Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines

Abstract

In order to compare their relative efficiencies as markers and to find the most suitable marker for maize diversity studies we evaluated 18 tropical maize inbred lines using a number of different loci as markers. The loci used were: 774 amplified fragment length polymorphisms (AFLPs); 262 random amplified polymorphic DNAs (RAPDs); 185 restriction fragment length polymorphisms (RFLPs); and 68 simple sequence repeats (SSRs). For estimating genetic distance the AFLP and RFLP markers gave the most correlated results, with a correlation coefficient of r = 0.87. Bootstrap analysis were used to evaluate the number of loci for the markers and the coefficients of variation (CV) revealed a skewed distribution. The dominant markers (AFLP and RAPD) had small CV values indicating a skewed distribution while the codominant markers gave high CV values. The use of maximum values of genetic distance CVs within each sample size was efficient in determining the number of loci needed to obtain a maximum CV of 10%. The number of RFLP and AFLP loci used was enough to give CV values of below 5%, while the SSRs and RAPD loci gave higher CV values. Except for RAPD, for all the markers genetic distance correlated with single cross performance and heterosis which showed that they could be useful in predicting single cross performance and heterosis in intrapopulation crosses for broad-based populations. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationships among tropical maize inbred lines with high accuracy.

Polyploidy creates higher diversity among Cynodon accessions as assessed by molecular markers

“…However, correlation between RAPD and the other markers was low (0.71). Garcia et al (2004) found similar results in maize (Zea mays L.).…”

“…The PCR-based DNA markers, such as RAPD and amplified fragment length polymorphism have been used in studies of genetic diversity, relatedness, phylogeny, and in identifying offtypes in cultivars of Cynodon (Vos et al 1995;CaetanoAnolles et al 1995;Zhang et al 1999;Karaca et al 2002;Garcia et al 2004;Wu et al 2005). While these studies provide baseline information on the variation in diversity, ploidy level and geographical distribution, more information on relationships between polyploidy and genetic diversity is needed to clarify evolution and relationships among Cynodon accessions with ploidy series.…”

Genetic Mapping in Cotton

“…Percent Disagreement Values (PDVs) distance matrix, tree clustering diagram and neighbor-joining stars are different statistical techniques to determine the extent of genetic diversity. Polymorphism Information Content (PIC) is another statistical technique that can be deployed to evaluate the polymorphism acquired through different techniques, primers or markers [35][36][37][38].…”

Genetic and Biochemical Diversity of Hypericum Perforatum L. Grown in the Caspian Climate of Iran

“…RAPD markers are a widely used in the genetic evaluation because they use small amounts of DNA to identify variations between plants at the DNA level and do not require information of the genome of interest. RAPD applications in plant breeding consist genetic mapping, Marker Assisted Selection (MAS) and transfer of useful genes and germplasm evaluation (Boonparkob, 1996;Garcia et al, 2004). RAPD marker is based on DNA amplification by non-specific primers and uses the polymerase chain reaction.…”