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.

When the allele of a wild species at a quantitative trait locus (QTL) conferring a desirable trait is introduced into cultivated species, undesirable effects on other traits may occur. These negative phenotypic effects may result from the presence of wild alleles at other closely linked loci that are transferred along with the desired QTL allele (i.e., linkage drag) and/or from pleiotropic effects of the desired allele. Previously, a QTL for resistance to Phytophthora infestans on chromosome 5 of Solanum habrochaites was mapped and introgressed into cultivated tomato (S. lycopersicum). Near-isogenic lines (NILs) were generated and used for fine-mapping of this resistance QTL, which revealed coincident or linked QTL with undesirable effects on yield, maturity, fruit size, and plant architecture traits. Subsequent higher-resolution mapping with chromosome 5 sub-NILs revealed the presence of multiple P. infestans resistance QTL within this 12.3 cM region. In our present study, these sub-NILs were also evaluated for 17 horticultural traits, including yield, maturity, fruit size and shape, fruit quality, and plant architecture traits in replicated field experiments over the course of two years. Each previously detected single horticultural trait QTL fractionated into two or more QTL. A total of 41 QTL were detected across all traits, with ∼30% exhibiting significant QTL × environment interactions. Colocation of QTL for multiple traits suggests either pleiotropy or tightly linked genes control these traits. The complex genetic architecture of horticultural and P. infestans resistance trait QTL within this S. habrochaites region of chromosome 5 presents challenges and opportunities for breeding efforts in cultivated tomato.

Previously, a Phytophthora infestans resistance QTL from Solanum habrochaites chromosome 11 was introgressed into cultivated tomato (S. lycopersicum). Fine mapping of this resistance QTL using near-isogenic lines (NILs) revealed some co-located QTL with undesirable effects on plant size, canopy density, and fruit size traits. Subsequently, higher-resolution mapping with sub-NILs detected multiple P. infestans resistance QTL within this 9.4-cM region of chromosome 11. In our present study, these same sub-NILs were also evaluated for 17 horticultural traits, including yield, maturity, fruit size and shape, fruit quality, and plant architecture traits in replicated field experiments over 2 years. The horticultural trait QTL originally detected by fine mapping each fractionated into two or more QTL at higher resolution. A total of 34 QTL were detected across all traits, with 14% exhibiting significant QTL × environment interactions (QTL × E). QTL for many traits were co-located, suggesting either pleiotropic effects or tight linkage among genes controlling these traits. Recombination in the pericentromeric region of the introgression between markers TG147 and At4g10050 was suppressed to approximately 29.7 Mbp per cM, relative to the genomewide average of 750 kbp per cM. The genetic architecture of many of the horticultural and P. infestans resistance traits that mapped within this chromosome 11 S. habrochaites region is complex. Complicating factors included fractionation of QTL, pleiotropy or tight linkage of QTL for multiple traits, pericentromeric chromosomal location(s), and/or QTL × E. High-resolution mapping of QTL in this region would be needed to determine which specific target QTL could be useful in breeding cultivated tomato.

White mold, caused by Sclerotinia sclerotiorum (Lib.) de Bary, causes major losses in dry and snap bean (Phaseolus vulgaris) production. With little genetic variation for white mold resistance in common bean, other potential sources for resistance must be investigated. Accessions of scarlet runner bean (P. coccineus) have been shown to have partial resistance exceeding any to be found in common bean. Resistance is quantitative with at least six QTL found in a P. coccineus intraspecific resistant × susceptible cross. Our goal is to transfer high levels of resistance from P. coccineus into commercially acceptable common bean lines. We developed interspecific advanced backcross populations for mapping and transfer of resistance QTL. 111 BC2F5 lines from a cross between OR91G and PI255956 have been tested in straw tests and oxalate tests, as well as in a field trial. The data show that the OR91G × PI255956 population carries a high level of resistance, but because of the quantitative nature of resistance, it may be necessary to intercross individuals to achieve higher levels. SSR, RAPD, and AFLP markers are being tested in the population to construct a linkage map for placement of QTL. QTL identified from each type of test (straw, oxalate, and field) may provide additional information about the genetic architecture of white mold resistance. Three other populations are from advanced backcrosses of the recurrent parents G122, OR91G, and MO162, with PI433251B as the donor parent in each. Analyses and advance of these populations will follow, the results of which should confirm QTL identified in the OR91G × PI255956 population, as well as possible additional resistance QTL from PI433251B.

Alleles conferring quantitative resistance to late blight disease [Phytophthora infestans (Mont.) de Bary] were introgressed into cultivated tomato [Solanum lycopersicum (L.)] from resistant wild tomato (Solanum habrochaites Knapp and Spooner). Two sets of sub‐near‐isogenic lines (sub‐NILs) were marker‐selected so that each contained resistance QTL alleles from S. habrochaites chromosome 5 or 11. We conducted a combining ability study with the sub‐NILs to evaluate the potential utility of the resistance QTL alleles for breeding F1 hybrid cultivars and identify sub‐NILs with the highest combining ability for late blight disease resistance. The sub‐NILs were mated with inbred testers in factorial mating designs (Design II). F1 hybrid progeny from these two sets of sub‐NILs, in which each hybrid was heterozygous for one or more QTL resistance alleles on chromosome 5 or 11, were evaluated for P. infestans resistance in replicated field and growth chamber experiments. Differences in combining ability were found in growth chamber but not field experiments, suggesting that sub‐NILs contributed similar levels of resistance to their F1 hybrid progeny in the field, but different levels in the growth chamber. Significant QTL × environment interactions were detected across field and growth chamber experiments. We identified sub‐NILs that expressed P. infestans resistance in F1 hybrid combinations, suggesting that these sub‐NILs could be useful for breeding F1 hybrid varieties with enhanced resistance. The expression of quantitative resistance to P. infestans in F1 hybrids derived from each sub‐NIL parent was provided by multiple QTL alleles from S. habrochaites.