Gene expression profile in response to Xanthomonas axonopodis pv. manihotis infection in cassava using a cDNA microarray

Abstract

A cassava cDNA microarray based on a large cassava EST database was constructed and used to study the incompatible interaction between cassava and Xanthomonas axonopodis pv. manihotis (Xam) strain CIO151. For microarray construction, 5700 clones from the cassava unigene set were amplified by polymerase chain reaction (PCR) and printed on glass slides. Microarray hybridization was performed using cDNA from cassava plants (resistant variety MBra685) collected at 12, 24, 48 h and 7 and 15 days post-infection as treatment and cDNA from mock-inoculated plants as control. A total of 199 genes were found to be differentially expressed (126 up-regulated and 73 down-regulated). A greater proportion of differentially-expressed genes was observed at 7 days after inoculation. Expression profiling and cluster analyses indicate that, in response to inoculation with Xam, cassava induces dozens of genes, including principally those involved in oxidative burst, protein degradation and pathogenesis-related (PR) genes. In contrast, genes encoding proteins that are involved in photosynthesis and metabolism were down regulated. In addition, various other genes encoding proteins with unknown function or showing no similarity to other proteins were also induced. Quantitative real time PCR experiments confirmed the reliability of our microarray data. In addition we showed that some genes are induced more rapidly in the resistant than in the susceptible cultivar.

Non-additive gene regulation in a citrus allotetraploid somatic hybrid between C. reticulata Blanco and C. limon (L.) Burm

“…The relative accumulation of the four mRNAs (alcohol dehydrogenase, phosphoenolpyruvate carboxylase kinase 2, putative sugar transporter and sucrose phosphatase) paralleled that observed by microarray hybridization, although the changes detected by both procedures were not quantitatively identical (Table 1). This variation is commonly observed in validation of microarray results by RT-PCR (Allen and Nuss, 2004;Lopez et al, 2005) and is probably due to intrinsic differences between both techniques.…”

COMPARING INOCULATION METHODS TO EVALUATE THE GROWTH OF Xanthomonas axonopodis pv. manihotis ON CASSAVA PLANTS

“…This could explain why most of the methods employed to quantify bacteria in planta produce a high variability, thereby making them inadequate for resistance screening and loss of pathogenicity assays. Additionally, microarray studies demonstrated that cassava gene expression upon Xam infection is quite delayed as compared to other pathosystems (López et al, 2005). This is also correlated to the observation that primary symptoms appear only 8 days-post inoculation of 4-month old susceptible cassava plants with a virulent strain of Xam (López et al, 2005).…”

“…Additionally, microarray studies demonstrated that cassava gene expression upon Xam infection is quite delayed as compared to other pathosystems (López et al, 2005). This is also correlated to the observation that primary symptoms appear only 8 days-post inoculation of 4-month old susceptible cassava plants with a virulent strain of Xam (López et al, 2005). At present, the reference method to evaluate cassava resistance is through area under the disease progress curve (AUDPC).…”

“…Only a few resistant cassava varieties have been reported, which are mainly non-commercial varieties (Restrepo et al, 2000a). Histological and molecular defense responses of cassava against Xam have shown to be activated in both resistant and susceptible varieties, but are faster and more intense in resistant plants (Kpémoua et al, 1996;López et al, 2005). As an important tool for improving the study of the cassava-Xam pathosystem, the cassava genome sequence was recently released (www.phytozome.net, Prochnik et al, 2012).…”

Unraveling the Dynamic Transcriptome

“…Currently, there are microarray projects for barley, Brassica, citrus, grape, maize, Medicago trunculata, poplar, potato, rice, soybean, sugarcane, tomato, wheat, strawberry, cassava, cacao, and others (Wang et al, 1998;Aharoni et al, 2000;Jones et al, 2002;Lopez et al, 2005;Rensink and Buell, 2005). These projects use a variety of platforms, including Affymetrix, Agilent, spotted cDNAs, and spotted oligonucleotides.…”