Development of sequence characterized amplified region (SCAR) marker for identifying drought tolerant sugarcane genotypes

• Published in: Australian Journal of Crop Science Vol. 6; no. 4; pp. 763 - 767
• Main Authors: Manoj Kumar Srivastava, Chang-Ning Li, Yang-Rui Li
• Format: Journal Article
• Language: English
• Published: Lismore, N.S.W Southern Cross Publishers 01.04.2012
• Subjects: Drought-tolerant plants; Effect of stress on; Environmental aspects; Plants; Sugarcane; Yields
• ISSN: 1835-2693

A sequence characterized amplified region (SCAR) marker was developed for screening drought tolerant genotypes in sugarcane. Of 150 RAPD decamer primers, used to identify polymorphism amongst five sugarcane genotypes (3 drought tolerant and 2 drought sensitive), 12 were found to be polymorphic. A 724 bp DNA fragment was amplified through PCR with primer OPAK 12 in drought tolerant genotypes ROC22 and GT 18, while it was absent in both sensitive genotypes. The DNA fragment was purified, cloned and sequenced. The DNA sequence of the RAPD marker OPAK 12724was used to generate SCAR marker, which was used for screening 23 genotypes, of which 13 were tolerant and 10 were susceptible to drought stress. SCAR amplification in 12 tolerant sugarcane genotypes, including one tolerant wild species, showed 92% specificity of marker and confirmed its location at the same loci as that of RAPD marker OPAK 12724. The amplified fragment showed 91% homology with Saccharum officinarumc DNA sequences identified in SUCEST project. However, no other known gene sequence in GenBank was found to show 100% similarity with this sequence. Possibly, it might be related to some conserved sequences of sugarcane genome, still unidentified for their genetic function. High effectiveness in the detection of drought tolerant genotypes, as well as wild species of sugarcane, showed that this marker is appropriate in assisting selection of genotypes with drought tolerance.