LTR retrotransposons and highly informative ISSRs in combination are potential markers for genetic fidelity testing of tissue culture-raised plants in sugarcane
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Testing the genetic fidelity of micropropagated clones with DNA markers could curtail the losses caused by somaclonal variation in sugarcane tissue culture industry. Evaluation of 32 inter-retrotransposon amplified polymorphism (IRAP) markers and 100 inter-simple sequence repeats (ISSRs) in 47 sugarcane accessions identified 20 (8 IRAPs and 12 ISSRs) polymorphic markers representing 98 loci. IRAP system was superior to ISSR in terms of marker index (2.68 as against 1.76), resolving power (2.85 as against 1.98), and polymorphic loci per assay (6 compared to 4.1), except mean polymorphic information content (0.31 and 0.34). Further evaluation of the 20 polymorphic markers in testing the genetic fidelity of micropropagated sugarcane clones identified a variant clone by three primers of ISSR and one IRAP marker (UBC810, UBC813, UBC840, and LTR6149 + 3′LTR). The unique amplicons from the somaclonal variant were validated by sequencing. Based on the number of bands amplified and proportion of polymorphic loci, a set of six ISSR and four IRAP markers has been recommended to test clonal fidelity for sugarcane tissue culture industry.
KeywordsGenetic fidelity testing IRAP ISSR Phylogeny Somaclonal variation Sugarcane
Our thanks are due for ICAR-NRCPB, New Delhi for extending all the facilities to carry out this work.
The Department of Biotechnology (DBT), Govt. of India through Biotech Consortium India Limited (BCIL), New Delhi funded the project on National Certification System for Tissue Culture-raised Plants (NCS-TCP).
- Ahmed TA, Zaidan SA, Elmeer K (2012) Inter-simple sequence repeat (ISSR) analysis of somaclonal variation in date palm plantlets regenerated from callus. In. Second Intl. Conf. Environ. Industrial Innovation, IPCBEE 35, pp 126–130Google Scholar
- Allendorf FW, Luikart G (2007) Conservation and the genetics of populations. Blackwell Publishing, Maden, p 642Google Scholar
- Campbell BC, LeMare S, Piperidis G, Godwin ID (2011) IRAP, a retrotransposon-based marker system for the detection of somaclonal variation in barley. Mol Breeding 27(2):193–206Google Scholar
- Devarumath R, Nandy S, Rani V, Marimuthu S, Muraleedharan N, Raina S (2002) RAPD, ISSR and RFLP fingerprints as useful markers to evaluate genetic integrity of micropropagated plants of three diploid and triploid elite tea clones representing Camellia sinensis (China type) and C. assamica ssp. assamica (Assam-India type). Plant Cell Rep 21(2):166–173Google Scholar
- Kour B, Kour G, Kaul S, Dhar MK (2014) In vitro mass multiplication and assessment of genetic stability of in vitro-raised Artemisia absinthium L. plants using ISSR and SSAP molecular markers. Adv Bot. https://doi.org/10.1155/2014/727020
- Lal N, Singh HN (1991) Correlation of fresh weight of callus to corresponding volumes in sugarcane. Indian J Plant Physiol XXXIV(3):261–263Google Scholar
- Liu ZL, Han FP, Tan M, Shan XH, Dong YZ, Wang XZ, Fedak G, Hao S, Liu B (2004) Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions. Theor Appl Genet 109(1):200–209CrossRefGoogle Scholar