Organellar Genome Diversity in <i>Saccharum</i> and <i>Erianthus</i> spp. revealed by PCR-RFLP

Abstract

The organellar genome diversity in Saccharum and Erianthus species was analysed by chloroplast deoxyribonucleic acid (cpDNA) and mitochondrial deoxyribonucleic acid (mtDNA) polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Six different chloroplast primers ( psbC - trnS , trnL , psaA , clpP , matK and ccsA ); and ten mitochondrial primers ( nad 1, nad 4/1-2, nad 4/2-3, nad 5/1-2, nad 5/4-5, 18S-5SrRNA , coxI , matR , cob and mttb ) were used to amplify the genes/intergenic spacers of 8 different members of Saccharum complex namely S . officinarum , S. robustum , S. spontaneum , S. barberi , E. arundinaceus, E. ciliaris , E. elegans and CoC 671 ( S . officinarum hybrid). The amplified PCR-products were digested with ten different restriction enzymes namely Alu I, BamH I, Bgl II, Dra I, EcoR I, Hae III, Hind III, Hinf I and Pst I, Taq I. Our results suggest that although monomorphic bands were observed with the PCR using chloroplast and mitochondrial primers; there exists restriction fragment length polymorphism in these genes/intergenic spacers. Out of the sixty primer-enzyme combinations studied, thirty primer-enzyme combinations revealed cpPCR-RFLP while out of hundred primer-enzyme combinations studied fifty-seven primer-enzyme combinations revealed mtPCR-RFLP in sugarcane. Differentiation in Saccharum and Erianthus species was found in the psbC - trnS region of the chloroplast digested using enzyme Hae III and also in the trnL region digested using enzyme Taq I. One new finding in our work was the mtPCR-RFLP revealed by nad 4/2-3region restriction digested using enzyme Alu I which was able to differentiate Saccharum species and Erianthus species. Our results may add to the knowledge about organellar genome diversity in sugarcane and may be useful for identification of sugarcane hybrids.