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

Antonio A F Garcia,Isaias O Geraldi,Anete P De Souza,Luciana L Benchimol,Cláudio L Souza Jr,Antônia M M Barbosa

doi:10.1590/s1415-47572004000400019

Abstract

In order to compare their relative efficiencies as markers and to find the most suitable marker for maize diversity studies we evaluated 18 inbred tropical maize 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 (SSR). 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 the RAPD markers, all the markers correlated genetic distance 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.

Highlights

The past limitations associated with pedigree data and morphological, physiological and cytological markers for assessing genetic diversity in cultivated and wild plant species have largely been circumvented by the development of DNA markers such as restriction fragment length polymorphisms (RFLPs; Botstein et al, 1980), random amplified polymorphic DNAs (RAPDs; Williams et al, 1990), amplified fragment length polymorphisms (AFLPs; Zabeau and Vos, 1993) and simple sequence repeats (SSRs, microsatellites; Tautz, 1989)
All of the 18 maize inbred lines studied by us had previously been investigated using the four different marker systems (RAPD: Lanza et al, 1997; RFLP: Benchimol et al, 2000; AFLP and SSR: Barbosa et al, 2003), the estimated means and ranges of the genetic distances and the level of polymorphism produced by each of the marker systems for the possible combinations of crosses between lines BR-105 and BR-106 being summarized in Tables 1 and 2
The highest genetic distance values occurred with crosses between inbred lines from different heterotic groups (BR-105 x BR-106), these results agreeing with the high level of heterosis exhibited when these populations are intercrossed (Naspolini Fo et al, 1981; Souza Jr. et al, 1993)

Summary

Introduction

The past limitations associated with pedigree data and morphological, physiological and cytological markers for assessing genetic diversity in cultivated and wild plant species have largely been circumvented by the development of DNA markers such as restriction fragment length polymorphisms (RFLPs; Botstein et al, 1980), random amplified polymorphic DNAs (RAPDs; Williams et al, 1990), amplified fragment length polymorphisms (AFLPs; Zabeau and Vos, 1993) and simple sequence repeats (SSRs, microsatellites; Tautz, 1989) These molecular markers have technical differences in terms of cost, speed, Send correspondence to Antonio A.F. Garcia, Escola Superior de Agricultura “Luiz de Queiroz”, Departamento de Genética, Caixa Postal 83, 13400-970 Piracicaba, SP, Brazil. The RAPD technology is well suited to DNA fingerprinting (dos Santos et al, 1994; Thormann et al, 1994) it does suffer from a certain lack of reproducibility due to mismatch annealing (Neale and Harry, 1994; Demeke et al, 1997; Karp et al, 1997)

Methods

Results

Conclusion