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loci, dQTL for different diseases were clustered,
suggesting the presence of genes conferring mul-
tiple disease resistance. Other QTL mapping
studies and analyses of introgression lines have
provided additional evidence for the existence of
MDR genes and loci in maize with respect to
a variety of disease combinations (Balint-Kurti
et al. 2010; Belcher et al. 2012; Chung et al. 2011;
Kerns et al. 1999; Welz et al. 1999; Zwonitzer
et al. 2010).
The questions remain as to whether the
observed MDR is due to linkage or pleiotropy
and whether MDR is the rule or the exception.
To address these questions, we examined MDR
to three foliar diseases of maize: GLS, SLB,
and NLB. These three diseases are caused
by fungi in the class Dothideomycetes and
share somewhat similar modes of pathogenesis
(Beckman and Payne 1982; Jennings 1957).
It may be that genes conferring MDR target
aspects of the pathogenesis process that are
shared among these pathogens. Analyzing the
disease ratings for an association panel of 300
diverse lines, Wisser et al. (2011) observed
significant genotypic correlations between
resistances to the three foliar diseases of maize,
supporting the MDR hypothesis. Using an initial
dataset of 858 SNPs, these authors reported the
association of a glutathione-S-transferase gene
with resistance to the three diseases.
Poland (2010) analyzed the correlations
among disease ratings for these same diseases
among the NAM founders (the 26 parents of
the population), across the 5,000 lines of the
population, and within the 25 individual fam-
ilies comprising the population. Correlations
between the diseases were the highest within the
diverse inbred founders, followed by the correla-
tions among the 5,000 recombinant inbred lines
(RILs), and correlations within RIL populations
were the weakest. The modest disease correla-
tions within RIL populations were not strongly
supportive of the MDR hypothesis, suggesting
instead that a large proportion of the strong cor-
relations among parental lines could be due to
the fact that some of the parental lines (those
bred for disease-conducive environments) carry
sets of resistance loci for multiple diseases.
A comparison of the QTL identified for SLB,
NLB, and GLS resistance in the NAM population
allows a fairly explicit examination of the MDR
hypothesis. A comparison of QTL and SNPs pro-
vides evidence for some loci with pleiotropic
effects. In the NAM population, 23 genetic posi-
tions were identified for which quantitative resis-
tance loci for two or more diseases co-localized.
At these loci, the estimated allele effects from
each founder inbred were compared. At seven
of these loci, allele effects were positively cor-
related, as would be expected for MDR genes
or loci (Poland 2010). When GWAS results for
NLB and SLB were compared, three genes (a
predicted leucine zipper transcription factor and
two unknown proteins) were identified as carry-
ing SNP loci with significant associations with
resistance to both diseases (Kump et al. 2011;
Poland et al. 2011).
While there is evidence that some individual
loci confer resistance to more than one disease,
this phenomenon does not apparently explain the
wider trends of pleiotropic QTL and correlated
resistances. From our work to date, it seems clear
that, at least with respect to SLB, GLS, and NLB,
most of the genetic disease resistance and in par-
ticular most of the dQTL of larger effect that
we observe are disease specific (Zwonitzer et al.
2010). While a number of lines of evidence sug-
gest the presence of MDR genes conferring resis-
tance to SLB, GLS, and NLB, it seems likely
that many of these MDR loci individually have
relatively small effects and may be below the
detection threshold as individual loci (Balint-
Kurti et al. 2010).
Both in terms of understanding the nature
of resistance and in choosing loci with com-
plementary functions, it would be desirable to
know the ways in which different QTL influence
the process of pathogenesis. Analysis of specific
dQTL using near-isogenic lines (NILs) differing
only for a specific locus permits a better under-
standing of their quantitative and qualitative phe-
notypes than can be achieved in segregating
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