Genome-wide identification of potato long intergenic noncoding RNAs responsive to <i>Pectobacterium carotovorum</i> subspecies <i>brasiliense</i> infection

BACKGROUND: Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression in both mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of long intergenic nocoding RNAs (lincRNAs) in plant defence responses are yet to be fully explored. RESULTS: In this study, we used strand-specific RNA sequencing to identify 1113 lincRNAs in potato (Solanum tuberosum) from stem tissues. The lincRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lincRNAs possess single exons. A time-course RNA-seq analysis between a tolerant and a susceptible potato cultivar showed that 559 lincRNAs are responsive to Pectobacterium carotovorum subsp. brasiliense challenge compared to mock-inoculated controls. Moreover, coexpression analysis revealed that 17 of these lincRNAs are highly associated with 12 potato defence-related genes. CONCLUSIONS: Together, these results suggest that lincRNAs have potential functional roles in potato defence responses. Furthermore, this work provides the first library of potato lincRNAs and a set of novel lincRNAs implicated in potato defences against P. carotovorum subsp. brasiliense, a member of the soft rot Enterobacteriaceae phytopathogens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2967-9) contains supplementary material, which is available to authorized users

The effect of β-aminobutyric acid (BABA) on root knot nematode and soft rot pathogen disease complexes in Solanum tuberosum plants

The efficacy of three elicitors, DL-β-aminobutyric acid (BABA), Acibenzolar-S-methyl (Bion) and Messenger (Harpin) on potato plants inoculated with Meloidogyne incognita second stage juveniles (J2s) was investigated in this study. The efficacy of each elicitor was evaluated based on galling index, egg numbers, total root knot nematode (RKN) population numbers, number of juveniles and the percentage of females in respective extracted populations per treatment at 28 and 56 dpi. There was a significant decrease in galling indices of all treated compared to untreated control plants. The highest percentage reduction was observed for 20 mM BABA-treated plants (33%) followed by 5mM BABA (23%), 50mg/L Bion (18%), 100mg/L Bion (15%) and Messenger (8%). The number of eggs extracted from plants treated with 20mM BABA was significantly lower (66%) compared to untreated controls. Furthermore, treating plants with 20mM BABA decreased the total RKN population numbers by 55% whilst the decrease observed for Bion and Messenger was between 24-39%. Of the three tested elicitors, 20mM BABA was found to be the most effective elicitor at both 28 and 56 dpi. Hence, it was selected for further testing against RKN and Pectobacterium carotovorum subsp. brasiliense (Pcb) disease complex. Efficacy was tested by comparing the colony forming units (cfu) of Pcb from treated and untreated control plants inoculated with M. incongita and Pcb simultaneously. The concentration of Pcb from untreated plants inoculated with both pathogens was significantly higher (3.3 × 103cfu/ml) compared to their treated counterparts (8.71 × 102cfu/ml). This suggests that BABA has the potential to decrease soft rot bacterial infections in RKN disease complexes by decreasing the rate of RKN infection. This is the first report where BABA is shown to decrease the infection rate of RKN as a primary causal agent in combination with a secondary pathogen.National Research Foundation, South Africa. AM received NRF Innovative and Potatoes South Africa Development Fund bursaries.http://link.springer.com/journal/106582016-05-21hb201