<p class="first" id="Par1">Sugarcane (
<i>Saccharum</i> sp.) is predominantly grown in both
tropics and subtropics in India, and the subtropics alone contribute more than half
of sugarcane production. Sugarcane active growth period in subtropics is restricted
to 8–9 months mainly due to winter’s low temperature stress prevailing during November
to February every year. Being a commercial crop, tolerance to low temperature is important
in sugarcane improvement programs. Development of cold tolerant sugarcane varieties
require a deep knowledge on molecular mechanism naturally adapted by cold tolerant
genotypes during low temperature stress. To understand gene regulation under low temperature
stress, control and stressed (10 °C, 24 h) leaf samples of cold tolerant
<i>S. spontaneum</i> IND 00-1037 collected from high altitude region in Arunachal
Pradesh were used for
transcriptome analysis using the Illumina NextSeq 500 platform with paired-end sequencing
method. Raw reads of 5.1 GB (control) and 5.3 GB (stressed) obtained were assembled
using trinity and annotated with UNIPROT, KEGG, GO, COG and SUCEST databases, and
transcriptome was validated using qRT-PCR. The differential gene expression (DGE)
analysis showed that 2583 genes were upregulated and 3302 genes were down-regulated
upon low temperature stress. A total of 170 cold responsive transcriptional factors
belonging to 30 families were differentially regulated. CBF6 (C-binding factor), a
DNA binding transcriptional activation protein associated with cold acclimation and
freezing tolerance was differentially upregulated. Many low temperature responsive
genes involved in various metabolic pathways, viz. cold sensing through membrane fluidity,
calcium and lipid signaling genes, MAP kinases, phytohormone signaling and biosynthetic
genes, antioxidative enzymes, membrane and cellular stabilizing genes, genes involved
in biosynthesis of polyunsaturated fatty acids, chaperones, LEA proteins, soluble
sugars, osmoprotectants, lignin and pectin biosynthetic genes were also differentially
upregulated. Potential cold responsive genes and transcriptional factors involved
in cold tolerance mechanism in cold tolerant
<i>S. spontaneum</i> IND 00-1037 were identified. Together, this study provides insights
into the cold
tolerance to low temperature stress in
<i>S. spontaneum</i>, thus opening applications in the genetic improvement of cold
stress tolerance in
sugarcane.
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<h5 class="section-title" id="d5072427e240">Electronic supplementary material</h5>
<p id="d5072427e242">The online version of this article (10.1007/s13205-018-1194-2)
contains supplementary
material, which is available to authorized users.
</p>
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