Ordas et al. BMC Genomics 2010, 11:174 http://www.biomedcentral.com/1471-2164/11/174 flowering time overlapped with the confidence interval of a QTL for yield. As the allele that increased flowering time decreased yield, the co-localization of the two QTLs could partially explain the significant and negative genetic correlations between flowering time and yield that we found. The QTL for plant height at bin 3.05 was consistently found in different genetic backgrounds and environments [7,33,59-62]. The confidence interval of this QTL overlapped with the confidence interval of the QTL for stalk tunnel length, agreeing with a pre- vious experiment [33]. Furthermore, in both experi- ments the allele associated to increased damage was also associated to increased plant height. The co-localization of the two QTLs, for plant height and stalk tunnel length, could contribute to the positive genetic correla- tion between both traits detected in this experiment. The confidence interval of the QTL for yield at bin 8.05 overlapped with the confidence interval of a QTL for stalk tunnel length and relative stalk tunnel length. Both the allele for decreased yield and the allele for increased stalk resistance were provided by the same line and, therefore, if the QTL would be used for increasing resis- tance to corn borers by MAS, a negative effect on yield could be expected. A negative relationship between resistance and yield was also found in selection pro- grams in which the yield decreased as an indirect conse- quence of selecting for increased resistance [19-21]. However, it is not possible to know if the co-localization of QTLs for different traits is due to linkage between different genes or pleitropism of a single gene. Conclusions We detected three genomic regions involved in resis- tance to stalk tunnelling by MCB that were close to genomic regions related to resistance to stalk tunnelling by ECB detected in genetically different populations. This indicates the importance of those genomic regions across corn borer species and maize populations. Our results, when compared with results from other authors, suggest that genes involved in cell wall biosynthesis or fortification could be good candidate genes for the QTLs detected for stem tunnelling in our experiment. Particularly, we proposed five candidate genes related to cell wall characteristics which could explain the QTL for stalk tunnelling at bin 3.05. The small proportion of genotypic variance explained by the QTLs suggest that there are also many other genes of small effect regulat- ing stem tunnelling by MCB. Therefore, we conclude that MAS seems not promising for this trait, although the genomic regions consistently detected are useful as starting points for the cloning of genes related to resis- tance. Two of the QTLs detected for stalk tunnelling Page 7 of 10 overlap with QTLs for agronomic traits, indicating the presence of pleitropism or linkage between genes. Methods Plant materials We developed a population of 178 RILs from the cross EP42 × EP39 by single-seed descent. EP42 is a yellow European flint line that was obtained from a local open pollinated variety from North-Western Spain (humid Spain), while EP39 is a yellow European flint line that was obtained from the race ‘Fino’ from Central Spain (dry Spain). EP42 is susceptible to MCB tunnelling, while EP39 is resistant to MCB attack [29,30]. The seed of the RILs was obtained by hand pollination in North- western Spain in 2005. Phenotypic analysis The parental inbred lines, the RILs, and EP39 × EP42 were evaluated in 2006 and 2007 in Pontevedra (42° 30’N, 8° 46’W), located in Northwestern Spain at the sea level, on the Atlantic coast. In Pontevedra, temperatures are relatively mild all year and the average annual rainfall is around 1700 mm. The evaluation was carried out under artificial infestation with corn borer eggs. At each environment, the treatments were arranged in a 16 × 12 a-lattice design with three replications per environment. For the evaluation of the RILs each plot consisted of one row with 13 hills per plot, rows were spaced 0.80 m apart and hills were spaced 0.21 m apart. Plots were over- planted and thinned obtaining a final density of approxi- mately 60 000 plants ha-1. The seedbed preparation was made according to the standard practices of the area: a chisel plow followed by a rotary tiller. Prior to emergence a pre-emergence herbicide was applied. When the plants were about 60 cm tall, later weeds were controlled by cultivation with a shovel cultivator. Fertilization was made with 105 Kg of N, 105 Kg of P2O5, and 105 Kg of K2O. Prior to flowering we applied 55 additional Kg of N. We irrigated with 60 L m-2 at flowering. For each plot, the date of silking was considered when 50% of the plants of the plot exerted the silks from within the husks. At silking, five plants for each plot were infested with a mass of ≈ 40 eggs of corn borer which were placed between the main ear and the stem [63]. At harvest, stems of the infested plants from each plot were dissected, the total tunnel length (cm) of each plant measured and the corn borer tunnelling reported both in centimetres (stalk tunnel length) and as ratio of tunnel length and plant height (relative stalk tunnel length). Kernel damage was estimated on a 9 point scale (9 = without injury; 1 = wholly damaged). The following agronomic traits were also taken: the number of days