In silico identification of candidate microRNAs and their targets in potato somatic hybrid Solanum tuberosum (+) S. pinnatisectum for late blight resistance

Abstract

We employed computational tools to identify candidate miRNAs from 153 putative known genes obtained from a previous microarray experiment by Singh et al. (2016) for late blight resistance. In this study, we identified eight miRNAs families (miR395, 821, 1030, 1510, 2673, 3979, 5021 and 5213) to the nine potato genes. Mature miRNAs located at different positions of pre-miRNAs are varied from 19 to 21 nucleotides in length. Of the total 343 published miRNAs in potato (miRBase), all identified miRNAs family are new to potato crop except miR395. In particular, these novel miRNAs were identified for pathogen-induced late blight resistance mechanism in interspecific potato somatic hybrid. Majority of the predicted target genes (Table 2) of these miRNAs are involved in different biological functions, including disease resistance proteins (NBS-LRR domains) and transcription factors families. This study offers an insight to identify potential candidate miRNAs and their targets to dissect late blight resistance mechanism in potato somatic hybrid Solanum tuberosum (+) S. pinnatisectum.

Screening of wild species and transcriptome profiling to identify differentially regulated genes in response to late blight resistance in potato

“…Our results are in agreement with earlier finding using microarray technology, indicating a strong association of disease resistance genes in conferring late blight resistance in potato cv. Kufri Girdhai ( Sundaresha et al., 2014 ; Singh et al., 2016 ). Allele mining study elucidates the involvement of the R genes ( Rpi-blb1 ) in wild species ( Tiwari et al., 2015 ).…”

Genome-Wide Characterization, Evolution, and Expression Profile Analysis of GATA Transcription Factors in Brachypodium distachyon

“…The results revealed that 16 BdGATA genes were predicted targets of 13 miRNAs. It should be noted that potato miR2673 targets seven GATA genes, and miR2673-GATA (PGSC id: DMT400024205) in potato was predicted to regulate resistance against late blight disease [ 24 ]. Furthermore, miR2673 was reported to implicate plant oxidative burst and HR via proline dehydrogenase [ 25 ].…”