Molecular Analysis of Cold Responsive (COR) Genes in Selected Sugarcane and Saccharum spontaneum L.

Shafee Ur Rehman, Khushi Muhammad, Hassan Sher, Youxiong Que, Rahmat Ali, Shahid Ali, Ishtiaq Hassan, Murad Ali Rahat


Background: Sugarcane (Saccharum derived) is an important commercially harvested crop in all parts of the world including tropical and subtropical areas. Saccharum hybrid is the tall perennial true grasses with sweet stalk rich in sucrose and it is the main source of sugar.

Methods: Initially, 23 genes differentially expressed during cold stress in other Andropogoneae tribe members were retrieved from NCBI GenBank and were investigated in the genome of selected sugarcane and Saccharum spontaneum L. Samples. Their presence in our samples was analyzed and confirmed through PCR and Agarose Gel Electrophoresis (AGE).

Results: Most of these (COR) genes (21/23) were confirmed in cold tolerant cultivars namely, SPSG-394, CP-851491 and Saccharum spontaneum L. while the least number of genes was observed in cold sensitive cultivar namely, CP-77400. Moreover 10 cold responsive genes, namely CBF1, CBF2, CBF3, COR 6.6, COR 78, COR 47, WCOR 80, WCOR14, C17 and 85KDA were sent for sequencing. Nucleotide sequences analysis of selected genes revealed the homology to stress responsive protein. Furthermore, during a conserved domain search, three conserved domains had been detected, namely gypsy transposon, zinc binding for reverse transcriptase and pepsin like aspartate proteases.

Conclusion: The analysis of cold responsive genes in sugarcane could help breeders to select cold tolerant sugarcane cultivars through PCR amplification.

Keywords:  NCBI; Sugarcane; COR genes; Conserved domain       

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