Identification of new microsatellite DNA markers for sugar and related traits in sugarcane

Abstract

Molecular studies in sugarcane are relatively limited because of the complex genetic structure, long life cycle and non availability of reliable sugarcane specific molecular markers. The use of DNA markers for the genetic analysis and manipulation of desirable agronomic traits has become an increasingly useful tool in sugarcane breeding. The objective of the present study was to evaluate the polymorphic potential of sugarcane microsatellite markers developed at National Research Centre on Plant Biotechnology, IARI, New Delhi in high and low sugar lines. These microsatellites markers were screened and validated for their polymorphic, genetic diversity, cross-transferability and comparative linkage mapping potential in high and low sugar bulk of two segregating progenies and 20 each, cultivated high and low sugar commercial varieties. One hundred sixty eight (28%) of the microsatellite markers were found to be highly robust and polymorphic with PIC values ranging from 0.51% to 0.84%. Forty three (0.26 %) markers contained dinucleotide repeats, fifty seven (0.34 %) markers contained trinucleotide repeats, twenty five (0.15 %) and forty three (0.26 %) markers contained composite repeats. The number of observed allele ranged from 2 to 11, with an average of five alleles detected per locus. A total of 977 polymorphic DNA bands were identified, with their fragment size ranging from 20 to 1380 bp. These microsatellite markers are an ideal resource for use in managing sugarcane germplasm, trait mapping and marker assisted breeding strategies. The wide cross — species transportability of these markers may extend their value to research involving other Saccharum species complex.