Using Maize Chromosome Segment Substitution Line Populations for the Identification of Loci Associated with Multiple Disease Resistance

Abstract

Southern Leaf Blight (SLB), Northern Leaf Blight (NLB), and Gray Leaf Spot (GLS) caused by Cochliobolus heterostrophus, Setosphaeria turcica, and Cercospora zeae-maydis respectively, are among the most important diseases of corn worldwide. Previously, moderately high and significantly positive genetic correlations between resistance levels to each of these diseases were identified in a panel of 253 diverse maize inbred lines. The goal of this study was to identify loci underlying disease resistance in some of the most multiple disease resistant (MDR) lines by the creation of chromosome segment substitution line (CSSL) populations in multiple disease susceptible (MDS) backgrounds. Four MDR lines (NC304, NC344, Ki3, NC262) were used as donor parents and two MDS lines (Oh7B, H100) were used as recurrent parents to produce eight BC3F4:5 CSSL populations comprising 1,611 lines in total. Each population was genotyped and assessed for each disease in replicated trials in two environments. Moderate to high heritabilities on an entry mean basis were observed (0.32 to 0.83). Several lines in each population were significantly more resistant than the MDS parental lines for each disease. Multiple quantitative trait loci (QTL) for disease resistance were detected for each disease in most of the populations. Seventeen QTL were associated with variation in resistance to more than one disease (SLB/NLB: 2; SLB/GLS: 7; NLB/GLS: 2 and 6 to all three diseases). For most populations and most disease combinations, significant correlations were observed between disease scores and also between marker effects for each disease. The number of lines that were resistant to more than one disease was significantly higher than would be expected by chance. Using the results from individual QTL analyses, a composite statistic based on Mahalanobis distance (Md) was used to identify joint marker associations with multiple diseases. Across all populations and diseases, 246 markers had significant Md values. However further analysis revealed that most of these associations were due to strong QTL effects on a single disease. Together, these findings reinforce our previous conclusions that loci associated with resistance to different diseases are clustered in the genome more often than would be expected by chance. Nevertheless true MDR loci which have significant effects on more than one disease are still much rarer than loci with single disease effects.

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

“…10% per NIL, compared with the expected 6.25% based on the breeding design; alleles from Ki3 were also more homozygous than expected (92% compared with the expected 78%) (Supporting Information Fig. S1; Lopez‐Zuniga et al ., ). Within each set of NILs there was little overlap between introgressed regions, and cumulatively they carried c .…”

Identification of quantitative trait loci associated with maize resistance to bacterial leaf streak

“…Additionally, DRIL78, a CSSL population, was evaluated. The parents of the population are NC344, an MDR line, and Oh7B, a multiple disease susceptible line (Lopez‐Zuniga et al., 2019; Wisser et al., 2011). The nomenclature for the population is as follows: disease resistance introgression line (DRIL) 7 (code for NC344), 8 (code for Oh7B).…”

“…Similarly, we examined the correlations between BLS, NCLB, SCLB, and GLS phenotypes in the DRIL78 population using data reported in Lopez‐Zuniga et al. (2019). Only lines with phenotypes for all the diseases were included in the analysis.…”

“…The genotypic dataset was generated using the Pioneer Illumina publicplex platform using 765 SNP markers and is available as supplemental data from Lopez‐Zuniga et al. (2019). The DRIL78 BLUPs were used as the phenotypic dataset.…”

“…We selected two NAM populations, Z022 (B73 × Oh43) and Z023 (B73 × Oh7B), to screen for their reaction to BLS. Additionally, we screened a complimentary chromosome segment substitution line (CSSL) population, referred to as the disease resistance introgression line 78 (DRIL78) population (NC344 × Oh7B) (Lopez‐Zuniga et al., 2019). The populations allowed us to investigate the genetic architecture of resistance to BLS in maize and the relationship between multiple foliar diseases.…”