The analogy of simple and inter simple sequence repeat markers in the assessment of genetic diversity of pumpkin accessions in Kenya

Abstract

Pumpkin is found growing in many parts of Kenya although its genetic variation has not been determined using available molecular markers. This study compared SSR and ISSR efficacy in assessing diversity of 139 pumpkin accessions using the multiplex ratio (MR), polymorphic information content (PIC), effective multiplex ratio (EMR), marker index (MI), different (Na) and effective (Ne) alleles, Shannon index (I), expected (He) and unbiased expected heterozygosity (UHe), analysis of molecular variance (AMOVA), clusters and mantel correspondence. DNA ranged from 27-2992ng/µl and 0.45-2.1 of 260/280nm. SSR detected 23 total alleles and 4.6 average alleles of 100-700bp. ISSR detected 152 total alleles and 21.7 average alleles of 200-2000bp. Amplified and polymorphic DNA bands were 437 and 117 for SSR, 512 and 391 for ISSR, respectively. Total and polymorphic bands MR was 87.4 and 29.4 for SSR, 73.1 and 55.9 for ISSR, respectively. PIC, EMR and MI for ISSR were higher than for SSR. Markers with high polymorphism portrayed high EMR and MI. SSR PKCT-122 and ISSR 17899A had the highest polymorphism, PIC, EMR and MI. Ne, I, He and UHe was high for SSR, while Na was high for ISSR. AMOVA revealed significant (P=0.01; P=0.02) differentiation. Genetic diversity was 14% and 7% among, 86% and 93% within accessions for SSR and ISSR, respectively. Three clusters independent of geographic origin were revealed. SSR and ISSR Euclidean matrices showed positive significant (r=0.272, P=0.0001) correlation, which implied they reflected the same genetic diversity. Hence, the genetic diversity of pumpkins can be assessed effectively using either SSR or ISSR markers.