Genome Mapping and Molecular Breeding of Tomato

The cultivated tomato, Lycopersicon esculentum, is the second most consumed vegetable worldwide and a well-studied crop species in terms of genetics, genomics, and breeding. It is one of the earliest crop plants for which a genetic linkage map was constructed, and currently there are several molecular maps based on crosses between the cultivated and various wild species of tomato. The high-density molecular map, developed based on an L. esculentum × L. pennellii cross, includes more than 2200 markers with an average marker distance of less than 1 cM and an average of 750 kbp per cM. Different types of molecular markers such as RFLPs, AFLPs, SSRs, CAPS, RGAs, ESTs, and COSs have been developed and mapped onto the 12 tomato chromosomes. Markers have been used extensively for identification and mapping of genes and QTLs for many biologically and agriculturally important traits and occasionally for germplasm screening, fingerprinting, and marker-assisted breeding. The utility of MAS in tomato breeding has been restricted largely due to limited marker polymorphism within the cultivated species and economical reasons. Also, when used, MAS has been employed mainly for improving simply-inherited traits and not much for improving complex traits. The latter has been due to unavailability of reliable PCR-based markers and problems with linkage drag. Efforts are being made to develop high-throughput markers with greater resolution, including SNPs. The expanding tomato EST database, which currently includes ∼214 000 sequences, the new microarray DNA chips, and the ongoing sequencing project are expected to aid development of more practical markers. Several BAC libraries have been developed that facilitate map-based cloning of genes and QTLs. Sequencing of the euchromatic portions of the tomato genome is paving the way for comparative and functional analysis of important genes and QTLs

Common QTL Affect the Rate of Tomato Seed Germination under Different Stress and Nonstress Conditions

The purpose of this study was to determine whether the rates of tomato seed germination under different stress and nonstress conditions were under common genetic controls by examining quantitative trait loci (QTL) affecting such traits. Seeds of BC1 progeny of a cross between a slow-germinating tomato breeding line and a rapid-germinating tomato wild accession were evaluated for germination under nonstress as well as cold, salt, and drought stress conditions. In each treatment, the most rapidly-germinating seeds were selected, grown to maturity, and subjected to molecular marker analysis. A selective genotyping approach detected between 6 and 9 QTL affecting germination rate under each of the four conditions, with a total of 14 QTL identified. Ten QTL affected germination rate under 2 or 3 conditions, which were considered germination-related common QTL. Four QTL affected germination rate only in one treatment, which were considered germination-related, condition-specific QTL . The results indicated that mostly the same QTL affected seed germination under different stress and nonstress conditions, supporting a previous suggestion that similar physiological mechanisms contribute to rapid seed germination under different conditions. Marker-assisted selection for the common QTL may result in progeny with rapid seed germinability under different conditions

A Solanum lycopersicum × Solanum pimpinellifolium Linkage Map of Tomato Displaying Genomic Locations of R-Genes, RGAs, and Candidate Resistance/Defense-Response ESTs

We have identified an accession (LA2093) within the tomato wild species Solanum pimpinellifolium with many desirable characteristics, including biotic and abiotic stress tolerance and good fruit quality. To utilize the full genetic potential of LA2093 in tomato breeding, we have developed a linkage map based on an F2 population of a cross between LA2093 and a tomato breeding line, using 115 RFLP, 94 EST, and 41 RGA markers. The map spanned 1002.4 cM of the 12 tomato chromosomes with an average marker distance of 4.0 cM. The length of the map and linear order of the markers were in good agreement with the published maps of tomato. The ESTs were chosen based on their sequence similarities with known resistance or defense-response genes, signal-transduction factors, transcriptional regulators, and genes encoding pathogenesis-related proteins. Locations of several ESTs and RGAs coincided with locations of several known tomato resistance genes and quantitative resistance loci (QRLs), suggesting that candidate-gene approach may be effective in identifying and mapping new R genes. This map will be useful for marker-assisted exploitation of desirable traits in LA2093 and other S. pimpinellifolium accessions, and possibly for utilization of genetic variation within S. lycopersicum

Identification and Mapping of Late Blight Resistance Quantitative Trait Loci in Tomato Accession PI 163245

Late blight (LB), caused by the oomycete (Mont.) de Bary, is one of the most devastating diseases of tomato ( L.) and potato ( tuberosum L. worldwide. The importance of LB on tomato has increased due to the occurrence of aggressive and fungicide-resistant clonal lineages of . Consequently, identification and characterization of new sources of genetic resistance to LB has become a priority in tomato breeding. Previously, we reported accession PI 163245 as a promising source of highly heritable LB resistance for tomato breeding. The purpose of this study was to identify and map quantitative trait loci (QTLs) associated with LB resistance in this accession using a trait-based marker analysis (a.k.a. selective genotyping). An F mapping population ( = 560) derived from a cross between a LB-susceptible tomato breeding line (Fla. 8059) and PI 163245 was screened for LB resistance, and the most resistant ( = 39) and susceptible ( = 35) individuals were selected for genotyping. Sequencing and comparison of the reduced representation libraries (RRLs) derived from genomic DNA of the two parents resulted in the identification of 33,541 putative single nucleotide polymorphism (SNP) markers, of which, 233 genome-wide markers were used to genotype the 74 selected F individuals. The marker analysis resulted in the identification of four LB resistance QTLs conferred by PI 163245, located on chromosomes 2, 3, 10, and 11. Research is underway to develop near-isogenic lines (NILs) for fine mapping the QTLs and develop tomato breeding lines with LB resistance introduced from PI 163245

HS-SPME-GC-MS Analyses of Volatiles in Plant Populations—Quantitating Compound × Individual Matrix Effects

Headspace solid-phase microextraction (HS-SPME) coupled to gas chromatography–mass spectrometry (GC-MS) is widely employed for volatile analyses of plants, including mapping populations used in plant breeding research. Studies often employ a single internal surrogate standard, even when multiple analytes are measured, with the assumption that any relative changes in matrix effects among individuals would be similar for all compounds, i.e., matrix effects do not show Compound × Individual interactions. We tested this assumption using individuals from two plant populations: an interspecific grape (Vitis spp.) mapping population (n = 140) and a tomato (Solanum spp.) recombinant inbred line (RIL) population (n = 148). Individual plants from the two populations were spiked with a cocktail of internal standards (n = 6, 9, respectively) prior to HS-SPME-GC-MS. Variation in the relative responses of internal standards indicated that Compound × Individual interactions exist but were different between the two populations. For the grape population, relative responses among pairs of internal standards varied considerably among individuals, with a maximum of 249% relative standard deviation (RSD) for the pair of [U13C]hexanal and [U13C]hexanol. However, in the tomato population, relative responses of internal standard pairs varied much less, with pairwise RSDs ranging from 8% to 56%. The approach described in this paper could be used to evaluate the suitability of using surrogate standards for HS-SPME-GC-MS studies in other plant populations

Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection

Genotyping-by-sequencing (GBS) was employed to construct a highly saturated genetic linkage map of a tomato ( L.) recombinant inbred line (RIL) population, derived from a cross between cultivar NC EBR-1 and the wild tomato L. accession LA2093. A pipeline was developed to convert single nucleotide polymorphism (SNP) data into genomic bins, which could be used for fine mapping of quantitative trait loci (QTL) and identification of candidate genes. The pipeline, implemented in a python script named SNPbinner, adopts a hidden Markov model approach for calculation of recombination breakpoints followed by genomic bins construction. The total length of the newly developed high-resolution genetic map was 1.2-fold larger than previously estimated based on restriction fragment length polymorphism (RFLP) and polymerase chain reaction (PCR)–based markers. The map was used to verify and refine QTL previously identified for two fruit quality traits in the RIL population, fruit weight (FW) and fruit lycopene content (LYC). Two well-described FW QTL ( and ) were localized precisely at their known underlying causative genes, and the QTL intervals were decreased by two- to tenfold. A major QTL for LYC content () was verified at high resolution and its underlying causative gene was determined to be ζ (). The RIL population, the high resolution genetic map, and the easy-to-use genotyping pipeline, SNPbinner, are made publicly available

SNPs called from the RNA-Seq data of RILs

SNPs called from the RNA-Seq data of RILs and their two parents, S. lycopersicum breeding line NC EBR-1 and S. pimpinellifolium accession LA2093. The file is in vcf format

gene models in non-reference genome

gene models annotated in the non-reference sequences of the tomato pan-genome, in gff3 forma

Data from: The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in TomLoxC promoter selected against during domestication. QTL mapping and analysis of transgenic plants reveal a novel role for TomLoxC in apocarotenoid production, which contributes to desirable tomato flavor. In orange-stage fruit, accessions harboring both the rare and common TomLoxC alleles (heterozygotes) have higher TomLoxC expression than those homozygous for either, and are resurgent in modern tomatoes. The tomato pan-genome adds depth and completeness to the reference genome, and is useful for future biological discovery and breeding