Morphological variation in tomato: a comprehensive study of quantitative trait loci controlling fruit shape and development

Variation in fruit morphology is a prevalent characteristic among cultivated tomato. The genetic and developmental mechanisms underlying similarities and differences in shape between the fruit of two elongated tomato varieties were investigated. Fruit from two F2 populations constructed from either Solanum lycopersicum cv. Howard German or cv. Banana Legs crossed with S. pimpinellifolium accession LA1589, and one BC1 population constructed with S. lycopersicum Howard German as the recurrent parent, were analysed for shape by using a new software program Tomato Analyzer. Quantitative trait loci (QTLs) controlling 15 individual shape attributes were mapped by both single and multitrait composite interval mapping in each population. In addition, principal components analysis and canonical discriminant analysis were conducted on these shape attributes to determine the greatest sources of variation among and between the populations. Individual principal components and canonical variates were subjected to QTL analysis to map regions of the genome influencing fruit shape in the cultivars. Common and unique regions, as well as previously known and novel QTLs, underlying fruit morphology in tomato were identified. Four major loci were found to control multiple fruit shape traits, principal components, and canonical variates in the populations. In addition, QTLs associated with the principal components better revealed regions of the genome that varied among populations than did the QTL associated with canonical variates. The QTL identified can be compared across additional populations of tomato and other fruit-bearing crop species.     

Quantitative genetic analysis of flowering time in tomato.

Artificial selection of cultivated tomato (Solanum lycopersicum L.) has resulted in the generation of early-flowering, day-length-insensitive cultivars, despite its close relationship to other Solanum species that need more time and specific photoperiods to flower. To investigate the genetic mechanisms controlling flowering time in tomato and related species, we performed a quantitative trait locus (QTL) analysis for flowering time in an F2 mapping population derived from S. lycopersicum and its late-flowering wild relative S. chmielewskii. Flowering time was scored as the number of days from sowing to the opening of the first flower (days to flowering), and as the number of leaves under the first inflorescence (leaf number). QTL analyses detected 2 QTLs affecting days to flowering, which explained 55.3% of the total phenotypic variance, and 6 QTLs for leaf number, accounting for 66.7% of the corresponding phenotypic variance. Four of the leaf number QTLs had not previously been detected for this trait in tomato. Colocation of some QTLs with flowering-time genes included in the genetic map suggests PHYB2, FALSIFLORA, and a tomato FLC-like sequence as candidate genes that might have been targets of selection during the domestication of tomato.     

Tomato fruit ascorbic acid content is linked with monodehydroascorbate reductase activity and tolerance to chilling stress

Quantitative trait loci (QTL) mapping is a step towards the identification of factors regulating traits such as fruit ascorbic acid content. A previously identified QTL controlling variations in tomato fruit ascorbic acid has been fine mapped and reveals that the QTL has a polygenic and epistatic architecture. A monodehydroascorbate reductase (MDHAR) allele is a candidate for a proportion of the increase in fruit ascorbic acid content. The MDHAR enzyme is active in different stages of fruit ripening, shows increased activity in the introgression lines containing the wild-type ( Solanum pennellii ) allele, and responds to chilling injury in tomato along with the reduced/oxidized ascorbate ratio. Low temperature storage of different tomato introgression lines with all or part of the QTL for ascorbic acid and with or without the wild MDHAR allele shows that enzyme activity explains 84% of the variation in the reduced ascorbic acid levels of tomato fruit following storage at 4 °C, compared with 38% at harvest under non-stress conditions. A role is indicated for MDHAR in the maintenance of ascorbate levels in fruit under stress conditions. Furthermore, an increased fruit MDHAR activity and a lower oxidation level of the fruit ascorbate pool are correlated with decreased loss of firmness because of chilling injury.     

The identification of a gene (Cwp1), silenced during Solanum evolution, which causes cuticle microfissuring and dehydration when expressed in tomato fruit

One of the most intriguing phenomena of fleshy fruit is the ability to maintain high water content at maturity, even following harvest. This is accomplished by a fruit cuticle that is highly impermeable to water diffusion. In this paper, we report on a novel genotype of tomato, developed via introgression from the wild species Solanum habrochaites, which is characterized by microfissuring of the fruit cuticle and dehydration of the mature fruit. The microfissure/dehydration phenotype is inherited as a single gene, termed Cwp1 (cuticular water permeability). The gene was fine mapped, and its identity was determined by map-based cloning and differential expression analysis in near-isogenic lines. Causality of the Cwp1 gene was shown by the heterologous transgenic expression of the gene in the cultivated tomato, which caused a microfissured fruit cuticle leading to dehydrated fruit. Cwp1 encodes for a protein of unidentified function in the DUF833 domain family. The gene is expressed in the fruit epidermis of the dehydrating genotype harbouring the wild-species introgression, but not in the cultivated tomato. It is expressed only in the primitive green-fruited wild tomato species, but is not expressed in the cultivated Solanum lycopersicum and the closely related Solanum cheesmaniae and Solanum pimpinellifolium, indicating a pre-adaptive role for Cwp1 silencing in the evolution and domestication of the cultivated tomato.     

Identification of fruit yield loci controlling the salt tolerance conferred by solanum rootstocks

The rootstock effect on the fruit yield of a grafted tomato variety was genetically analyzed under salinity using as rootstock two populations of F(9) lines developed from a salt sensitive genotype of Solanum lycopersicum var. cerasiforme, as female parent, and two salt tolerant lines, as male parents, from S. pimpinellifolium, the P population (123 lines), and S. cheesmaniae, the C population (100 lines). There were rootstock lines from the two populations (up to 65% in the P population) that raised the fruit yield of the commercial hybrid under saline conditions. It is shown that this salt tolerance rootstock effect is a heritable trait (h (2) near 0.3), governed by at least eight QTLs. The most relevant component was the number of fruits. Thus most detected QTLs correspond to this component. In general, QTL gene effects are medium-sized, with contributions from 8.5 up to 15.9% at most, and the advantageous allele comes from the wild, salt tolerant species. Only two fruit yield QTLs on chromosomes P9 and C11 might correspond to fruit yield QTLs of the non-grafted lines indicating their root system dependence. A fruit yield QTL on chromosome 3 is acting epistatically in both populations. The epistatic interactions found were dominant and they were unveiled using the associated marker as cofactor in the composite interval mapping methodology. Therefore, an efficient and profitable utilization of wild germplasm can be carried out through the improvement of rootstocks that confer salt tolerance in terms of fruit yield to the grafted variety.     

Identification of growth processes involved in QTLs for tomato fruit size and composition

Many quantitative trait loci (QTLs) for quality traits havebeen located on the tomato genetic map, but introgression offavourable wild alleles into large fruited species is hamperedby co-localizations of QTLs with antagonist effects. The aimof this study was to assess the growth processes controlledby the main QTLs for fruit size and composition. Four nearlyisogenic lines (NILs) derived from an intraspecific cross betweena tasty cherry tomato (Cervil) and a normal-tasting large fruittomato (Levovil) were studied. The lines carried one (L2, L4,and L9) or five (Lx) introgressions from Cervil on chromosomes1, 2, 4, and 9. QTLs for fruit size could be mainly associatedwith cell division processes in L2 and L9, whereas cell expansionwas rather homogeneous among the genotypes, except Cervil forwhich the low expansion rate was attributed to low cell plasticity.The link between endoreduplication and fruit size remained unclear,as cell or fruit sizes were positively correlated with the cellDNA content, but not with the endoreduplication factor. QTLsfor fruit composition reflected differences in water accumulationrather than in sugar accumulation, except in L9 for which theup-regulation of sucrose unloading and hexose transport and/orstarch synthesis was suggested. This may explain the increasedamount of carbon allocated to cell structures in L9, which couldbe related to a QTL for fruit texture. In Lx, these effectswere attenuated, except on fruit size and cell division. Finally,the region on top of chromosome 9 may control size and compositionattributes in tomato, by a combination of QTL effects on celldivision, cell wall synthesis, and carbon import and metabolism. Key words: Cell division and expansion, endoreduplication, fruit quality, near isogenic line, osmotic regulation, quantitative trait locus, Solanum lycopersicum, starch, sugar and acid contents Received 22 July 2008; Revised 17 October 2008 Accepted 20 October 2008     

Genealogy and fine mapping of obscuravenosa, a gene affecting the distribution of chloroplasts in leaf veins, and evidence of selection during breeding of tomatoes (Lycopersicon esculentum; Solanaceae)

In the processes of plant domestication and variety development, some traits are under direct selection, while others may be introduced by indirect selection or linkage. In the cultivated tomato (Lycopersicon esculentum = Solanum lycopersicum), and all other Solanaceae examined, chloroplasts are normally absent from subepidermal and mesophyll cells surrounding the leaf veins, and thus, veins appear clear upon subillumination. The tomato mutant obscuravenosa (obv), in contrast, contains chloroplasts in cells around the vein, and thus, veins appear as dark as the surrounding leaf tissue. Among tomato cultivars, the obv allele is common in processing varieties bred for mechanical harvest, but is otherwise rare. We traced the source of obv in processing tomatoes to the cultivar Earliana, released in the 1920s. The obv locus was mapped to chromosome 5, bin 5G, using introgression lines containing single chromosome segments from the wild species L. pennellii. This region also contains a quantitative trait locus (QTL) for plant height, pht5.4, which cosegregated with SP5G, a paralog of self-pruning (sp), the gene that controls the switch between determinate and indeterminate growth in tomato. The pht5.4 QTL was partially dominant and associated with a reduced percentage of red fruit at harvest. Our data suggest that the prevalence of obv in nearly all processing varieties may have resulted from its tight linkage to a QTL conferring a more compact, and horticulturally desirable, plant habit.     

Genetic dissection of vitamin E biosynthesis in tomato

Vegetables are critical for human health as they are a source of multiple vitamins including vitamin E (VTE). In plants, the synthesis of VTE compounds, tocopherol and tocotrienol, derives from precursors of the shikimate and methylerythritol phosphate pathways. Quantitative trait loci (QTL) for α-tocopherol content in ripe fruit have previously been determined in an Solanum pennellii tomato introgression line population. In this work, variations of tocopherol isoforms (α, β, γ, and δ) in ripe fruits of these lines were studied. In parallel all tomato genes structurally associated with VTE biosynthesis were identified and mapped. Previously identified VTE QTL on chromosomes 6 and 9 were confirmed whilst novel ones were identified on chromosomes 7 and 8. Integrated analysis at the metabolic, genetic and genomic levels allowed us to propose 16 candidate loci putatively affecting tocopherol content in tomato. A comparative analysis revealed polymorphisms at nucleotide and amino acid levels between Solanum lycopersicum and S. pennellii candidate alleles. Moreover, evolutionary analyses showed the presence of codons evolving under both neutral and positive selection, which may explain the phenotypic differences between species. These data represent an important step in understanding the genetic determinants of VTE natural variation in tomato fruit and as such in the ability to improve the content of this important nutriceutical.     

Combining ecophysiological modelling and quantitative trait locus analysis to identify key elementary processes underlying tomato fruit sugar concentration

A mechanistic model predicting the accumulation of tomato fruit sugars was developed in order (i) to dissect the relative influence of three underlying processes: assimilate supply (S), metabolic transformation of sugars into other compounds (M), and dilution by water uptake (D); and (ii) to estimate the genetic variability of S, M, and D. The latter was estimated in a population of 20 introgression lines derived from the introgression of a wild tomato species (Solanum chmielewskii) into S. lycopersicum, grown under two contrasted fruit load conditions. Low load systematically decreased D in the whole population, while S and M were targets of genotype × fruit load interactions. The sugar concentration positively correlated to S and D when the variation was due to genetic introgressions, while it positively correlated to S and M when the variation was due to changes in fruit load. Co-localizations between quantitative trait loci (QTLs) for sugar concentration and QTLs for S, M, and D allowed hypotheses to be proposed on the processes putatively involved at the QTLs. Among the five QTLs for sugar concentration, four co-localized with QTLs for S, M, and D with similar allele effects. Moreover, the processes underlying QTLs for sugar accumulation changed according to the fruit load condition. Finally, for some genotypes, the processes underlying sugar concentration compensated in such a way that they did not modify the sugar concentration. By uncoupling genetic from physiological relationships between processes, these results provide new insights into further understanding of tomato fruit sugar accumulation.     

Yield quantitative trait loci from wild tomato are predominately expressed by the shoot

Plant yield is the integrated outcome of processes taking place above and below ground. To explore genetic, environmental and developmental aspects of fruit yield in tomato, we phenotyped an introgression line (IL) population derived from a cross between the cultivated tomato (Solanum lycopersicum) and a wild species (Solanum pennellii). Both homozygous and heterozygous ILs were grown in irrigated and non-irrigated fields and evaluated for six yield components. Thirteen lines displayed transgressive segregation that increased agronomic yield consistently over 2?years and defined at least 11 independent yield-improving QTL. To determine if these QTL were expressed in the shoots or the roots of the plants, we conducted field trials of reciprocally grafted ILs; out of 13 lines with an effect on yield, 10 QTL were active in the shoot and only IL8-3 showed a consistent root effect. To further examine this unusual case, we evaluated the metabolic profiles of fruits from both the homo- and heterozygous lines for IL8-3 and compared these to those obtained from the fruit of their equivalent genotypes in the root effect population. We observed that several of these metabolic QTL, like the yield QTL, were root determined; however, further studies will be required to delineate the exact mechanism mediating this effect in this specific line. The results presented here suggest that genetic variation for root traits, in comparison to that present in the shoot, represents only a minor component in the determination of tomato fruit yield.     

Mapping of yield-related QTLs in pepper in an interspecific cross of <Emphasis Type="Italic">Capsicum annuum</Emphasis> and <Emphasis Type="Italic">C. frutescens</Emphasis>

An advanced backcross QTL study was performed in pepper using a cross between the cultivated species Capsicum annuum cv. Maor and the wild C. frutescens BG 2816 accession. A genetic map from this cross was constructed, based on 248 BC(2) plants and 92 restriction fragment length polymorphism (RFLP) markers distributed throughout the genome. Ten yield-related traits were analyzed in the BC(2) and BC(2)S(1) generations, and a total of 58 quantitative trait loci (QTLs) were detected; the number of QTLs per trait ranged from two to ten. Most of the QTLs were found in 11 clusters, in which similar QTL positions were identified for multiple traits. Unlike the high percentage of favorable QTL alleles discovered in wild species of tomato and rice, only a few such QTL alleles were detected in BG 2816. For six QTLs (10%), alleles with effects opposite to those expected from the phenotype were detected in the wild species. The use of common RFLP markers in the pepper and tomato maps enabled possible orthologous QTLs in the two species to be determined. The degree of putative QTL orthology for the two main fruit morphology traits-weight and shape-varied considerably. While all eight QTLs identified for fruit weight in this study could be orthologous to tomato fruit weight QTLs, only one out of six fruit shape QTLs found in this study could be orthologous to tomato fruit shape QTLs.     

Mapping of QTLs for lycopene and other fruit traits in a Lycopersicon esculentum × L. pimpinellifolium cross and comparison of QTLs across tomato species

Quantitative trait loci (QTLs) for several fruit traits in tomato were mapped and characterized in a backcross population of an interspecific cross between Lycopersicon esculentum fresh-marker breeding line NC84173 and L. pimpinellifolium accession LA722. A molecular linkage map of this cross that was previously constructed based on 119 BC1 individuals and 151 RFLP markers was used for the QTL mapping. The parental lines and 119 BC1S1 families (self-pollinated progeny of BC1 individuals) were grown under field conditions at two locations, Rock Spring, PA, and Davis, CA, and fruits were scored for weight (FW), polar (PD) and equatorial diameters (ED), shape (FS), total soluble solids content (SSC), pH and lycopene content (LYC). For each trait, between 4 and 10 QTLs were identified with individual effects ranging between 4.4% and 32.9% and multilocus QTL effects ranging between 39% and 75% of the total phenotypic variation. Most QTL effects were predictable from the parental phenotypes, and several QTLs were identified that affected more than one trait. A few pairwise epistatic interactions were detected between QTL-linked and QTL-unlinked markers. Despite great differences between PA and CA growing conditions, the majority of FW QTLs (78%) and SSC QTLs (75%) in the two locations shared similar genomic positions. Almost all of the QTLs that were identified in the present study for FW and SSC were previously identified in six other studies that used different interspecific crosses of tomato; this indicates conservation of QTLs for fruit traits across tomato species. Altogether, the seven studies identified at least 28 QTLs for FW and 32 QTLs for SSC on the 12 tomato chromosomes. However, for each trait a few major QTLs were commonly identified in 4 or more studies; such ‘popular’ QTLs should be of considerable interest for breeding purposes as well as basic research towards cloning of QTLs. Notably, a majority of QTLs for increased SSC also contributed to decreased fruit size. Therefore, to significantly increase SSC of the cultivated tomato, some compromise in fruit size may be unavoidable. This revised version was published online in June 2006 with corrections to the Cover Date.     

Genetic analysis of organoleptic quality in fresh market tomato. 1. Mapping QTLs for physical and chemical traits

Improving organoleptic quality is an important but complex goal for fresh market tomato breeders. A total of 26 traits involved in organoleptic quality variation were evaluated, in order to understand the genetic control of this characteristic. A recombinant inbred line (RIL) population was developed from an intraspecific cross between a cherry tomato line with a good overall aroma intensity and an inbred line with a common taste but with bigger fruits. Physical traits included fruit weight, diameter, color (L,a,b), firmness and elasticity. Chemical traits were dry matter weight, titratable acidity, pH, and the contents of soluble solids, sugars, lycopene, carotene and 12 aroma volatiles. RILs showed a large range of variation for most of the traits and many of them were transgressive. Some correlations between aroma volatiles were in accordance with the metabolic pathway they originated from. A total of 81 significant QTLs were detected for the 26 traits by simple and composite interval mapping. They were mainly distributed in a few regions on chromosomes 2, 3, 4, 8, 9, 11 and 12. Major QTLs (R²>30%) were detected for fruit weight, diameter, and color, and for six aroma volatiles. Co-localization of QTLs controlling correlated traits was mainly found on chromosome 2. QTLs for fruit weight and sugar content or dry matter weight were often co-localized. However, a QTL for soluble-solids content and dry matter weight have been detected on chromosome 9 in a region without fruit weight QTLs. QTLs for seven aroma volatiles, lycopene content and fruit color were also co-localized. The QTL localizations were compared with those detected in crosses between Lycopersicon esculentum and wild tomato species. Received: 19 January 2000 / Accepted: 26 May 2000     

Identification of novel quantitative trait loci for increased lycopene content and other fruit quality traits in a tomato recombinant inbred line population

Epidemiological and clinical studies indicate that a steady dietary intake of bioavailable lycopene, a C₄₀ carotenoid and potent natural antioxidant, may be associated with a decreased incidence of prostate cancer in humans. Since fresh tomatoes and processed tomato products represent approximately 85% of the average human??s dietary lycopene intake, the identification of novel genetic factors which regulate high fruit lycopene content in tomato is imperative for the improvement of nutritional quality in this commercially valuable specialty crop. To understand the genetic control of the extraordinarily high fruit lycopene content in an accession (LA2093) of the tomato wild species Solanum pimpinellifolium, a quantitative trait locus (QTL) mapping study was conducted using a recombinant inbred line (RIL) population of a cross between LA2093 and a cultivated tomato (S. lycopersicum) breeding line, NCEBR-1. The parental lines, F1 progeny, and F7-F10 RIL populations were grown in replicated field trials in four successive years and evaluated for lycopene content as well as several other traits, including fruit fresh weight, soluble solids content, pH of puree, and plant maturity. The lycopene content of ripe fruit was estimated using three methods: high-performance liquid chromatography (HPLC), spectrophotometry, and colorimetric assays. Based on these measurements, QTL were identified and compared across generations. Among the QTL identified for lycopene, two QTL, located on chromosomes 7 and 12, had very large effects and were consistent across generations. The genomic intervals in which these two QTL reside do not correspond to known map positions of carotenoid biosynthetic genes, indicating that these QTL may represent novel alleles with potentially important implications for tomato breeding as well as increased understanding of carotenoid accumulation in tomato. Several QTL were also identified for fruit weight, soluble solids content and plant maturity. The potential implications of these results for tomato crop improvement are discussed.     

Mode of inheritance of primary metabolic traits in tomato

To evaluate components of fruit metabolic composition, we have previously metabolically phenotyped tomato (Solanum lycopersicum) introgression lines containing segmental substitutions of wild species chromosome in the genetic background of a cultivated variety. Here, we studied the hereditability of the fruit metabolome by analyzing an additional year's harvest and evaluating the metabolite profiles of lines heterozygous for the introgression (ILHs), allowing the evaluation of putative quantitative trait locus (QTL) mode of inheritance. These studies revealed that most of the metabolic QTL (174 of 332) were dominantly inherited, with relatively high proportions of additively (61 of 332) or recessively (80 of 332) inherited QTL and a negligible number displaying the characteristics of overdominant inheritance. Comparison of the mode of inheritance of QTL revealed that several metabolite pairs displayed a similar mode of inheritance of QTL at the same chromosomal loci. Evaluation of the association between morphological and metabolic traits in the ILHs revealed that this correlation was far less prominent, due to a reduced variance in the harvest index within this population. These data are discussed in the context of genomics-assisted breeding for crop improvement, with particular focus on the exploitation of wide biodiversity.     

Increase in tomato locule number is controlled by two single-nucleotide polymorphisms located near WUSCHEL

In tomato (Solanum lycopersicum) fruit, the number of locules (cavities containing seeds that are derived from carpels) varies from two to up to 10 or more. Locule number affects fruit shape and size and is controlled by several quantitative trait loci (QTLs). The large majority of the phenotypic variation is explained by two of these QTLs, fasciated (fas) and locule number (lc), that interact epistatically with one another. FAS has been cloned, and mutations in the gene are described as key factors leading to the increase in fruit size in modern varieties. Here, we report the map-based cloning of lc. The lc QTL includes a 1,600-bp region that is located 1,080 bp from the 3' end of WUSCHEL, which encodes a homeodomain protein that regulates stem cell fate in plants. The molecular evolution of lc showed a reduction of diversity in cultivated accessions with the exception of two single-nucleotide polymorphisms. These two single-nucleotide polymorphisms were shown to be responsible for the increase in locule number. An evolutionary model of locule number is proposed herein, suggesting that the fas mutation appeared after the mutation in the lc locus to confer the extreme high-locule-number phenotype.     

RFLP Mapping in Soybean: Association between Marker Loci and Variation in Quantitative Traits

Quantitative trait loci (QTLs) have been mapped to small intervals along the chromosomes of tomato (Lycopersicon esculentum), by a method we call substitution mapping. The size of the interval to which a QTL can be mapped is determined primarily by the number and spacing of previously mapped genetic markers in the region surrounding the QTL. We demonstrate the method using tomato genotypes carrying chromosomal segments from Lycopersicon chmielewskii, a wild relative of tomato with high soluble solids concentration but small fruit and low yield. Different L. chmielewskii chromosomal segments carrying a common restriction fragment length polymorphism were identified, and their regions of overlap determined using all available genetic markers. The effect of these chromosomal segments on soluble solids concentration, fruit mass, yield, and pH, was determined in the field. Many overlapping chromosomal segments had very different phenotypic effects, indicating QTLs affecting the phenotype(s) to lie in intervals of as little as 3 cM by which the segments differed. Some associations between different traits were attributed to close linkage between two or more QTLs, rather than pleiotropic effects of a single QTL: in such cases, recombination should separate desirable QTLs from genes with undesirable effects. The prominence of such trait associations in wide crosses appears partly due to infrequent reciprocal recombination between heterozygous chromosomal segments flanked by homozygous regions. Substitution mapping is particularly applicable to gene introgression from wild to domestic species, and generally useful in narrowing the gap between linkage mapping and physical mapping of QTLs.     

A genetic map of candidate genes and QTLs involved in tomato fruit size and composition

In order to screen for putative candidate genes linked to tomato fruit weight and to sugar or acid content, genes and QTLs involved in fruit size and composition were mapped. Genes were selected among EST clones in the TIGR tomato EST database (http://www.tigr.org/tdb/tgi/lgi/) or corresponded to genes preferentially expressed in the early stages of fruit development. These clones were located on the tomato map using a population of introgression lines (ILs) having one segment of Lycopersicon pennellii (LA716) in a L. esculentum (M82) background. The 75 ILs allowed the genome to be segmented into 107 bins. Sixty-three genes involved in carbon metabolism revealed 79 loci. They represented enzymes involved in the Calvin cycle, glycolysis, the TCA cycle, sugar and starch metabolism, transport, and a few other functions. In addition, seven cell-cycle-specific genes mapped into nine loci. Fourteen genes, primarily expressed during the cell division stage, and 23 genes primarily expressed during the cell expansion stage, revealed 24 and 26 loci, respectively. The fruit weight, sugars, and organic acids content of each IL was measured and several QTLs controlling these traits were mapped. Comparison between map location of QTLs and candidate gene loci indicated a few candidate genes that may influence the variation of sugar or acid contents. Furthermore, the gene/QTL locations could be compared with the loci mapped in other tomato populations.     

The genetic and functional analysis of flavor in commercial tomato: the FLORAL4 gene underlies a QTL for floral aroma volatiles in tomato fruit

Tomato (Solanum lycopersicum L.) has become a popular model for genetic studies of fruit flavor in the last two decades. In this article we present a study of tomato fruit flavor, including an analysis of the genetic, metabolic and sensorial variation of a collection of contemporary commercial glasshouse tomato cultivars, followed by a validation of the associations found by quantitative trait locus (QTL) analysis of representative biparental segregating populations. This led to the identification of the major sensorial and chemical components determining fruit flavor variation and detection of the underlying QTLs. The high representation of QTL haplotypes in the breeders’ germplasm suggests that there is great potential for applying these QTLs in current breeding programs aimed at improving tomato flavor. A QTL on chromosome 4 was found to affect the levels of the phenylalanine‐derived volatiles (PHEVs) 2‐phenylethanol, phenylacetaldehyde and 1‐nitro‐2‐phenylethane. Fruits of near‐isogenic lines contrasting for this locus and in the composition of PHEVs significantly differed in the perception of fruity and rose‐hip‐like aroma. The PHEV locus was fine mapped, which allowed for the identification of FLORAL4 as a candidate gene for PHEV regulation. Using a gene‐editing‐based (CRISPR‐CAS9) reverse‐genetics approach, FLORAL4 was demonstrated to be the key factor in this QTL affecting PHEV accumulation in tomato fruit.