Molecular Characterization of Early Maturing Sugarcane Clones Using Microsatellite Markers

Abstract

Sugarcane is an important cash crop of the entire world including India. It alone contributes to 75% of the worldwide sugar trade. Molecular markers are powerful tools and provide the basis for the estimation of genetic variability to start reasonable breeding program. Microsatellite markers have unique ability to determine the extent of genetic divergence among sugarcane genotypes. The objective of this study was to evaluate the genetic divergence of 12 early maturing sugarcane clones using 11 SSR markers. A total 55 alleles were found during the amplification of the primers out of which 21 alleles were found unique and 34 alleles were shared. The number of shared alleles per locus ranged from two out of five alleles in the case of primer NKS 1 and nine out of ten alleles in NKS 34. Similarly no. of unique alleles per locus ranged from one out of ten alleles in NKS 34, three out of six alleles in NKS 57. The primer pairs NKS 1 and NKS 8 generated considerably greater percentage of unique alleles. The PIC values revealing allelic diversity and frequency among the genotypes varied from 0.034 in case of NKS 48 to 0.778 in case of NKS 9 with an average of 0.549. Pair-wise combinations of CoSe15451 and CoSe15452 showed the highest similarity with the value of similarity coefficient (0.890). The lowest value of similarity coefficient was found to be 0.490 in the pair CoBln15501 and CoSe01421. The dendogram based on SSR marker analysis grouped the 12 sugarcane clones into four clusters which shows the CoSe15451 and CoSe15452 clones had maximum similarity and CoBln15501 and CoSe15452 clones had maximum diversity between each other.

Molecular Characterization of Mid-late Maturing Sugarcane Clones by Using Microsatellite Markers

“…Fresh leaf samples of each genotype were taken and put into zip lock bags then put immediately into an isotherm bucket containing ice gel pads and brought to the molecular laboratory of Plant Breeding and Genetics, Faculty of Agriculture, and samples were utilized for extraction of DNA". [24].…”

“…Storage of PCR products was done at 4°C before loading. Amplification was done using a thermal cycler Benchtop, USA model number K960" [24].…”

“…An electrophoretic system (BIORAD) was used to run amplified products along with a 50bp ladder (Thermo Scientific). The banding pattern was observed using a gel documentation system (Chemi Imager™ Ready)" [24].…”

“…Genotypic data in the form of digits of the different band sizes were fed into an MS Excel sheet for further analysis. The observed bands in Gel Documentation System were in decreasing order of the molecular weights for each primer" [24]. The amplification products were viewed under UV light and photographs were saved for the experimental evaluation.…”

“…The PIC values revealing allelic diversity and frequency among the genotypes varied from 0.36 in the case of NKS 57 to 0.90 in the case of NKS 1 with an average of 0.62. The work of several scientists indicated that PIC values varied for SSR markers used in sugarcane" [34], and Singh et al [24]. "Polymorphic information content (PIC) is a measure of the relative information content of a marker that indicates whether the marker is useful in determining polymorphism in germplasm" [26].…”