Congruence of random amplification of polymorphic deoxyribonucleic acid (RAPD) and simple sequence repeats (SSR) markers in genetic characterization of willow (Salix spp.)

Abstract

Willow (Salix spp.) includes closely related dioecious polyploid species, which are obligate outcrossers. Natural populations of willows and their hybrids are represented by a mixture of highly heterozygous genotypes sharing a common gene pool. Random amplified polymorphism DNAs (RAPD) and microsatellites (simple sequence repeats, SSRs) are useful methods for studying genetic diversity of willow (Salix spp.). RAPD delivers a large number of data points from a single experiment and is a useful method for distinguishing between closely related individuals. SSR markers are very robust tools, and we have identified several markers that show high levels of polymorphism in willow. Genetic characterization of 94 genotypes (four female, ten male, and 80 half sibs) of Salix collected from Naganji Nursery of University of Horticulture and Forestry, Solan, Himachal Pradesh, India were analyzed using 10 SSRs and 15 RAPDs PCR-based molecular markers. RAPD analysis yielded 87 polymorphic fragments (98.9%), with an average of 5.8 polymorphic fragments per primer. Similarly, SSR analysis produced 33 bands, out of which 26 were polymorphic (78.8%) with an average of 2.6 polymorphic fragments per primer. The genetic diversity was high among the genotypes (Nei’s genetic diversity = 0.354 and Shannon’s information index = 0.536) as measured by combination of both RAPD and SSR markers. The mean coefficient of gene differentiation (Gst) was 0.037, indicating 96.6% of the genetic diversity resided within the genotypes. It was found that the genetic diversity among genotypes was broader, suggesting the importance and feasibility of introducing elite genotypes from different hybrids for willows germplasm conservation and breeding programs.

Keywords: Salix sp., female, male, half sibs, molecular markers, genetic diversity, Random amplified polymorphism DNAs (RAPD), simple sequence repeats (SSRs).

African Journal of Biotechnology, Vol 13(31) 3217-3229