Insights into the mechanism underlying Fusarium wilt race 4 (FOV4) resistance by comparative root transcriptional analysis using Pima-S6, Gossypium barbadense L

Authors: Ulloa, Mauricio; ODILON OJEDA-RIVERA, JONATHAN - Texas Tech University; LOPEZ-ARRENDONDO, DAMAR - Texas Tech University; Jobe, Timothy; HERRERA-ESTRELLA, LUIS - Texas Tech University

Submitted to: National Center for Biotechnology Information (NCBI)
Publication Type: Other
Publication Acceptance Date: 11/30/2023
Publication Date: 1/8/2024
Citation: Ulloa, M., Odilon Ojeda-Rivera, J., Lopez-Arrendondo, D., Jobe, T.O., Herrera-Estrella, L. 2024. Insights into the mechanism underlying Fusarium wilt race 4 (FOV4) resistance by comparative root transcriptional analysis using Pima-S6, Gossypium barbadense L. National Center for Biotechnology Information (NCBI).

Interpretive Summary:

Technical Abstract: A highly pathogenic soil borne fungus responsible for Fusarium wilt [Fusarium oxysporum f. sp. vasinfectum (FOV)] race 4 (FOV4) represents a continuing threat to cotton (Gossypium spp.) production in the southwest states of the US, including California, New Mexico, and Texas. In general, the Pima (G. barbadense L.) cotton gene-pool shows more susceptibility to this pathogen compared to Upland (G. hirsutum L.) cotton. Fortunately, some Pima cultivars, such as Pima S6, are resistant to FOV4 infection. To gain insights into the mechanism(s) underlying FOV4 resistance, comparative transcriptional analyses were performed on FOV4-resistant Pima-S6, and FOV4-susceptible Pima S-7 and Pima 3-79 cotton. Roots were harvested, control (no inoculation) and inoculated (1 x 10-6 conidia per ml), from each genotype at 11 days after inoculation (dai) for RNA extraction. The root infection protocol was performed in the greenhouse according to the previously described root-cut dip method. Eighteen Pima cotton libraries (nine control and nine inoculated) were aligned to our assembly of the Pima-S6 G. barbadense genome. All libraries were sequenced using Illumina technology. Gene expression was quantified using the pseudo-alignment RNA-seq quantification program kallisto version 0.46.1. A principal component analysis of transcriptional FOV4 infection responses on these genotypes indicated a differential response between resistant Pima-S6, and susceptible Pimas S-7 and 3-79. Pima-S6 libraries cluster more closely and separated from those of Pima 3-79 and Pima S-7 in response to FOV4 treatments. Overall, the data indicated that susceptible genotypes share a more significant portion of their transcriptional response to FOV4 among themselves than with Pima-S6, and that the transcriptional response of the resistant Pima-S6 cultivar is specific and different from that of the susceptible cultivars. Enriched GO categories in Pima-S6 included biological processes such as the metabolism of small molecules, phenylpropanoid biosynthesis and metabolism, ABC-type transporter activity, lipid metabolism, regulation of enzymatic activity, diterpenoid biosynthetic processes, and phytohormone signaling-related processes. Transcriptomic profiling enabled the identification of candidate genes potentially involved in the mechanism of FOV4-resistance, protecting the Pima-S6 cotton cultivar from this pathogenic fungus. Our results highlight an important role for the phenylpropanoid synthesis pathway and create opportunities for further studies of gene discovery and biomarker-SNP development for marker-associated selection (MAS) and breeding for FOV4 resistance.