Fractionation, Stability, and Isolate-Specificity of QTL for Resistance toPhytophthora infestansin Cultivated Tomato (Solanum lycopersicum)

Abstract

Cultivated tomato (Solanum lycopersicum) is susceptible to late blight, a major disease caused by Phytophthora infestans, but quantitative resistance exists in the wild tomato species S. habrochaites. Previously, we mapped several quantitative trait loci (QTL) from S. habrochaites and then introgressed each individually into S. lycopersicum. Near-isogenic lines (NILs) were developed, each containing a single introgressed QTL on chromosome 5 or 11. NILs were used to create two recombinant sub-NIL populations, one for each target chromosome region, for higher-resolution mapping. The sub-NIL populations were evaluated for foliar and stem resistance to P. infestans in replicated field experiments over two years, and in replicated growth chamber experiments for resistance to three California isolates. Each of the original single QTL on chromosomes 5 and 11 fractionated into between two and six QTL for both foliar and stem resistance, indicating a complex genetic architecture. The majority of QTL from the field experiments were detected in multiple locations or years, and two of the seven QTL detected in growth chambers were co-located with QTL detected in field experiments, indicating stability of some QTL across environments. QTL that confer foliar and stem resistance frequently co-localized, suggesting that pleiotropy and/or tightly linked genes control the trait phenotypes. Other QTL exhibited isolate-specificity and QTL × environment interactions. Map-based comparisons between QTL mapped in this study and Solanaceae resistance genes/QTL detected in other published studies revealed multiple cases of co-location, suggesting conservation of gene function.

Linkage Relationships Among Multiple QTL for Horticultural Traits and Late Blight (P. infestans) Resistance on Chromosome 5 Introgressed from Wild TomatoSolanum habrochaites

“…Genomic DNA extractions, genotyping with chromosome 5 PCR-based markers (SCAR, CAPS, and SSR), primer sequences, enzymatic reaction conditions, and restriction enzymes used for each marker have been described by Johnson et al (2012).…”

“…In a companion study (Johnson et al 2012), we mapped the chromosome 5 resistance QTL reported by Brouwer and St. Clair (2004) at higher resolution with sub-NILs. We found that the resistance QTL located in a 12.3 cM region subsequently fractionated into two and three QTL groups for foliar and stem resistance, respectively.…”

Exploiting Differential Gene Expression and Epistasis to Discover Candidate Genes for Drought-Associated QTLs in Arabidopsis thaliana

“…There is significant physiological crosstalk between shade avoidance, drought physiology, and phenology (Maliakal Schmitt et al, 2003), raising the possibility that CSA1 pleiotropically affects phenological and physiological traits in the TSUxKAS population, a hypothesis that requires further testing. Several studies have found that single QTL peaks can fractionate into multiple linked peaks, each caused by separate, but linked polymorphisms (Studer and Doebley, 2011;Johnson et al, 2012). To examine this possibility, we screened for QTLs with multiple strong candidate genes with correlated expression patterns.…”

Unraveling Genomic Complexity at a Quantitative Disease Resistance Locus in Maize

“…Pleiotropy remains uncommon in maize, and correlated responses may be due to While in some cases single genes or alleles common across diverse germplasm confer disease resistance, increasingly, the role of structural variation in plants is being explored and its effects on phenotypic variation recognized (Springer et al 2009;Chia et al 2012;McHale et al 2012). As quantitative trait loci (QTL) are subjected to fine mapping, some loci fractionate into many QTL, each conditioned by one or more genes (Steinmetz et al 2002;Studer and Doebley 2011;Johnson et al 2012). In some cases, the allele effect conditioned by each QTL is small enough that the individual locus cannot be identified in isolation (Buckler et al 2009;Poland et al 2011).…”

“…As quantitative trait loci (QTL) are subjected to fine mapping, some loci fractionate into many QTL, each conditioned by one or more genes (Steinmetz et al 2002;Studer and Doebley 2011;Johnson et al 2012). In some cases, the allele effect conditioned by each QTL is small enough that the individual locus cannot be identified in isolation (Buckler et al 2009;Poland et al 2011).…”