Validation and Characterization of Maize Multiple Disease Resistance QTL

Abstract

Southern Leaf Blight, Northern Leaf Blight, and Gray Leaf Spot, caused by ascomycete fungi, are among the most important foliar diseases of maize worldwide. Previously, disease resistance quantitative trait loci (QTL) for all three diseases were identified in a connected set of chromosome segment substitution line (CSSL) populations designed for the identification of disease resistance QTL. Some QTL for different diseases co-localized, indicating the presence of multiple disease resistance (MDR) QTL. The goal of this study was to perform an independent test of several of the MDR QTL identified to confirm their existence and derive a more precise estimate of allele additive and dominance effects. Twelve F 2:3 family populations were produced, in which selected QTL were segregating in an otherwise uniform genetic background. The populations were assessed for each of the three diseases in replicated trials and genotyped with markers previously associated with disease resistance. Pairwise phenotypic correlations across all the populations for resistance to the three diseases ranged from 0.2 to 0.3 and were all significant at the alpha level of 0.01. Of the 44 QTL tested, 16 were validated (identified at the same genomic location for the same disease or diseases) and several novel QTL/disease associations were found. Two MDR QTL were associated with resistance to all three diseases. This study identifies several potentially important MDR QTL and demonstrates the importance of independently evaluating QTL effects following their initial identification.

Genome-wide association studies in tropical maize germplasm reveal novel and known genomic regions for resistance to Northern corn leaf blight

“…Another haplotype identified on chromosomal bin 9.03 (Hap_9.2) identified in CAAM and DTMA panels was found to be located in close physical proximity to two closely spaced SNPs at 99.41 Mb identified in the Iodent material in a GWAS study conducted by Van Inghelandt et al 21 . QTLs for resistance to NCLB and for multiple disease resistance on chromosomal region 4.05 have been identified in various studies 11,59,62 , and our study also identified two haplotype blocks Hap_4.2 and Hap_4.3 in this chromosomal bin. Overall, it was found that several SNPs/haplotypes identified in this study are in close proximity to previously reported major genes and QTL clusters, but many novel genomic regions were also discovered that could be environment and germplasm-specific.…”

“…Meta-QTL studies on resistance to multiple foliar diseases identified about 147 multiple disease resistance mQTLs for three foliar diseases, NCLB, Southern leaf blight (SLB) and Gray leaf spot (GLS) and identified bins 3.04-08, 5.04-07, and 8.05-06 that are significant for resistance to these diseases 10 . QTLs on chromosome 3 bin 3.04-08 has been identified in many studies for NCLB and SLB 11 . QTLs on chromosome bin 5.04 and 5.06-07 were detected in different mapping studies for NCLB and GLS resistance 11 .…”

Analysis of leaf microbiome composition of near‐isogenic maize lines differing in broad‐spectrum disease resistance

“…To test our hypotheses, we compared microbiome composition of near-isogenic plants with and without introgressed chromosome segments that conferred MDR (Lopez-Zuniga et al, 2019;Martins et al, 2019). Two MDR inbred lines (NC304 and Ki3) were crossed with H100, a disease-susceptible line.…”

“…4). However, the effects of these introgressions on the microbiome were much more variable among environments than their effects on disease resistance (Lopez-Zuniga et al, 2019;Martins et al, 2019). This suggests that changes in the relative abundance of potentially protective microbes is unlikely to be a major mechanism by which these particular MDR alleles confer improved disease resistance.…”

“…Our data enabled us to test several hypotheses. First, because these MDR lines were selected for resistance to three different fungal pathogens (Lopez‐Zuniga et al ., ; Martins et al ., ), we hypothesised that the introgressed alleles would have stronger effects on the fungi than bacteria. Second, because these loci have known effects on disease resistance, we hypothesised that their effects on the microbiome would be stronger in environments with higher disease pressure (Fig.…”