Cotton Genomics and Genetics 2016, Vol.7, No.2, 1-23
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Cotton (
Gossypium
spp.,) is a highly preferred natural textile fiber because of its economic value and comfort and
cotton seed oil is a significant food source for human and livestock.
Gossypium
consists of at least 45 diploid and
5 allotetraploid species; however, only four species
viz., G. hirsutum,
G. barbadense,
G. arboreum
and
G.
herbaceum
(described in the order of highest to lowest global acreage), have been domesticated for their abundant
seed trichomes and provide the foundation for the global textile industry. India has the largest area dedicated to
cotton production worldwide; however, the cotton fiber production is largely limited by water stress since more
than 60% of this area is under rainfed (Boopathi and Pathmanaban, 2012). Genetic improvement of cotton with
drought resistance will be a viable and cost effective option to mitigate such losses. Though significant
advancement has been documented, the progress in this direction is not up to the expected level due to lack of
knowledge on drought resistance mechanisms. Although progress has been made in unravelling the complex
stress response mechanisms, particularly in the identification of water stress responsive protein-coding genes, the
key factors such as miRNAs that regulate the expression of these genes remain unclear. Such gap severely
hampers the precise manipulation of drought resistance in cotton. Even though there is no direct proof that
miRNAs are the crucial regulatory elements in development of drought tolerance in cotton, we postulate that
differential expression of miRNAs might be involved in such complex process. As a first step towards the
understanding of their regulatory mechanisms and networks of target genes in drought tolerance in cotton,
differential expression of miRNAs between drought tolerant (
Gossypium hirsutum
cv. KC3) and drought
susceptible (
G.
barbadense
cv. Suvin) cotton lines were compared in the present study under water stressed and
irrigated conditions in the field using a deep sequencing approach.
In general, miRNAs are being identified in plants by forward genetics (whereby miRNAs are isolated from an
organism showing abnormal phenotypic characteristics), reverse genetics (whereby a specific gene is knocked out
or over expressed), cDNA sequencing and computational prediction approaches (Ambros, 2004). In the early days,
the identification of cotton miRNAs depended largely on computational approaches based on the conserved
characteristics of miRNAs (Qiu et al., 2007; Zhang et al., 2007; Barozai et al., 2007), which was accomplished by
searching the cotton genomic sequences and/or ESTs that were homologous to known mature miRNAs or pre -
miRNAs. Later, after complete sequencing of
G. raimondii
(Wang et al., 2012) and
G. arboreum
(Li et al., 2014)
it was proposed that there were totally 348 and 431 miRNA sequences, respectively in these two species.
The first experimental validation and exploration of cotton miRNAs by cloning and sequencing identified only
three cotton miRNAs (Abdurakhmonov et al., 2008). However, recently deep sequencing has emerged as an
effective approach for large-scale miRNA discovery. Small RNA libraries prepared from cotton ovules and
seedlings have been analysed by high-throughput sequencing (Kwak et al., 2009; Ruan et al., 2009). Pang et al.
(2009) reported 27 conserved and four novel miRNA families from
G. hirsutum
by sequencing the small RNAs of
leaves and ovules. Along with data from microarrays and Northern blots, they examined the changing pattern of
certain miRNAs and their targets. Similar comparative miRNAome analysis revealed seven fiber initiation-related
miRNAs expressed in cotton ovules besides 36 novel miRNAs and two conserved miRNAs (Wang et al., 2012).
Targets of these miRNAs were experimentally validated and they described complex regulatory networks that
coordinate fiber initiation responses. Yin et al. (2012) reported genome-wide profiling of miRNAs and other small
non-coding RNAs in the
Verticillium dahliae
inoculated cotton roots. Small RNAs and their targets were also
identified during cotton somatic embryogenesis through high-throughput small RNA and degradome sequencing
(Yang et al., 2013). Zhang et al. (2013) have identified 93 miRNAs, including 63 novel miRNAs that are involved
in fiber initiation and seed development. Similarly, 257 novel miRNAs were reported by Xue et al. (2013) in
elongating cotton fiber cells. In another comparative miRNA expression study, Wei et al. (2013) identified sixteen
conserved miRNA families during anther development in genetic male sterile and wild type cotton. Chen et al.
(2013) has studied genetic variation of miRNAs and their target genes and they were genetically mapped in cotton.
Despite of these progresses, only 378 mature miRNA sequences from cotton (
Gossypium
spp.), were described in
miRBase (
Release 21; June, 2014). As several thousands of miRNAs
were identified in plants, this number is extremely lesser than the expected number of miRNAs in cotton and they
