SuperSAGE revealed different classes of early resistance response genes in Capsicum chinense plants harboring L 3 -resistance gene infected with Pepper mild mottle virus

Abstract

We used SuperSAGE, an improved version of serial analysis of gene expression, to explore transcriptome changes early in the L 3 -mediated resistance response of pepper plants against a tobamovirus. Capsicum chinense plants homozygous for the L 3 resistance gene were infected with virulent and avirulent strains of Pepper mild mottle virus (PMMoV). Plants were maintained at a temperature nonpermissive for the resistance gene to allow the viruses to spread, then transferred to a permissive temperature for 3 h and subsequently analyzed. In the incompatible reaction, we selected 152 SuperSAGE tags (each 26 nucleotides long) possibly corresponding to upregulated genes, and 84 tags for downregulated genes. Approximately 70% of tags had matching ESTs in the genus Capsicum, other genera within the Solanaceae and/or other families of plants. More than 90% of tags with EST matches could be annotated with either functionally characterized or uncharacterized proteins. We compared genes annotated by SuperSAGE tags and those annotated by partial cDNA that was obtained using the SuperSAGE tag sequences as rapid amplification of the cDNA ends-PCR primers. Of genes annotated by SuperSAGE tags, c. 90% were consistent with those annotated by longer cDNA sequences. We cloned 17 full-length cDNAs from different SuperSAGE tags and confirmed that these genes were upregulated during normal infection in the incompatible interaction. We identified several early resistance response genes including a Ran/TC4 protein and a b-oxidation multifunctional protein, indicating that SuperSAGE is a powerful tool for investigating plant-pathogen interactions.

Physiological and molecular analysis of polyethylene glycol‐induced reduction of aluminium accumulation in the root tips of common bean (Phaseolus vulgaris)

“…SuperSAGE is an improved version of SAGE which overcomes the limitations of SAGE by producing 26-bp-long fragments from defined positions in cDNAs, providing sufficient sequence information to unambiguously characterize the mRNAs (Matsumura et al, 2003;Molina et al, 2008). This technique has been applied successfully in several gene expression studies (Matsumura et al, 2003;Hamada et al, 2008;Molina et al, 2008;Gilardoni et al, 2010).…”

Mutations That Determine Resistance Breaking in a Plant RNA Virus Have Pleiotropic Effects on Its Fitness That Depend on the Host Environment and on the Type, Single or Mixed, of Infection

“…Since TMGMV and PMMoV differ in Ϸ30% of amino acid positions at the CP, the analysis was restricted to PMMoV. Most reported PMMoV isolates are of pathotype P 1,2 (22), and different mutations at the CP have been reported as determinants of pathotypes P 1,2,3 and P 1,2,3,4 (27,30,(34)(35)(36). We addressed the following specific questions: (i) if resistance-breaking mutations in PMMoV CP have associated fitness costs in susceptible hosts, (ii) if pleiotropic effects of resistance-breaking mutations vary according to the genotype of the susceptible host, and (iii) if pleiotropic effects of resistance-breaking mutations vary according to the type, single or mixed, of infection.…”

Ecological genetics and genomics of plant defences: evidence and approaches

“…2003; Restrepo et al. 2005; Hamada et al. 2008), developmental changes in gene expression (Obermeier et al.…”