Cotton Genomics and Genetics 2016, Vol.7, No.2, 1-23
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In our previous study in cotton, we have computationally identified miR319 and established through
in silico
analysis that miR319 might be involved in abiotic stress resistance (Boopathi and Pathmanaban, 2012).
Interestingly, miR319 was found to be induced 4.939 folds in KC3-WS (Supplementary Table 1). Transgenic
plants overexpressing miR319 displayed morphological changes and exhibited enhanced drought and salt
tolerance associated with increased leaf wax content and water retention but reduced sodium uptake (Zhou et al.,
2013). As one of the first experimentally characterized and most conserved miRNA families, the miR319 targets
Teosinte Branched / Cycloidea / Proliferating cell factors (TCP) genes, which encode plant -specific transcription
factors sharing a conserved TCP domain with a basic helix-loop-helix structure. The TCP family is known to be
largely involved in plant development such as the control of cell proliferation in leaf morphogenesis (Axtell and
Bowman, 2008; Zhou et al., 2013).
It is known that miR393 was commonly up regulated during drought stress in Arabidopsis, rice and sugarcane
(Ding et al., 2013). The target of miR393 encodes
TIR1 (transport inhibitor response 1)
, an auxin receptor in
Arabidopsis. The TIR1 enzyme is a positive regulator of auxin signalling by promoting the degradation of
Aux/IAA proteins through ubiquitination. Thus, increased levels of miR393 would down regulate auxin signalling
and may reduce plant growth under drought stress (Ding et al., 2013). It was also shown in this study that miR393
was down regulated more than two folds in KC3-WS; Supplementary Table 1) which might favour the growth of
KC3 under drought. Similarly, more than two fold down regulation of miR394 was noticed in KC3-WS.
Downregulated miR394 was noticed in Populus, whose predicted targets are annotated as dehydration-responsive
protein and F-box proteins, which were reported to play significant roles in the abiotic stress-response pathway
(Shuai et al., 2013).
High induction of 36 members of miR396 (maximum of 11.456 folds) was displayed in KC3-WS in this study
(Supplementary Table 1). miR396 family was found to have maximum number of members in this study and
interestingly, all were up regulated in KC3-WS. Up regulation of miR396 under water stress was also noticed in
Arabidopsis and tobacco (Liu et al., 2009; Yang and Yu, 2009). miR396 has been shown to target six growth
regulating factor (GRF) transcription factors with roles in the coordination of cell division and differentiation
during leaf development in Arabidopsis (Wang et al., 2011). Transgenic Arabidopsis plants overexpressing
miR396 displayed narrow-leaf phenotypes because of reduction in cell number, achieved through repression of
the expression of GRF genes and were more tolerant to drought than wild-type plants, likely because of the lower
stomatal density (Liu et al., 2009). Overexpression of miR396 also conferred increased tolerance to drought stress
in tobacco (Yang and Yu, 2009). These observations suggest that miR396 plays important roles not only in leaf
development but also in drought tolerance in plants (Ding et al., 2013).
Three members of miR399 were up regulated (maximum of 7.150 fold) in KC3-WS (Supplementary Table 1).
miR399 was found as one of the largest family in plants and it appears to target four sites in the 5′ UTR of a
putative ubiquitin conjugating enzyme E2 (UBC; Sunkar and Zhu, 2004). It was found that there is no substantial
regulation of miR399 by salt, drought, or cold stress. Low K or low N did not induce the expression of miR399.
But miR399 was highly induced (whereas the target UBC mRNA was reduced) by low-phosphate (Pi) stress (Lu
and Huang, 2008; Mantri et al., 2013).
Interestingly, 15 members of miR482 were up regulated (to the maximum tune of 15.957 folds) in KC3 under
water limited conditions (however, one member of miR482 was down regulated (2.085 fold); Supplementary
Table 1). Up regulation of miR482 under drought was reported in finger millet (Nageshbabu et al., 2013). Four
UDP-glucosyltransferases (UDPGs) were found to be targeted by miR482 (Shuai et al., 2013). The UDPGs are
enzymes that attach a sugar molecule to a specific acceptor in plants. As in Arabidopsis, the UDPG is a key
regulator of stress adaption through auxin IBA (Tognetti et al., 2010) and plays a role in fine-tuning nitrogen
assimilation in cassava
(Kannangara et al., 2011). miR482 has also shown to target resistance gene receptor
kinases (Nageshbabu et al., 2013; Shuai et al., 2013) and involved in disease resistance in cotton (Zhu et al., 2013)
and soybean nodulation (Nageshbabu et al., 2013). The ability of drought stress to increase and decrease the
