Quantitative trait locus analysis in crosses between outbred lines with dominance and inbreeding

In an effort to determine the genetic basis of exceptionally large tomato fruits, QTL analysis was performed on a population derived from a cross between the wild species Lycopersicon pimpinellifolium (average fruit weight, 1 g) and the L. esculentum cultivar var. Giant Heirloom, which bears fruit in excess of 1000 g. QTL analysis revealed that the majority (67%) of phenotypic variation in fruit size could be attributed to six major loci localized on chromosomes 1-3 and 11. None of the QTL map to novel regions of the genome-all have been reported in previous studies involving moderately sized tomatoes. This result suggests that no major QTL beyond those already reported were involved in the evolution of extremely large fruit. However, this is the first time that all six QTL have emerged in a single population, suggesting that exceptionally large-fruited varieties, such as Giant Heirloom, are the result of a novel combination of preexisting QTL alleles. One of the detected QTL, fw2.2, has been cloned and exerts its effect on fruit size through global control of cell division early in carpel/fruit development. However, the most significant QTL detected in this study (fw11.3, lcn11.1) maps to the bottom of chromosome 11 and seems to exert its effect on fruit size through control of carpel/locule number. A second major locus, also affecting carpel number (and hence fruit size), was mapped to chromosome 2 (fw2.1, lcn2.1). We propose that these two carpel number QTL correspond to the loci described by early classical geneticists as fasciated (f) and locule number (lc), respectively.     

QTLs mapping for fruit size and shape in chromosomes 2 and 4 in pepper and a comparison of the pepper QTL map with that of tomato

Quantitative trait locus (QTL) mapping for fruit weight and shape in pepper (Capsicum spp.) was performed using C. chinense and C. frutescens introgression lines of chromosomes 2 and 4. In chromosome 2, a single major fruit-weight QTL, fw2.1, was detected in both populations that explained 62% of the trait variation. This QTL, as well as a fruit-shape QTL, fs2.1, which had a more minor effect, were localized to the tomato fruit-shape gene ovate. The cloned tomato fruit-weight QTL, fw2.2, did not play a major role in controlling fruit size variations in pepper. In chromosome 4, two fruit-weight QTLs, fw4.1 and fw4.2, were detected in the same genomic regions in both mapping populations. In addition, a single fruit-shape QTL was detected in each of the mapping populations that co-localized with one of the fruit-weight QTLs, suggesting pleiotropy or close linkage of the genes controlling size and shape. fw2.1 and fw4.2 represent major fruit-weight QTLs that are conserved in the three Capsicum species analyzed to date for fruit-size variations. Co-localization of the pepper QTLs with QTLs identified for similar traits in tomato suggests that the pepper and tomato QTLs are orthologous. Compared to fruit-shape QTLs, fruit-weight QTLs were more often conserved between pepper and tomato. This implies that different modes of selection were employed for these traits during domestication of the two Solanaceae species.S. Zygier and A. Ben Chaim contributed equally to this work.     

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.     

fw2.2 directly affects the size of developing tomato fruit, with secondary effects on fruit number and photosynthate distribution

fw2.2 is a quantitative trait locus responsible for approximately 30% of the difference in fruit size between large, domesticated tomatoes (Lycopersicon esculentum Mill.) and their small-fruited wild relatives. The gene underlying this quantitative trait locus was cloned recently and shown to be associated with altered cell division in ovaries (Frary et al., 2000). However, it was not known whether the change in fruit size is associated with other changes in plant morphology or overall fruit yield-changes that could potentially cause the fruit weight phenotype. To shed light on this issue, a detailed comparison was made between nearly isogenic lines differing for alleles at this locus to search for pleiotropic effects associated with fw2.2. Field observations show that although the small-fruited nearly isogenic line produced smaller ovaries and fruit as expected, this was compensated by a larger number of fruit-due mainly to a significantly greater number of inflorescences-but with no net change in total fruit mass yield. This strongly suggests that fw2.2 may have a pleiotropic effect on how the plant distributes photosynthate among fruit. In a flower removal experiment to control for differences in inflorescence size and number, fruit size remained significantly different between the nearly isogenic lines. These observations indicate that the primary effect of fw2.2 is in controlling ovary and fruit size, and that other associated phenotypic effects are secondary.     

Evaluating the genetic basis of multiple-locule fruit in a broad cross section of tomato cultivars

Lycopersicon esculentum accessions bearing fasciated (multiloculed) fruit were characterized based on their flower organ and locule number phenotypes. Greenhouse and field evaluations indicate that increases in locule number are associated with increases in the number of other floral organs (e.g., sepals, petals, stamens) in all stocks. F₁ complementation, F₂ segregation analysis, and genetic mapping indicate that at least four loci account for increases in the number of carpels/locules in these stocks. The most significant of these map to the bottoms of chromosomes 2 and 11 and correspond to the locule number and fasciated loci. All stocks tested were fixed for mutations at the fasciated locus, which maps to the 0.5-cM interval between the markers T302 and cLET24J2A and occurs in at least three allelic forms (wild type and two mutants). One of the fasciated mutant alleles is associated with nonfused carpels and repressed recombination and may be due to a small inversion or deletion. The other two loci controlling locule number correspond to the lcn1.1 and lcn2.2 loci located on chromosomes 1 and 2, respectively.     

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.     

QTL analysis of morphological traits in eggplant and implications for conservation of gene function during evolution of solanaceous species

An interspecific F(2) population from a cross between cultivated eggplant, Solanum melongena, and its wild relative, S. linnaeanum, was analyzed for quantitative trait loci (QTL) affecting leaf, flower, fruit and plant traits. A total of 58 plants were genotyped for 207 restriction fragment length polymorphism (RFLP) markers and phenotyped for 18 characters. One to eight loci were detected for each trait with a total of 63 QTL identified. Overall, 46% of the QTL had allelic effects that were the reverse of those predicted from the parental phenotypes. Wild alleles that were agronomically superior to the cultivated alleles were identified for 42% of the QTL identified for flowering time, flower and fruit number, fruit set, calyx size and fruit glossiness. Comparison of the map positions of eggplant loci with those for similar traits in tomato, potato and pepper revealed that 12 of the QTL have putative orthologs in at least one of these other species and that putative orthology was most often observed between eggplant and tomato. Traits showing potential orthology were: leaf length, shape and lobing; days to flowering; number of flowers per inflorescence; plant height and apex, leaf and stem hairiness. The functionally conserved loci included a major leaf lobing QTL ( llob6.1) that is putatively orthologous to the potato leaf ( c) and/or Petroselinum ( Pts) mutants of tomato, two flowering time QTL ( dtf1.1, dtf2.1) that also have putative counterparts in tomato and four QTL for trichomes that have potential orthologs in tomato and potato. These results support the mounting evidence of conservation of gene function during the evolution of eggplant and its relatives from their last common ancestor and indicate that this conservation was not limited to domestication traits.     

Characterization offs8.1, a major QTL influencing fruit shape in tomato

In two previous quantitative trait locus (QTL) mapping studies conducted inLycopersicon esculentum x L. pimpinellifolium BC₁ and BC₂ populations we had localized a major QTL for fruit shape,fs8.1, to a ca. 20 cM interval on the short arm of chromosome 8, flanked by markers TG176 and CT92. At this QTL the allele from the wild species reduces the length of fruit, giving round-shaped fruit. In order to define more precisely the location offs8.1, near-isogenic lines (NILs) segregating for the region of interest were developed. The results from substitution mapping show that no recombination occurred betweenfs8.1 and the marker CD40 in 322 meioses. The gene action forfs8.1 was determined in a BC₄F₃ population to be partial dominance. The main effect offs8.1 is exerted on fruit length while fruit diameter is not significantly affected. A highly significant correlation (r=0.89;P<0.01) was found between fruit shape and ovary shape indicating that thefs8.1 gene product acts early in ovary development (preanthesis). Implications for the evolution of fruit shape and the feasibility of map-based cloning of this QTL are discussed.     

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.     

fw 2.2:a major QTL controlling fruit weight is common to both red- and green-fruited tomato species

We have shown that a major QTL for fruit weight (fw2.2) maps to the same position on chromosome 2 in the green-fruited wild tomato species, Lycopersicon pennellii and in the red-fruited wild tomato species, L. pimpinellifolium. An introgression line F₂ derived from L. esculentum (tomato) x L. pennellii and a backcross 1 (BC₁) population derived from L. esculentum x L. pimpinellifolium both place fw2.2 near TG91 and TG167 on chromosome 2 of the tomato highdensity linkage map. fw2.2 accounts for 30% and 47% of the total phenotypic variance in the L. pimpinellifolium and L. pennellii populations, respectively, indicating that this is a major QTL controlling fruit weight in both species. Partial dominance (d/a of 0.44) was observed for the L. pennellii allele of fw 2.2 as compared with the L. esculentum allele. A QTL with very similar phenotypic affects and gene action has also been identified and mapped to the same chromosomal region in other wild tomato accessions: L. cheesmanii and L. pimpinellifolium. Together, these data suggest that fw2.2 represents an orthologous QTL (i.e., derived by speciation as opposed to duplication) common to most, if not all, wild tomato species. High-resolution mapping may ultimately lead to the cloning of this key locus controlling fruit development in tomato.     

fs8.1, a major QTL, sets the pattern of tomato carpel shape well before anthesis

fs8.1 is a major fruit-shape QTL differentiating fresh-market and processing tomatoes. Mature fruits from plants with the wild-type fresh-market alleles are round, whereas those with alleles from processing variety E6203 are elongated (sometimes referred to as blocky or square tomatoes). Fine mapping was undertaken to determine whether the effect is due to a single gene or several tightly linked genes. RAPD and RFLP linkage analysis, and substitution mapping of nearly isogenic lines (NILs) segregating for the 22.8 cM-TG176-CT92 interval at the top of chromosome 8 in tomato were used for high-resolution mapping. For the 1212 gametes screened in F₂ and F₃ families, it was determined that fs8.1 maps as a single locus near the centromere of chromosome 8. A comparative developmental study of fs8.1 NILs revealed that fs8.1 alleles exert their effects on fruit shape early in carpel development at least 6 days before anthesis. Field evaluations of the NILs indicate that fs8.1 affects not only fruit shape, fruit length, and fruit weight but also the number of flowers and fruits per inflorescence, and the harvest index. The date of first flower and fruit diameter were not significantly affected. Received: 19 July 1999 / Accepted: 16 December 1999     

Fine mapping of QTLs of chromosome 2 affecting the fruit architecture and composition of tomato

Negative correlations between quality traits and fruit size may hamper the breeding of fresh market tomato varieties for better organoleptic qualities. In a recent QTL analysis, QTLs with large effects on fruit weight, locule number and several quality traits were detected in the distal 50 cM of chromosome 2, but favorable alleles for fruit weight and locule number were unfavorable to quality traits. Substitution mapping was undertaken to determine whether the effects were due to a single QTL or to several tightly linked QTLs. Several chromosomal segments were characterized using near-isogenic lines. Five of them appeared to be involved in one or several traits. Considering the five segments from the top to the bottom of the region, the QTLs detected in each segment controlled the variation of: (1) fruit weight, (2) soluble solids content and dry matter weight, (3) fruit weight, (4) locule number and (5) fruit weight, dry matter weight, total sugars, titratable acidity and soluble solids content. This last cluster illustrates an antagonism between fruit weight and four quality traits, as favorable alleles are not conferred by the same parent in both cases. Nevertheless, several antagonistic QTLs were separated from each other in the first four segments, holding the promise for marker-assisted improvement of fruit quality traits without compromising the fruit size.     

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.     

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.     

Developmental characterization of the fasciated locus and mapping of Arabidopsis candidate genes involved in the control of floral meristem size and carpel number in tomato.

Mutation at the fasciated locus was a key step in the production of extreme fruit size during tomato domestication. To shed light on the nature of these changes, near-isogenic lines were used for a comparative developmental study of fasciated and wild-type tomato plants. The fasciated gene directly affects floral meristem size and is expressed before the earliest stages of flower organogenesis. As a result, mature fruit of fasciated mutants have more carpels (locules) and greater fruit diameter and mass. The discovery that fasciated affects floral meristem size led to a search for candidate genes from Arabidopsis known to be involved in floral meristem development. Putative homologs were identified in a large tomato EST database, verified through phylogenetic analyses, and mapped in tomato; none mapped to the fasciated locus; however, putative homologs of WUS and WIG mapped to the locule number locus on chromosome 2, the second major transition to large tomato fruit, with WUS showing the highest association. In other cases, minor QTLs for floral organ number (lcn2.2) and (stn11.2) co-localized with a CLV1 paralog and with the syntenic region containing the CLV3 gene in Arabidopsis, respectively.     

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     

Genetic and molecular regulation of fruit and plant domestication traits in tomato and pepper

Tomato and pepper are two Solanaceous fruit crops that display an enormous diversity in fruit morphology. In this review, we will present an overview of the history of tomato and pepper and discuss key plant traits that were specifically selected during domestication of the two species. The traits discussed are fruit weight, shape, colour, ripening, pungency and plant architecture. We will review these characteristics as well as the genetic loci or genes that control these features, questioning whether mutations at orthologous loci occurred independently in these two species or whether unique plant and fruit features resulted in selection at different genes.     

Both additivity and epistasis control the genetic variation for fruit quality traits in tomato

The effect of a gene involved in the variation of a quantitative trait may change due to epistatic interactions with the overall genetic background or with other genes through digenic interactions. The classical populations used to map quantitative trait loci (QTL) are poorly efficient to detect epistasis. To assess the importance of epistasis in the genetic control of fruit quality traits, we compared 13 tomato lines having the same genetic background except for one to five chromosome fragments introgressed from a distant line. Six traits were assessed: fruit soluble solid content, sugar content and titratable acidity, fruit weight, locule number and fruit firmness. Except for firmness, a large part of the variation of the six traits was under additive control, but interactions between QTL leading to epistasis effects were common. In the lines cumulating several QTL regions, all the significant epistatic interactions had a sign opposite to the additive effects, suggesting less than additive epistasis. Finally the re-examination of the segregating population initially used to map the QTL confirmed the extent of epistasis, which frequently involved a region where main effect QTL have been detected in this progeny or in other studies.