Identification and molecular mapping of loci controlling fruit ripening time in tomato

Using RAPD marker analysis, two quantitative trait loci (QTLs) associated with earliness due to reduced fruit-ripening time (days from anthesis to ripening = DTR) were identified and mapped in an F₂ population derived from a cross between Lycopersicon esculentum’E6203’ (normal ripening) and Lycopersicon esculentum’Early Cherry’ (early ripening). One QTL, on chromosome 5, was associated with a reduction in both ripening time (5 days) and fruit weight (29.3%) and explained 15.8 and 13% of the total phenotypic variation for DTR and fruit weight, respectively. The other QTL, on chromosome 12, was primarily associated with a reduction only in ripening time (7 days) and explained 12.3% of the total phenotypic variation for DTR. The gene action at this QTL was found to be partially dominant (d/a=0.41). Together, these two QTLs explained 25.1% of the total phenotypic variation for DTR. Additionally, two QTLs associated with fruit weight were identified in the same F₂ population and mapped to chromosomes 4 and 6, respectively. Together, these two QTLs explained 30.9% of the total phenotypc variation for fruit weight. For all QTLs, the ’Early Cherry’ alleles caused reductions in both ripening time and fruit weight. The polymorphic band for the most significant RAPD marker (OPAB-06), linked to the reduced ripening time QTL on chromosome 12, was converted to a cleaved amplified polymorphism (CAP) assay for marker-aided selection and further introgression of early ripening time (DTR) into cultivated tomato. Received: 15 March 1999 / Accepted: 29 April 1999     

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.     

Fine mapping of fw3.2 controlling fruit weight in tomato

Tomato (Solanum lycopersicum) is an important crop in the Solanaceae family. One of the key traits selected during domestication is fruit mass which is controlled by many quantitative trait loci. The fruit weight locus fw3.2 is one of the major loci responsible for fruit mass in tomato. Identification of the underlying gene will improve our understanding of the molecular mechanism of fruit development while also providing insights into genes that were selected during domestication. We fine mapped fw3.2 to a 51.4-kb interval corresponding to a region comprising seven candidate genes. Gene action showed that the allele from cultivated tomato was additive to dominant in giving rise to an enlarged fruit. Fruit shape analysis indicated that fw3.2 primarily played a role in controlling fruit weight, with a minor effect on fruit shape. Gene expression and nucleotide diversity were investigated and the likelihood of the genes control fruit mass is discussed.     

Identification and characterization of a novel locus controlling early fruit development in tomato

Cultivated tomatoes (Lycopersicon esculen- tum) encompass a wide range of fruit size and shape variants. This variation provides the basis for dissecting the genetic and molecular pathways of ovary and fruit development. One fruit shape variant is displayed by the cultivar Sun 1642 (TA491). TA491 has an elongated fruit phenotype, while the wild relative L. pimpinellifolium LA1589 produces fruit that are nearly perfect spheres, a shape typical of wild tomatoes. Developmental studies indicated that the differences in fruit shape between TA491 and LA1589 are determined by events occurring immediately after pollination and extending to 14 days post-pollination. Quantitative trait mapping revealed a single major locus on chromosome 7 (named sun) to be responsible for the differential development of TA491 and LA1589 fruit. Other fruit shape loci characterized in tomato (e.g. fs8.1 and ovate) exert their effects before anthesis and early in ovary development. sun is the first major locus identified in tomato controlling fruit shape through post-pollination events. Received: 17 November 2000 / Accepted: 24 November 2000     

Quantitative trait loci pyramiding for fruit quality traits in tomato

Fruit quality is a major focus for most conventional and innovative tomato breeding strategies, with particular attention being paid to fruit antioxidant compounds. Tomatoes represent a major contribution to dietary nutrition worldwide and a reservoir of diverse antioxidant molecules. In a previous study, we identified two Solanum pennellii introgression lines (IL7-3 and IL12-4) harbouring quantitative trait loci (QTL) that increase the content of ascorbic acid (AsA), phenols and soluble solids (degrees Brix; °Bx) in tomato fruit. The purpose of the present work was to pyramid into cultivated varieties the selected QTL for enhanced antioxidant and °Bx content. To better understand the genetic architecture of each QTL, the two ILs were crossed to the recurrent parent M82 (ILH7-3 and ILH12-4) and between them (ILH7-3+12-4). F1 hybrids (ILH7-3+12-4) were then selfed up to obtain F3 progenies in order to stabilize the favourable traits at the homozygous condition. Species-specific molecular markers were identified for each introgressed region and allowed us to select four F2 genotypes carrying both introgressions at the homozygous condition. The F3 double homozygous plants displayed AsA, total phenols and °Bx content significantly higher than M82. Therefore, they may represent suitable genetic material for breeding schemes aiming to increase antioxidant content in tomato fruit.     

The climacteric in ripening tomato fruit

Phosphofructokinase is identified as the regulator reaction activated at the onset of the climacteric rise in respiration of the ripening tomato fruit (Lycopersicon esculentum Mill). The concentration of ATP in the fruit increases to a maximum value after the climacteric peak of respiration is past. Orthophosphate is proposed as the most probable activator of phosphofructokinase in the ripening fruit.     

Heterozygosity levels in a mammal: A determination derived from allele frequencies at loci controlling gross morphology

Summary Estimates of heterozygosity derived from electrophoretic data may seriously underestimate the true levels of genetic variability. An estimate derived from allele frequencies in Felis that relate to macroscopic morphological traits appears to be congruent with several theoretical predictions of heterozygosity levels.     

Genetic mapping of quantitative trait loci controlling fruit size and shape in papaya

Papaya (Carica papaya L.) is a pan-tropical tree that bears fruit exhibiting a wide range of size and shape. Depending on variety and environment, papaya fruit may weigh from 0.2 kg up to 10 kg. Papaya fruit shape is a sex-linked trait ranging from spherical to ovate, cylindrical or pyriform. An F2 mapping population, produced from a cross between the Thai variety Khaek Dum, bearing 1.2 kg, red-fleshed fruit, and variety 2H94, a Hawaii Solo type bearing a 0.2 kg, yellow-fleshed fruit, was used to identify quantitative trait loci (QTLs) that influence papaya fruit characters including weight, diameter, length and shape. Fruit phenotype data, collected from two subpopulations planted in successive growing seasons, showed striking differences by year indicating significant genotype × environment interactions. Fourteen QTL with phenotypic effects ranging from 5 to 23% were identified across six linkage groups (LGs) with clusters of two or more QTL on LGs 02, 03, 07 and 09. These loci contain homologs to the tomato fruit QTL ovate, sun and fw2.2 regulating fruit size and shape. The papaya fruit QTL provide a starting point for dissecting the genetic pathways leading to extreme fruit size and shape and may prove useful for papaya breeders attempting to tailor new varieties to specific consumer markets.     

Gentiobiose: a novel oligosaccharin in ripening tomato fruit

Two neutral disaccharides, gentiobiose [beta- D-Glc p-(1-->6)- D-Glc] and nigerose [alpha- D-Glc p-(1-->3)- D-Glc], were detected in tomato ( Lycopersicon esculentum Mill.) pericarp and locule. Gentiobiose was present in the locule of green fruit and ripe fruit at 0.88 and 5.8 micro mol (kg fresh weight)(-1), respectively. When vacuum-infiltrated into green tomato fruit, exogenous gentiobiose (50 or 200 micro g per fruit) hastened the initiation of ripening (as judged by colour change) by 1-3 days relative to fruit that were infiltrated with glucose or isomaltose. Nigerose plus gentiobiose was particularly effective, but nigerose alone had no significant effect. The endogenous disaccharides were found to be present in the apoplastic fluid of the fruit, compatible with a proposed intercellular signalling role. The origin and metabolic fate of the disaccharides were investigated. Phenolic esters of these disaccharides were not detectable in tomato fruit and it is therefore unlikely that the free disaccharides were formed from a pool of such esters. An alternative possible biosynthetic origin, via transglycosylation, is discussed. When [(14)C]gentiobiose was vacuum-infiltrated into unripe or ripe fruit, the disaccharide remained intact for at least 1 h but was largely degraded within 24 h. The results suggest that gentiobiose is a new, naturally occurring oligosaccharin with a rapid turnover rate.     

Identifying the loci responsible for natural variation in fruit size and shape in tomato

Fruit size and shape are two major factors determining yield, quality and consumer acceptability for many crops. Like most traits important to agriculture, both are quantitatively inherited. Despite their economic importance none of the genes controlling either of these traits have been cloned, and little is known about the control of the size and shape of domesticated fruit. Tomato represents a model fruit-bearing domesticated species characterized by a wide morphological diversity of fruits. The many genetic and genomic tools available for this crop can be used to unraveal the molecular bases of the developmental stages which presumably influence fruit architecture, size and shape. The goal of this review is to summarize data from the tomato QTL studies conducted over the past 15 years, which together allow the identification of the major QTLs responsible for fruit domestication in tomato. These results provide the starting point for the isolation of the genes involved in fruit-size/shape determination in tomato and potentially other fruit-bearing plants. Received: 21 January 1999 / Accepted: 12 March 1999     

Genetic loci controlling lethal cell death in tomato caused by viral satellite RNA infection

Cucumber mosaic virus (CMV) associated with D satellite RNA (satRNA) causes lethal systemic necrosis (LSN) in tomato (Solanum lycopersicum), which involves programmed cell death. No resistance to this disease has been found in tomato. We obtained a line of wild tomato, S. habrochaitis, with a homogeneous non-lethal response (NLR) to the infection. This line of S. habrochaitis was crossed with tomato to generate F1 plants that survived the infection with NLR, indicating that NLR is a dominant trait. The NLR trait was successfully passed on to the next generation. The phenotype and genotype segregation was analyzed in the first backcross population. The analyses indicate that the NLR trait is determined by quantitative trait loci (QTL). Major QTL associated with the NLR trait were mapped to chromosomes 5 and 12. Results from Northern blot and in situ hybridization analyses revealed that the F1 and S. habrochaitis plants accumulated minus-strand satRNA more slowly than tomato, and fewer vascular cells were infected. In addition, D satRNA-induced LSN in tomato is correlated with higher accumulation of the minus-strand satRNA compared with the accumulation of the minus strand of a non-necrogenic mutant D satRNA.     

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.     

Characteristics of a membrane-associated lipoxygenase in tomato fruit

Microsomal membranes isolated from the pericarp of maturegreen tomato (Lycopersicon esculentum) fruit rapidly metabolize exogenous radiolabeled linoleic acid into fatty acid oxidation products at 22°C. The reaction is strongly inhibited by n-propyl gallate, an inhibitor of lipoxygenase. The membranes also rapidly metabolize 16:0/18:2^* phosphatidylcholine into radiolabeled oxidation products that comigrate on TLC plates with those formed from free linoleic acid. At 30°C, the formation of fatty acid oxidation products from 16:0/18:2^* phosphatidylcholine is slower, and there is an initial accumulation of radiolabeled linoleic acid that is not evident at 22°C, which can be attributed to the action of lipolytic acyl hydrolase. Radiolabeled phosphatidic acid and diacylglycerol are also formed during metabolism of 16:0/18:2^* phosphatidylcholine by the microsomal membranes, and there is no breakdown of either linoleic acid or phosphatidylcholine by heat-denatured membranes. When Triton X-100 treated membranes were used, the same patterns of metabolite formation from radiolabeled linoleic acid and 16:0/18:2^* phosphatidylcholine were observed. Thus, the enzymes mediating the breakdown of these radiolabeled compounds appear to be tightly associated with the membranes. Collectively, the data indicate that there is a lipoxygenase associated with microsomal membranes from tomato fruit that utilizes free fatty acid substrate released from phospholipids. The microsomal lipoxygenase is strongly active over a pH range of 4.5 to 8.0, comprises approximately 38% of the total (microsomal plus soluble) lipoxygenase activity in the tissue, has an apparent K_m of 0.52 millimolar and an apparent V_max of 0.186 millimoles per minute per milligram of protein. The membranous enzyme also cross-reacts with polyclonal antibodies raised against soybean lipoxygenase-1 and has an apparent molecular mass of 100 kilodaltons.     

The genetic basis of pear-shaped tomato fruit

Molecular-marker analysis of a cross between yellow pear, a tomato variety bearing small, pear-shaped fruit, and the round-fruited, wild species, Lycopersicon pimpinellifolium LA1589, revealed that pear-shaped fruit is determined largely by a major QTL on chromosome 2 and, to a lesser extent, a minor QTL on chromosome 10. The locus on chromosome 2 was also detected in a cross between yellow pear and the round-fruited introgression line (IL2–5) which carried the distal portion of chromosome 2 from the Lycopersicon pennellii genome. Based on its map position, we propose that the locus detected on chromosome 2 is the same as a locus referred to as ovate in the early tomato literature (Linstrom 1926, 1927). The fruit-shape index (length/diameter) and neck constriction were highly correlated in both populations suggesting that ovate exerts control over both traits or that the genes for these traits are tightly linked on chromosome 2. Using two-way ANOVA test, the minor QTL on chromosome 10 showed no significant interaction with the ovate locus on chromosome 2 with respect to the fruit-shape index. For ovate round fruit was dominant to elongated fruit in the L. pimpinellifolium populations, but additive in the IL2–5 population. Thus far, no genes controlling fruit shape have been cloned. The molecular mapping of the ovate locus may ultimately lead to its isolation via map-based cloning. Received: 8 January 1999 / Accepted: 30 January 1999     

Candidate genes and quantitative trait loci affecting fruit ascorbic acid content in three tomato populations

Fresh fruit and vegetables are a major source of ascorbic acid (vitamin C), an important antioxidant for the human diet and also for plants. Ascorbic acid content in fruit exhibits a quantitative inheritance. Quantitative trait loci (QTL) for ascorbic acid content have been mapped in three tomato populations derived from crosses between cultivated tomato varieties (Solanum lycopersicum accessions) and three related wild species or subspecies. The first population consists of a set of introgression lines derived from Solanum pennellii, each containing a unique fragment of the wild species genome. The second population is an advanced backcross population derived from a cross between a cultivated tomato and a Solanum habrochaites (formerly Lycopersicum hirsutum) accession. The third population is a recombinant inbred line population derived from the cross between a cherry tomato line and a large fruited line. Common regions controlling ascorbic acid content have been identified on chromosomes 2, 8, 9, 10, and 12. In general, the wild alleles increased ascorbic acid content, but some improvement could also be provided by S. lycopersicum. Most QTLs appeared relatively stable over years and in different environments. Mapping of candidate genes involved in the metabolism of ascorbic acid has revealed a few colocations between genes and QTLs, notably in the case of a monodehydroascorbate reductase gene and a QTL present in two of the populations on chromosome 9 (bin 9-D), and a previously mapped GDP-mannose epimerase and a QTL on chromosome 9 (bin 9-J).     

Solubilisation of tomato fruit pectins by ascorbate: a possible non-enzymic mechanism of fruit softening

The aim of this work was to test the hypothesis that endogenous ascorbate, released into the apoplast by membrane permeabilisation early in fruit ripening, could promote the solubilisation and depolymerisation of polysaccharides, and thus contribute to fruit softening. In vitro, ascorbate (1 mM), especially in the presence of traces of either Cu²⁺ or H₂O₂, solubilised up to 40% of the total pectin from the alcohol-insoluble residue of mature-green tomato (Lycopersicon esculentum Mill.) fruit. Solubilisation was due to the action of ascorbate-generated hydroxyl radicals (^·OH), which can cause non-enzymic scission of polysaccharides. The pectins solubilised by ascorbate in vitro were polydisperse (4–1,000 kDa), partially esterified and galactose-rich. Excised pieces of living tomato fruit released ascorbate into the medium (apoplast); the ability of different tissues to do this increased in the order pericarp < placenta < locule. In all three tissues, but especially in the locule, the ability to release ascorbate increased during ripening. The Cu content of each tissue also increased during ripening, whereas neither Fe nor Mn showed a similar trend. We suggest that progressively increasing levels of Cu and ascorbate in the fruit apoplast would lead to elevated ^·OH production there and thus to non-enzymic scission of pectins during ripening. Such scission could contribute to the natural softening of the fruit. De-esterified citrus pectin was more susceptible to ascorbate-induced scission in vitro than methylesterified pectin, suggesting a possible new significance for pectin methylesterase activity in fruit ripening. In conclusion, non-enzymic mechanisms of fruit softening should be considered alongside the probable roles of hydrolases, xyloglucan endotransglucosylases and expansins.Abbreviations AIR alcohol-insoluble residue - Ara l-arabinose - DMSO dimethylsulphoxide - endo-PG endo-polygalacturonase - Gal d-galactose - GalA d-galacturonic acid - Glc d-glucose - k_·OH rate constant for reaction with the hydroxyl radical - K_av elution from Sepharose column relative to the void volume (K_av=0.0) and totally included volume (K_av=1.0) - MG mature-green - PME pectin methylesterase - Rha l-rhamnose - RR red-ripe     

Identification of restriction fragment length polymorphisms linked to genes controlling soluble solids content in tomato fruit

Summary Gene(s) conferring high soluble solids (SS) in tomato fruit had been backcrossed previously from a wild tomato species, Lycopersicon chmielewskii LA1028 ( 10% SS), into a L. esculentum cultivar, VF36 ( 5% SS), to derive a BC₅S₅ line, LA1563, similar to VF 36 but with 7–8% SS. DNAs from these lines and a tomato breeding line, H2038, were screened for restriction fragment length polymorphisms (RFLPs) using four restriction endonucleases and sixty clones chosen at random from a tomato cDNA library. Most of the cDNA clones (56) identified the same RFLP in VF 36 and LA1563 and a different RFLP in LA1028. However, two cDNA clones identified the same RFLP in LA1563 and LA1028 and a different RFLP in VF36. To determine whether RFLPs identified by these two cDNA clones were linked to SS genes, a H2038 x LA1563 F₂ population was screened for segregation of the RFLPs and for SS content. The segregation ratios of these RFLPs were consistent with ratios expected for codominant alleles at unlinked loci. Analysis of variance of SS content for different RFLP genotypic classes indicated that RFLP alleles at one of the loci were linked to genes controlling SS content. The RFLP allele from the high SS tomato line, LA1563, was associated with significantly higher SS content and, therefore, could be useful in selecting for high SS gene(s) in a tomato breeding program.     

A comparative analysis into the genetic bases of morphology in tomato varieties exhibiting elongated fruit shape

Fruit shape is a quantitatively inherited character. In tomato, two major loci, sun and ovate, control fruit shape index, which is the ratio of fruit height over width. In this study, we measured many additional fruit shape features in three inter-specific F₂ populations using the software application Tomato Analyzer. These populations were derived from varieties carrying elongated fruit but for which the major shape loci differed. We compared the effect of the major fruit shape loci with overall shape, as well as with the distal and proximal end shape features in each population. sun and ovate represented the largest effect on fruit shape in the Howard German and Sausage F₂ populations, respectively. The largest effect QTL in the Rio Grande population carrying neither sun nor ovate, were fs8.1 on chromosome 8 and tri2.1/dblk2.1 on chromosome 2. These latter loci were also segregating in the other two populations, thus indicating common regions that control shape across the three populations. The phenotypic analyses showed that sun and ovate contributed to almost all aspects of shape such as the distal and proximal end features. In Rio Grande however, the largest effect QTL did not control all aspects of shape and the distal and proximal features were distinctly controlled in that population. Combined, our results implied that within the cultivated tomato germplasm pool the largest effect on elongated fruit shape was controlled by a combination of the loci sun, ovate, fs8.1 and tri2.1/dblk2.1. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.