Abundant mapping information is available on quantitative trait loci (QTL); the challenge is how to apply this genetic information in marker-assisted breeding programs. Our aim is to combine this information into an integrated scheme whereby marker-assisted breeding can be applied in crop improvement programs targeting more than one trait. The advent of marker technology in the 1980s dramatically enhanced the efficiency of plant breeding since most programs apply marker-assisted breeding to increase the efficiency of selection and to significantly shorten the development time of varieties. The availability and advances in automated technology allow the generation of large-scale marker data sets that help determine the genetic basis and selection of more than one trait. The ability to combine favourable alleles at several loci will lead to the development of superior varieties in a shorter and more economical time frame due to increased reliability and efficiency.

DNA-based markers can ensure the presence of multiple genes, hence our attempt to apply this concept in applying and selecting stable and durable resistance of plant varieties for maize streak virus (MSV), northern corn leaf blight (NCLB) and gray leaf spot (GLS) disease resistance. We selected markers on chromosome 1 (bin 1.04–1.05), chromosome 2 (bin 2.09), chromosome 4 (bin 4.08) and chromosome 8 (bin 8.06).

One major QTL for MSV disease resistance was mapped on chromosome 1 (umc029–umc167). The gene seemed allelic or identical to ms1, a major resistance gene. The mapping population was from Lo951 (Italian, susceptible) to CML 202 (African line from the International Maize and Wheat Improvement Center (CIMMYT), resistant). The same region was identified for Tzi4 (International Institute for Tropical Agriculture—IITA). QTLs for NCLB disease resistance were mapped on chromosomes 2 and 8 in the maize population Lo951 (Italian, susceptible) and CML 202 (African line from CIMMYT, resistant): chromosome 2 (umc371–umc381), chromosome 8 (umc323–umc030). The region on chromosome 8 may coincide with that of the major gene Ht2. The study found the QTLs for GLS resistance on chromosome 2 (Bnlg1520) and chromosome 4 (umc127). The QTLs were mapped in a population developed from Pa405 (susceptible) and V0613Y (resistant) at Ohio (USA) and Cedar (South Africa). Combining markers for traits located in different regions of the genome will enable us to check if the genetic factors contributing to resistance are a part of a cluster of resistance or tolerance genes. The QTLs on chromosome 1 may have resistance to other diseases such as GLS, MSV and NCLB. A QTL for drought tolerance is in another region of chromosome 1.

Marker-assisted breeding techniques are not a replacement for classical breeding and selection techniques; rather, where successful, they can be a powerful tool to accelerate the rate of development and durability of plant disease-resistance traits for breeders.