Modulation of miRNA expression in natural populations of A. thaliana along a wide altitudinal gradient of Indian Himalayas

Abstract

Plant populations growing along an altitudinal gradient are exposed to different environmental conditions. They are excellent resources to study regulatory mechanisms adopted by plants to respond to different environmental stresses. Regulation by miRNA is one of such strategies. Here, we report how different miRNAs are preferentially expressed in the three natural populations of A. thaliana originating from a wide altitudinal range. The expression level of miRNAs was mostly governed by temperature and radiation. Majority of the identified miRNAs expressed commonly in the three populations. However, 30 miRNAs expressed significantly at different level between the low and the high altitude populations. Most of these miRNAs regulate the genes associated with different developmental processes, abiotic stresses including UV, cold, secondary metabolites, etc. Further, the expression of miR397 and miR858 involved in lignin biosynthesis and regulation of secondary metabolites respectively, may be regulated by light intensity. A few miRNAs expressed at increasing level with the increase in the altitude of the site indicating environment driven tight regulation of these miRNAs. Further, several novel miRNAs and isomiR diversity specific to the Himalayas are reported which might have an adaptive advantage. To the best of our knowledge, this is the first report on miRNA expression from natural plant populations.

Abolished miR158 activity leads to 21-nucleotide tertiary phasiRNA biogenesis that targetsNHX2inArabidopsis thaliana

“…Effects of single nucleotide polymorphisms in the MIRNA have also been reported (Ryan et al, 2010;Todesco et al, 2012). In our previous study, we observed negligible expression of miR158 in a particular A. thaliana population of Indian west Himalayas under different growing conditions (Tripathi et al, 2019). These populations are reported from elevation range of 700 m above mean sea level (amsl) to 3400 m amsl having varied climatic conditions.…”

“…Our previous analyses of small RNA profiling of the three populations Deh, Mun, and Chit showed negligible expression of miR158 in Mun as compared to the other two populations, both under field and controlled growth conditions (Table S4 of (Tripathi et al, 2019)). To reconfirm the negligible expression of miR158 in Mun, we analyzed its expression under native, controlled and common garden conditions along with miR158 SALK mutant using quantitative real time PCR (qRT-PCR).…”

“…It was clearly evident that the abundance of PDPs was more in Mun than Deh and Chit (P value = 0.005645, F = 4.32423) ( Table 1; Supplemental Figure 12A). Since above small RNA libraries were prepared from pooled leaf samples of several plants of each population (Tripathi et al, 2019), we re-examined the data using small RNA sequence data from randomly selected individual plants of each variant types. Small RNA data from individual DTL, ITL and NTL plant reconfirmed the above observations (Table 1; Figure 4D).…”

“…RNA samples having RIN >7 were used for small RNA library preparation. Four pooled small RNA libraries corresponding to Deh, Mun, Chit and Col-0 was prepared and used as replicates of earlier sequenced data from the same populations (Tripathi et al, 2019). Further, for each plant type individual libraries were prepared and sequenced in replicates, except for DTL, miR158 OE and pseudo-PPR OE (one of these libraries failed the quality control).Libraries were prepared using NEB Next Small RNA Library Prep Set (New England Biolabs) and sequencing was carried out using Illumina HiSeq 4000 in single-end mode by outsourcing.…”

MicroRNA775 and targetGalactosyltransferase(GALT9) module regulates recovery from submergence induced senescence by modulatingSAGsinArabidopsis thaliana

“…miR775 was reported to be highly upregulated in response to the hypoxic conditions in different microarray and expression studies, in stresses such as flooding and high altitude in Arabidopsis (Moldovan et al ., 2010, Liu et al ., 2012, Jin et al ., 2017, Tripathi et al ., 2019). To analyze the effect on miR775 and its target gene GALT9 abundance in Arabidopsis seedlings during submergence we analyzed the tissue-specific expression of MIR775 and its target GALT9 during submergence stress using pMIR775A: GUS and pGALT9:GUS transgenic plants ( Figure 4 a-j ).…”