Integration of Stress and Growth-Related Responses by microRNAs in Andean Potatoes

Compared to commercial cultivars, farmer-selected landraces of andigena potatoes (Solanum tuberosum ssp. andigenum) are well-adapted to the chronic stress environments that characterize the Andean ecosystem. Our comparison of representative Andean cultivars (Sullu, Guincho Negra, Negra Ojosa) with several tuberosum cultivars (Atlantic, Russet Burbank, Bora Valley) revealed that the hardiness of the andigena potatoes (especially the cultivar Sullu) is manifested in terms of their high capacity for regrowth under sub-optimal conditions. Guided by the baseline physiological data, we conducted parallel analysis of coding and non-coding RNA components of the stress response transcriptome of the andigena cultivar Sullu by RNA-SEQ. Transcriptome and microRNA profiles were configured relative to the reference potato libraries and the physiological/molecular implications were inferred based on the mapping of homologous genes in the Arabidopsis co-expression network. The gene expression signatures of Sullu revealed key transcriptional and post-transcriptional regulatory nodes associated with dormancy and growth modulation under stressful environments. Target-miRNA relationship confirmed stress-inducible downregulation of HD-ZIP-Phavulota and Myb101 by the most abundantly expressed miR166 and miR159, respectively. Other predicted target transcription factors with high expression level in other potato cultivars such as APETALA2, TGA4, and Nuclear factor-Y were expressed very weakly in Sullu library. Overall, gene expression signatures revealed from transcript and small RNA profiling indicate that the modulatory effects of miRNAs are critical to acclimation and adaptation.