN - Retired ARS Employee; CHEE, PENG - University Of Georgia; McCarty Jr, Jack; Jenkins, Johnie; NICHOLS, ROBERT - Cotton, Inc

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/23/2025
Publication Date: 2/19/2025
Citation: Wubben, M., Khanal, S., Gaudin, A.G., Callahan, F.E., Chee, P.W., Mccarty Jr, J.C., Jenkins, J.N., Nichols, R.L. 2025. Transcriptome profiling and RNA-Seq SNP analysis of reniform nematode (Rotylenchulus reniformis) resistant cotton (Gossypium hirsutum) identifies activated defense pathways and candidate resistance genes. Frontiers in Plant Science. 16:1532943. https://doi.org/10.3389/fpls.2025.1532943.
DOI: https://doi.org/10.3389/fpls.2025.1532943

Interpretive Summary: The reniform nematode (RN) is a serious pathogen of cotton that is grown throughout the southeastern United States and Texas. A popular source of cotton resistance to RN comes from the wild accession 'GB713'. It was previously shown that GB713 RN resistance is largely controlled by a single genetic locus on cotton chromosome 21 that is named Renbarb2. In the present study, we set out to determine how Renbarb2 mediates resistance to RN by measuring the expression of all cotton genes in plant roots infected or not infected with RN that are resistant or susceptible to the nematode at three timepoints following RN inoculation. Across all timepoints, we discovered modified expression of 1099 genes in RN-infected resistant roots versus only 141 differentially expressed genes (DEGs) in RN-infected susceptible roots. In resistant roots, genes that were involved in defense/resistance responses were prevalent. Furthermore, in resistant roots, transcription factor genes of many different varieties were induced at that later timepoint, indicating that the resistance response was ongoing. Lastly, we identified genes within the Renbarb2 locus that have a strong possibility of being responsible for 'turning on' the resistance response. These new data provide a way forward for identifying the gene required for Renbarb2 resistance and the development of new resistant cotton cultivars.

Technical Abstract: The reniform nematode (Rotylenchulus reniformis Linford & Oliveira) is a serious pathogen of Upland cotton (Gossypium hirsutum L.) wherever it is grown throughout the United States. Upland cotton resistance to R. reniformis derived from the G. barbadense accession GB713 is largely controlled by the Renbarb2 locus on chromosome 21. Renbarb2 has proven useful as a tool to mitigate annual cotton yield losses due to R. reniformis infection; however, very little is known about the molecular aspects of Renbarb2-mediated resistance and the gene expression changes that occur in resistant plants during the course of R. reniformis infection. In this study, two nearly isogenic lines (NILs), with and without the Renbarb2 locus, were inoculated with R. reniformis and RNAs extracted and sequenced from infected and control roots at 5-, 9-, and 13-dai (days after inoculation). A total of 1099 differentially expressed genes (DEGs) were identified in the resistant NIL while 141 DEGs were discovered from the susceptible NIL. In resistant plants, biological processes related to oxidation-reduction reactions and redox homeostasis were enriched at each timepoint with such genes being up-regulated at 5- and 9-dai but then being down-regulated at 13-dai. DEGs associated with cell wall reinforcement and defense responses were also up-regulated at early timepoints in resistant roots. In contrast, in susceptible roots, defense-related gene induction was only present at 5-dai and was comprised of far fewer genes than in the resistant line. ERF, WRKY, and NAC transcription factor DEGs were greatly enriched at 13-dai in resistant roots but were absent in the susceptible. Cluster analysis of resistant and susceptible DEGs revealed an ‘early’ and ‘late’ response in resistant roots that was not present in the susceptible NIL. SNP analysis of transcripts within the Renbarb2 QTL interval identified five genes having non-synonymous mutations shared by other Renbarb2 germplasm lines. The basal expression of a single candidate gene, Gohir.D11G302300, a CC-NBS-LRR homolog, was ~3.5-fold greater in resistant roots versus susceptible. These data help us to understand the Renbarb2-mediated resistance response and provides a short list of candidate resistance genes that potentially mediate that resistance.