Quantitative trait loci (QTL) analyses in pepper are common for horticultural, disease resistance, and fruit quality traits; although none of the studies to date have used sequence-based markers associated with genes. In this study we measured plant architectural, phenological, and fruit quality traits in a pepper mapping population consisting of 92 recombinant inbred lines derived from a cross between Capsicum frutescens acc. 2814-6 and C. annuum var. NuMexRNAKY. Phenotypic measurements were correlated to loci in a high-density EST-based genetic map. In total, 96 QTL were identified for 38 traits, including 12 QTL associated with capsaicinoid levels. Twenty-one loci showed correlation among seemingly unrelated phenotypic categories, highlighting tight linkage or shared genetics between previously unassociated traits in pepper.

For many horticultural crops, selection is based on quality as well as yield. To investigate the distribution of trait variation and identify those attributes appropriate for developing selection indices, we collected and organized information related to fruit size, shape, color, soluble solids, acid, and yield traits for 143 processing tomato (Solanum lycopersicum L.) lines from North America. Evaluation of the germplasm panel was conducted in a multiyear, multilocation trial. Data were stored in a flat-file format and in a trait ontology database, providing a public archive. We estimated variance components and proportion of variance resulting from genetics for each trait. Genetic variance was low to moderate (range, 0.03–0.51) for most traits, indicating high environmental influence on trait expression and/or complex genetic architecture. Phenotypic values for each line were estimated across environments as best linear unbiased predictors (BLUPs). Principal components (PC) analysis using the trait BLUPs provided a means to assess which traits explained variation in the germplasm. The first two PCs explained 28.0% and 16.2% of the variance and were heavily weighted by measures of fruit shape and size. The third PC explained 12.9% of the phenotypic variance and was determined by fruit color and yield components. Trait BLUPs and the first three PCs were also used to explore the relationship between phenotypes and the origin of the accessions. We were able to differentiate germplasm for fruit size, fruit shape, yield, soluble solids, and color based on origin, indicating regional breeding programs provide a source of trait variation. These analyses suggest that multitrait selection indices could be established that encompass quality traits in addition to yield. However, such indices will need to balance trait correlations and be consistent with market valuation.

Sucrose synthase (SuSy) is the main sucrose breakdown enzyme in plant sink tissues, including nodules, and is a possible candidate for the diversion of plant carbon to arbuscular mycorrhizal (AM) fungi in roots. We tested the involvement of SuSy in AM symbiosis of Glomus intraradices and Pisum sativum (pea). We observed that peas deficient in the predominant root isoform of SuSy were colonized successfully by AM fungi similar to wild-type roots. SuSy protein levels did not increase in roots as AM symbiosis developed, although SuSy protein levels did increase in nodules as the rhizobium symbiosis developed. Our results lead us to conclude that, unlike nodule symbiosis, SuSy protein does not limit or regulate carbon transfer in the AM symbiosis.