Molecular characterization of cassava mosaic disease (CMD) resistant varieties and wild relatives of cassava (Manihot esculenta Crantz) using SSR and SNP markers

Abstract

In the present study an attempt was made to estimate the extent of genetic diversity between 25 CMD resistant, 16 susceptible and seven wild relatives of cassava using 14 SSR and two SNP primers. Out of the 16 primers, nine primers was analysed using PAGE and remaining seven using capillary electrophoresis on genetic analyzer. The primers produced a total of 53 alleles across the 48 cassava accessions. NS198 was found to be highly polymorphic with 6 alleles followed by NS169, SSR36 and SSR39 (5allelles). The two SNP marker analysis on genetic analyzer namely SNPAPX3 and SNP ERF revealed that out of the two peaks generated, one of the peak at a range of 650-690 and 500-530bp respectively was common to all the 48 accessions and the other peak was variable between samples. The dendrogram constructed with 16 primers using UPGMA had four major clusters which clearly distinguished the resistant, susceptible and wild collections of cassava. The close observation made on one of the sub cluster within major resistant cluster revealed the resistant cultivars TME3 and TME4 were closely related with a similarity coefficient of 0.98. Clustering analysis was well supported by PCA, made representation of distinct location of CMD resistant, susceptible and wild relatives of cassava on 2D and 3D dimensions. Comparison of PIC value for all the 16 primers found out the PIC value for individual SSR markers is higher than the individual SNP PIC value at a range of 0.19 - 0.24. SSR PIC values ranged from 0.347 in SSR32 with observed heterozygosity (He) 0.447 to 0.72 in NS198 with He 0.76. Based on the PIC ranges NS198, NS169, SSRY39, RME-1, SSR106 and NS158 were selected as highly polymorphic markers.