Cotton Genomics and Genetics 2016, Vol.7, No.2, 1-23
10
Continuing Table 4
S. No Contig number Mature sequence
Reads (RPKM)*
Fold Change
$
KC3-WS Suvin-WS
22.
Contig_15717
GGCUGUGGUUGAUUCGGCAAGA
8.49962
6.45096
4.137 down
23.
Contig_20599
UGAAACAAACAUAUUUACAUUGUCGAUACA
6.82977
4.41854
5.319 down
24.
Contig_21324
UCACAUUUACUUGGCAAGUGAU
7.86219
6.18793
3.191 down
25.
Contig_20427
UGGCAAGUGAUUGUGCGCCACG
7.9402
5.45096
5.614 down
26.
Contig_21332
AACAUGGCGAAUAAUAUGAUGGAAAU
6.62118
7.94692
2.506 up
27.
Contig_18969
UCACAGGGAUCAAAAUUGGGA
8.84684
6.25504
6.028 down
28.
Contig_7495
UCCAGAAGAUACAUUAGCACCAUGGGAUAU
7.56674
5.74047
3.546 down
29.
Contig_5490
GGAAGUGGGGUGCGAGGAAAGAUCA
11.78397 13.88125
4.279 up
30.
Contig_17372
AUCAACCGUGUUACUCUGUCUAAUC
9.36582
8.07389
2.448 down
31.
Contig_15837
UUUCUAAAGCUCUAGAUAACGUUA
10.22495 8.49536
3.316 down
32.
Contig_16924
AGCUCGUUAUCGAGAAUUCAAUAUGUUGUGUC
5.95905
3.32543
6.205 down
33.
Contig_12125
UGAGGGUCCAAGACUGACCUCC
9.0142
10.64736
3.101 up
34.
Contig_20315
UCAGCGCGACCUGCCGACGUG
7.66627
3.93311
13.298 down
35.
Contig_4359
UGGACUUGGAUACGUUGAAGAAGUGG
8.09512
11.56163
11.054 up
36.
Contig_14297
GUAAGGGAGAUCCUAGAUUCA
9.34434
6.51808
7.092 down
Note
:
*- RPKM: reads per kilo base million;
$
- Differential expression in fold change (up or down regulation in Suvin-WS)
Interestingly, high level expression miR2 in root tissues were reported in Mangrove (Khraiwesh et al., 2013) and
more specifically differential expression of miR2 under drought was noticed in maize (Xu et al., 2010). Another
report in cucumber has also shown that miR2 targeted a gene coding a tetratricopeptide repeat-containing protein
(Martinez et al., 2011) that usually interacts with heat shock proteins (Yin et al., 2011). Thus, it can be strongly
hypothesised that vigorous up regulation of hme-bantam and miR2 in the drought tolerant KC3 accelerates anti-
apoptotic activity in the cells during water stress and provide useful leads to promote research that confirms that
these miRNAs endorses drought tolerance in cotton. Similarly several other conserved miRNAs identified in this
study were found to be linked to water or other abiotic stresses and cellular processes.
For example, miR14 was 76.243 fold down regulated in Suvin under water stress in this study (Supplementary
Table 1). The targets for mir14 include cell-death effectors other than
hid
(Xu et al., 2003) and mutants of miR14
were shown to be sensitive to high salinity (Leung and Sharp, 2010)
.
In foxtail millet, miR14 has reported to
target GRAS transcription factor that has been involved in development and other processes (Yi et al., 2013).
This study has identified that there were nine members of small RNAs (maximum of 4.058 fold down regulated)
under water stressed conditions in Suvin and all of them have shown > 90% percent identify with miR156 family.
Squamosa Promoter Binding like (SPL) proteins are negatively regulated by the miR156, whose cellular levels are
higher in younger plants and progressively decrease as the plant ages and especially during flowering (Wu et al.,
2009; Yamaguchi et al., 2009). Among the miRNA-target that were studied in cotton, miR156-SPL2, shown
significant regulation relationship in roots and leaves under salinity stress (Wang et al., 2013). Up regulation of
miR156 in rice shoot and root tissues in response to heat (Sailaja et al., 2014) and drought (Zhou et al., 2010)
stresses was also reported as it found in KC3-WS in this study. Further, high-throughput sequencing and
expression analysis of microRNAs and their targets under salt stress in
Caragana intermedia
has shown that the
miR156 family exhibited the highest abundance among all of the miRNA families (Zhu et al., 2013).
More than 8 fold up regulation of miR159 was noticed in KC3-WS when compared with Suvin-WS
(Supplementary Table 1). Ding et al. (2013)
reviewed that miR159 was induced by ABA and drought treatments
and miR159 play a key role in ABA response by directing the degradation of MYB mRNAs. Bertolinia et al.
(2013) addressed the role of miR159 in reprogramming leaf growth during drought stress in
Brachypodium
