Wide-genome QTL mapping of fruit quality traits in a tomato RIL population derived from the wild-relative species Solanum pimpinellifolium L.

Abstract

QTL and candidate genes associated to fruit quality traits have been identified in a tomato genetic map derived from Solanum pimpinellifolium L., providing molecular tools for marker-assisted breeding. The study of genetic, physiological, and molecular pathways involved in fruit development and ripening has considered tomato as the model fleshy-fruited species par excellence. Fruit quality traits regarding organoleptic and nutritional properties are major goals for tomato breeding programs since they largely decide the acceptance of tomato in both fresh and processing markets. Here we report the genetic mapping of single-locus and epistatic quantitative trait loci (QTL) associated to the fruit size and content of sugars, acids, vitamins, and carotenoids from the characterization of a RIL population derived from the wild-relative Solanum pimpinellifolium TO-937. A genetic map composed of 353 molecular markers including 13 genes regulating fruit and developmental traits was generated, which spanned 1007 cM with an average distance between markers of 2.8 cM. Genetic analyses indicated that fruit quality traits analyzed in this work exhibited transgressive segregation and that additive and epistatic effects are the major genetic basis of fruit quality traits. Moreover, most mapped QTL showed environment interaction effects. FrW7.1 fruit size QTL co-localized with QTL involved in soluble solid, vitamin C, and glucose contents, dry weight/fresh weight, and most importantly with the Sucrose Phosphate Synthase gene, suggesting that polymorphisms in this gene could influence genetic variation in several fruit quality traits. In addition, 1-deoxy-D-xylulose 5-phosphate synthase and Tocopherol cyclase genes were identified as candidate genes underlying QTL variation in beta-carotene and vitamin C. Together, our results provide useful genetic and molecular information regarding fruit quality and new chances for tomato breeding by implementing marker-assisted selection.

Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of solanum pimpinellifolium using genotyping by sequencing

“…Most of these low resolution linkage maps were constructed with RFLP (Restriction Fragment Length Polymorphism), COSII and SSR markers. Four recently constructed linkage maps contain SNP markers designed from the Solanaceae Genomics Network [10] and Tomato Mapping Resource databases [11–14]. The maps introduced by Salinan et al [13] and Capel et al [14], respectively, contained 112 and 233 SNP markers genotyped in S. pimpinellifolium and S. lycopersicum using the high-resolution melting (HRM) method.…”

“…Four recently constructed linkage maps contain SNP markers designed from the Solanaceae Genomics Network [10] and Tomato Mapping Resource databases [11–14]. The maps introduced by Salinan et al [13] and Capel et al [14], respectively, contained 112 and 233 SNP markers genotyped in S. pimpinellifolium and S. lycopersicum using the high-resolution melting (HRM) method. Another map with 440 markers was constructed with SNPs discovered by Restriction site Associated DNA Sequencing (RAD-Seq) technology and VeraCode SNP makers [15].…”

Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits

“…In tomato ( Solanum lycopersicum L.), QTLs were mapped for fruit quality traits measured under optimal watering conditions using linkage (Causse et al , 2001; Saliba-Colombani et al , 2001; Tieman et al , 2006; Zanor et al , 2009 b ; Capel et al , 2015) and association mapping (Xu et al , 2013; Ruggieri et al , 2014; Sauvage et al , 2014; Sacco et al , 2015). The studies of QTLs by water regime interactions focused on introgression lines between the cultivated tomato and its wild relatives (mainly S. habrochaites and S. pennellii ), leading to low mapping resolution (Semel et al , 2007; Gur et al , 2011; Arms et al , 2015).…”

Genes and Genomic Regions Related to the Production of Volatile Compounds in the Tomato Fruit

“…A S. lycopersicum x S. pimpinellifolium recombinant inbred line (RIL) population has been used in this work which had previously been employed for the localization of QTL involved in pest resistance (Salinas et al, 2013) and other fruit-quality components (Capel et al, 2015). Line TO-937 was derived from a S.…”

“…Up to 9 QTLs for the carotenoids lycopene and β-carotene had been identified previously in the same RIL population (Capel et al, 2015).…”