Differentially expressed genes in mycorrhized and nodulated roots of common bean are associated with defense, cell wall architecture, N metabolism, and P metabolism

Abstract

Legumes participate in two important endosymbiotic associations, with phosphorus-acquiring arbuscular mycorrhiza (AM, soil fungi) and with nitrogen-fixing bacterial rhizobia. These divergent symbionts share a common symbiotic signal transduction pathway that facilitates the establishment of mycorrhization and nodulation in legumes. However, the unique and shared downstream genes essential for AM and nodule development have not been identified in crop legumes. Here, we used ion torrent next-generation sequencing to perform comparative transcriptomics of common bean (Phaseolus vulgaris) roots colonized by AM or rhizobia. We analyzed global gene expression profiles to identify unique and shared differentially expressed genes (DEGs) that regulate these two symbiotic interactions, and quantitatively compared DEG profiles. We identified 3,219 (1,959 upregulated and 1,260 downregulated) and 2,645 (1,247 upregulated and 1,398 downregulated) unigenes that were differentially expressed in response to mycorrhizal or rhizobial colonization, respectively, compared with uninoculated roots. We obtained quantitative expression profiles of unique and shared genes involved in processes related to defense, cell wall structure, N metabolism, and P metabolism in mycorrhized and nodulated roots. KEGG pathway analysis indicated that most genes involved in jasmonic acid and salicylic acid signaling, N metabolism, and inositol phosphate metabolism are variably expressed during symbiotic interactions. These combined data provide valuable information on symbiotic gene signaling networks that respond to mycorrhizal and rhizobial colonization, and serve as a guide for future genetic strategies to enhance P uptake and N-fixing capacity to increase the net yield of this valuable grain legume.

Cysteine-Rich Receptor-Like Kinase Gene Family Identification in the Phaseolus Genome and Comparative Analysis of Their Expression Profiles Specific to Mycorrhizal and Rhizobial Symbiosis

“…Previously, we performed global transcriptome profiling in Phaseolus vulgaris L. cv. Negro Jamapa roots colonized with Rhizophagus irregularis spores, or Rhizobium tropici strain CIAT899 [46]. The present study utilizes the same transcriptomic data to obtain the expression profiles of CRK family genes under both types of symbiotic conditions.…”

“…Negro Jamapa seeds and germinated them as described by Nanjareddy et al [47]. Two-day-old germinated seedlings were transplanted into sterile vermiculite and were inoculated with R. irregularis or R. tropici according to Nanjareddy et al [46]. Uninoculated P. vulgaris plants served as controls.…”

Influence of alternative soil amendments on mycorrhizal fungi and cowpea production

“…For example, we found substantial differences between AM benefits to grain yield and nutritional quality of six Sorghum bicolor genotypes ( Cobb et al., 2016 ). Previous research indicates positive mycorrhizal responsiveness for cowpea and common beans ( Phaseolus vulgaris L.) ( Nanjareddy et al., 2017 ; Oruru et al., 2018 ). Therefore, we focused on the influence of conventional and alternative nutrient management on AM fungi and the production/nutrition of common bean and cowpea.…”

In BPS1 Downregulated Roots, the BYPASS1 Signal Disrupts the Induction of Cortical Cell Divisions in Bean-Rhizobium Symbiosis

“…Seeds of the common bean ( P. vulgaris L.) cultivar Negro Jamapa were surface sterilized and germinated in the dark for two days [ 28 ]. The two-day-old seedlings were transferred to pots with sterile vermiculite, inoculated with freshly cultured Rhizobium tropici (strain CIAT899) at an OD 600 of 0.05, and irrigated with Broughton & Dilworth (B & D) [ 29 ] medium without nitrate.…”