Differentially Expressed Genes in Resistant and Susceptible Common Bean (Phaseolus vulgaris L.) Genotypes in Response to Fusarium oxysporum f. sp. phaseoli

Abstract

Fusarium wilt of common bean (Phaseolus vulgaris L.), caused by Fusarium oxysporum Schlechtend.:Fr. f.sp. phaseoli (Fop), is one of the most important diseases of common beans worldwide. Few natural sources of resistance to Fop exist and provide only moderate or partial levels of protection. Despite the economic importance of the disease across multiple crops, only a few of Fop induced genes have been analyzed in legumes. Therefore, our goal was to identify transcriptionally regulated genes during an incompatible interaction between common bean and the Fop pathogen using the cDNA amplified fragment length polymorphism (cDNA-AFLP) technique. We generated a total of 8,730 transcript-derived fragments (TDFs) with 768 primer pairs based on the comparison of a moderately resistant and a susceptible genotype. In total, 423 TDFs (4.9%) displayed altered expression patterns after inoculation with Fop inoculum. We obtained full amplicon sequences for 122 selected TDFs, of which 98 were identified as annotated known genes in different functional categories based on their putative functions, 10 were predicted but non-annotated genes and 14 were not homologous to any known genes. The 98 TDFs encoding genes of known putative function were classified as related to metabolism (22), signal transduction (21), protein synthesis and processing (20), development and cytoskeletal organization (12), transport of proteins (7), gene expression and RNA metabolism (4), redox reactions (4), defense and stress responses (3), energy metabolism (3), and hormone responses (2). Based on the analyses of homology, 19 TDFs from different functional categories were chosen for expression analysis using quantitative RT-PCR. The genes found to be important here were implicated at various steps of pathogen infection and will allow a better understanding of the mechanisms of defense and resistance to Fop and similar pathogens. The differential response genes discovered here could also be used as molecular markers in association mapping or QTL analysis.

Combined De Novo Transcriptome and Metabolome Analysis of Common Bean Response to Fusarium oxysporum f. sp. phaseoli Infection

“…We validated the expression profiles of eight common bean genes of particular interest ( Figure 5). The Actin gene was used as an internal control to standardize the data, and the amount of target gene transcript was normalized compared to the constitutive abundance of common bean Actin gene [3,28]. Among the common bean DEGs analyzed, five genes were upregulated in FO-24 as compared to CK-24 i.e., PHAVU_007G070400g, PHAVU_004G134300g, PHAVU_011G042100g, PHAVU_008G232600g, and PHAVU_007G185300g.…”

“…Since its first identification in USA in 1929, this disease has been detected in all bean growing areas such as Africa, East Asia, Europe, Latin America, United Sates, and China [1,2]. Sever fusarium wilt epidemics have been reported in Heilongjiang and other common bean growing areas of China where beans follow vegetables [3]. High moisture, excessive irrigation, or poorly drained fields and a lack of rotation encourage the disease and FOP can persist in the soil indeterminately because of the production of chlamydospores and to the colonization of plant residues including roots of non-susceptible crops cultivated in rotation [3,4].…”

“…Sever fusarium wilt epidemics have been reported in Heilongjiang and other common bean growing areas of China where beans follow vegetables [3]. High moisture, excessive irrigation, or poorly drained fields and a lack of rotation encourage the disease and FOP can persist in the soil indeterminately because of the production of chlamydospores and to the colonization of plant residues including roots of non-susceptible crops cultivated in rotation [3,4]. The majority of studies showed that invasion begins with the hyphal network development around root hairs followed by penetration and colonization of the epidermis and subsequently into the vascular tissues of the root.…”

“…In common bean, only a limited number of studies have been conducted to understand the mechanism and pathways involved in response to FOP infection. A recent study using cDNA amplified fragment length polymorphism technique reported transcript-derived fragments functionally characterized as metabolism, signal transduction, protein synthesis and processing, development and cytoskeletal organization, redox reaction, defense and stress response, transport proteins, and gene expression and RNA metabolism related genes/proteins [3]. However proteomic and metabolomics scale responses of common bean against FOP infection is poorly understood.…”

Transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. medicaginis during colonisation of resistant and susceptible Medicago truncatula hosts identifies differential pathogenicity profiles and novel candidate effectors

“…Various sources of host resistance in chickpeas and other legumes have been identified, but the underlying genetic or molecular mechanisms (e.g. Resistance or Pathogenesis-Related genes, signalling pathways) are yet to be fully elucidated [3, 20, 24, 25]. Parallel to this, genetic and molecular mechanisms responsible for individual F. oxysporum f. sp.…”