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.     

Mapping of two suppressors of OVATE (sov) loci in tomato

Tomato fruit shape varies significantly in the cultivated germplasm. To a large extent, this variation can be explained by four genes including OVATE. While most varieties with the OVATE mutation bear elongated fruits, some accessions carry round fruit, suggesting the existence of suppressors of OVATE in the germplasm. We developed three intraspecific F₂ populations with parents that carried the OVATE mutation but differed in fruit shape. We used a bulk segregant analysis approach and genotyped the extreme classes using a high-throughput genotyping platform, the SolCAP Infinium Assay. The analyses revealed segregation at two quantitative trait loci (QTLs), sov1 and sov2. These loci were confirmed by genotyping and QTL analyses of the entire population. More precise location of those loci using progeny testing confirmed that sov1 on chromosome 10 controlled obovoid and elongated shape, whereas sov2 on chromosome 11 controlled mainly elongated fruit shape. Both loci were located in intervals of <2.4 Mb on their respective chromosomes.     

Diallel analysis of production traits among domestic, exotic and mutant germplasms of Lycopersicon

The effects of wild germplasm on tomato fruit shelf life have not yet been completely evaluated. Three different genotypes of Lycopersicon esculentum (a cultivated variety, a homozygote for nor and a homozygote for rin), LA1385 of L. esculentum var. cerasiforme, LA722 of L. pimpinellifolium, and 10 diallel hybrids were assayed. Mean values of fruit shelf life, weight, shape, and mean number of flowers per cluster were analyzed after Griffing (1956, Aust. J. Biology 9: 463-493), method 2, model 1. Both general and specific combining abilities (GCA and SCA) were significant for the four traits. Negative unidirectional dominance was detected for fruit weight and shelf life, while bidirectional dominance was detected for fruit shape and mean number of flowers per cluster. SCA was greater than GCA for shelf life, so nonadditive effects predominantly accounted for this trait. In the heterozygous state, rin had smaller mean effects than nor. Wild accessions were able to prolong shelf life per se, and in crosses to the cultivated variety. The cross between the homozygote for nor and LA722 yielded the longest shelf life among hybrids.     

SUN regulates vegetative and reproductive organ shape by changing cell division patterns

One of the major genes controlling the elongated fruit shape of tomato (Solanum lycopersicum) is SUN. In this study, we explored the roles of SUN in vegetative and reproductive development using near isogenic lines (NILs) that differ at the sun locus, and SUN overexpressors in both the wild species LA1589 (Solanum pimpinellifolium) and the cultivar Sun1642 background. Our results demonstrate that SUN controls tomato shape through redistribution of mass that is mediated by increased cell division in the longitudinal and decreased cell division in the transverse direction of the fruit. The expression of SUN is positively correlated with slender phenotypes in cotyledon, leaflet, and floral organs, an elongated ovary, and negatively correlated with seed weight. Overexpression of SUN leads to more extreme phenotypes than those shown in the NILs and include thinner leaf rachises and stems, twisted leaf rachises, increased serrations of the leaflets, and dramatically increased elongation at the proximal end of the ovary and fruit. In situ hybridizations of the NILs showed that SUN is expressed throughout the ovary and young fruit, particularly in the vascular tissues and placenta surface, and in the ovules and developing seed. The phenotypic effects resulting from high expression of SUN suggest that the gene is involved in several plant developmental processes.     

Genomic variation in tomato,from wild ancestors to contemporary breeding accessions

Background

Domestication modifies the genomic variation of species. Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,008 tomato accessions including Solanum lycopersicum var. lycopersicum (SLL), S. lycopersicum var. cerasiforme (SLC), and S. pimpinellifolium (SP) that were genotyped using 7,720 SNPs. Additionally, we explored the allelic frequency of six loci affecting fruit weight and shape to infer patterns of selection.

Results

Our results revealed a pattern of variation that strongly supported a two-step domestication process, occasional hybridization in the wild, and differentiation through human selection. These interpretations were consistent with the observed allele frequencies for the six loci affecting fruit weight and shape. Fruit weight was strongly selected in SLC in the Andean region of Ecuador and Northern Peru prior to the domestication of tomato in Mesoamerica. Alleles affecting fruit shape were differentially selected among SLL genetic subgroups. Our results also clarified the biological status of SLC. True SLC was phylogenetically positioned between SP and SLL and its fruit morphology was diverse. SLC and “cherry tomato” are not synonymous terms. The morphologically-based term “cherry tomato” included some SLC, contemporary varieties, as well as many admixtures between SP and SLL. Contemporary SLL showed a moderate increase in nucleotide diversity, when compared with vintage groups.

Conclusions

This study presents a broad and detailed representation of the genomic variation in tomato. Tomato domestication seems to have followed a two step-process; a first domestication in South America and a second step in Mesoamerica. The distribution of fruit weight and shape alleles supports that domestication of SLC occurred in the Andean region. Our results also clarify the biological status of SLC as true phylogenetic group within tomato. We detect Ecuadorian and Peruvian accessions that may represent a pool of unexplored variation that could be of interest for crop improvement.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1444-1) contains supplementary material, which is available to authorized users.     

Phylogenetic analyses provide the first insights into the evolution of OVATE family proteins in land plants

Background and Aims

The OVATE gene encodes a nuclear-localized regulatory protein belonging to a distinct family of plant-specific proteins known as the OVATE family proteins (OFPs). OVATE was first identified as a key regulator of fruit shape in tomato, with nonsense mutants displaying pear-shaped fruits. However, the role of OFPs in plant development has been poorly characterized.

Methods

Public databases were searched and a total of 265 putative OVATE protein sequences were identified from 13 sequenced plant genomes that represent the major evolutionary lineages of land plants. A phylogenetic analysis was conducted based on the alignment of the conserved OVATE domain from these 13 selected plant genomes. The expression patterns of tomato SlOFP genes were analysed via quantitative real-time PCR. The pattern of OVATE gene duplication resulting in the expansion of the gene family was determined in arabidopsis, rice and tomato.

Key Results

Genes for OFPs were found to be present in all the sampled land plant genomes, including the early-diverged lineages, mosses and lycophytes. Phylogenetic analysis based on the amino acid sequences of the conserved OVATE domain defined 11 sub-groups of OFPs in angiosperms. Different evolutionary mechanisms are proposed for OVATE family evolution, namely conserved evolution and divergent expansion. Characterization of the AtOFP family in arabidopsis, the OsOFP family in rice and the SlOFP family in tomato provided further details regarding the evolutionary framework and revealed a major contribution of tandem and segmental duplications towards expansion of the OVATE gene family.

Conclusions

This first genome-wide survey on OFPs provides new insights into the evolution of the OVATE protein family and establishes a solid base for future functional genomics studies on this important but poorly characterized regulatory protein family in plants.     

Morphological variation and evolutionary significance of <Emphasis Type="Italic">Coccinia grandis</Emphasis> (L.) Voigt: an under-exploited cucurbitaceous vegetable crop

Morphological variation was analyzed in wild accessions and cultivars of the vegetatively propagated dioecious Coccinia grandis. Variations of 43 morphological characters, 19 qualitative and 23 quantitative traits, were analyzed among 40 female accessions, including 25 cultivars and 15 wild accessions. Multivariate statistical analyses were used to group accessions according to their morphological similarity. Principal component (PC) analysis revealed that the first three PCs accounted for 50% of the total variance, and differences among the accessions were evidenced principally in relation to fruit characteristics such as fruit weight, fruit length and the number of seeds in each fruit. Analysis of variance carried out in the entire germplasm revealed significant differences within the germplasm, whereas ANOVA carried out between the wild accessions and the cultivars proved the null hypothesis that there are no significant differences between the two groups, and differences were observed only in fruit characters that are targets of human selection. Principal component analysis, UPGMA cluster analysis and discriminant factor analysis revealed strong overlaps between the two groups indicating the ongoing process of evolution and selection in the 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.     

Fruit Development, Ripening and Quality Related Genes in the Papaya Genome

Papaya (Carica papaya L.) is the first fleshy fruit with a climacteric ripening pattern to be sequenced. As a member of the Rosids superorder in the order Brassicales, papaya apparently lacks the genome duplication that occurred twice in Arabidopsis. The predicted papaya genes that are homologous to those potentially involved in fruit growth, development, and ripening were investigated. Genes homologous to those involved in tomato fruit size and shape were found. Fewer predicted papaya expansin genes were found and no Expansin Like-B genes were predicted. Compared to Arabidopsis and tomato, fewer genes that may impact sugar accumulation in papaya, ethylene synthesis and response, respiration, chlorophyll degradation and carotenoid synthesis were predicted. Similar or fewer genes were found in papaya for the enzymes leading to volatile production than so far determined for tomato. The presence of fewer papaya genes in most fruit development and ripening categories suggests less subfunctionalization of gene action. The lack of whole genome duplication and reductions in most gene families and biosynthetic pathways make papaya a valuable and unique tool to study the evolution of fruit ripening and the complex regulatory networks active in fruit ripening.     

Genetic relationships and evolution in <Emphasis Type="Italic">Cucurbita pepo</Emphasis> (pumpkin,squash, gourd) as revealed by simple sequence repeat polymorphisms

Genetic relationships among 104 accessions of Cucurbita pepo were assessed from polymorphisms in 134 SSR (microsatellite) and four SCAR loci, yielding a total of 418 alleles, distributed among all 20 linkage groups. Genetic distance values were calculated, a dendrogram constructed, and principal coordinate analyses conducted. The results showed 100 of the accessions as distributed among three clusters representing each of the recognized subspecies, pepo, texana, and fraterna. The remaining four accessions, all having very small, round, striped fruits, assumed central positions between the two cultivated subspecies, pepo and texana, suggesting that they are relicts of undescribed wild ancestors of the two domesticated subspecies. In both, subsp. texana and subsp. pepo, accessions belonging to the same cultivar-group (fruit shape) associated with one another. Within subsp. pepo, accessions grown for their seeds or that are generalists, used for both seed and fruit consumption, assumed central positions. Specialized accessions, grown exclusively for consumption of their young fruits, or their mature fruit flesh, or seed oil extraction, tended to assume outlying positions, and the different specializations radiated outward from the center in different directions. Accessions of the longest-fruited cultivar-group, Cocozelle, radiated bidirectionally, indicating independent selection events for long fruits in subsp. pepo probably driven by a common desire to consume the young fruits. Among the accessions tested, there was no evidence for crossing between subspecies after domestication.     

Tomato genetic resources and activities in Poland

The vegetables germplasm conservation programme in Poland was started in 1982, activities under this program resulted up to this date in building up a tomato germplasm collection of 782 accessions that are available for distribution to breeders and researchers in Poland and abroad. Between 1990 and 1999 we distributed 651 tomato seed samples to breeders and scientists in Poland, and 95 samples to users abroad. During 1990 – 1999 the 652 tomato accessions were evaluated for 43 traits of plants and fruits. Work is in progress to expand the collection and identify useful characteristics of the collected material, and to make use of them in breeding and other research works.     

Conservation of gene function in the solanaceae as revealed by comparative mapping of domestication traits in eggplant

Quantitative trait loci (QTL) for domestication-related traits were identified in an interspecific F(2) population of eggplant (Solanum linnaeanum x S. melongena). Although 62 quantitative trait loci (QTL) were identified in two locations, most of the dramatic phenotypic differences in fruit weight, shape, color, and plant prickliness that distinguish cultivated eggplant from its wild relative could be attributed to six loci with major effects. Comparison of the genomic locations of the eggplant fruit weight, fruit shape, and color QTL with the positions of similar loci in tomato, potato, and pepper revealed that 40% of the different loci have putative orthologous counterparts in at least one of these other crop species. Overall, the results suggest that domestication of the Solanaceae has been driven by mutations in a very limited number of target loci with major phenotypic effects, that selection pressures were exerted on the same loci despite the crops' independent domestications on different continents, and that the morphological diversity of these four crops can be explained by divergent mutations at these loci.     

Tomato TILLING technology: development of a reverse genetics tool for the efficient isolation of mutants from Micro-Tom mutant libraries

To accelerate functional genomic research in tomato, we developed a Micro-Tom TILLING (Targeting Induced Local Lesions In Genomes) platform. DNA pools were constructed from 3,052 ethyl methanesulfonate (EMS) mutant lines treated with 0.5 or 1.0% EMS. The mutation frequency was calculated by screening 10 genes. The 0.5% EMS population had a mild mutation frequency of one mutation per 1,710 kb, whereas the 1.0% EMS population had a frequency of one mutation per 737 kb, a frequency suitable for producing an allelic series of mutations in the target genes. The overall mutation frequency was one mutation per 1,237 kb, which affected an average of three alleles per kilobase screened. To assess whether a Micro-Tom TILLING platform could be used for efficient mutant isolation, six ethylene receptor genes in tomato (SlETR1-SlETR6) were screened. Two allelic mutants of SlETR1 (Sletr1-1 and Sletr1-2) that resulted in reduced ethylene responses were identified, indicating that our Micro-Tom TILLING platform provides a powerful tool for the rapid detection of mutations in an EMS mutant library. This work provides a practical and publicly accessible tool for the study of fruit biology and for obtaining novel genetic material that can be used to improve important agronomic traits in tomato.     

CHLOROPLAST DNA POLYMORPHISM SUGGESTS NIGERIAN CENTER OF DOMESTICATION FOR THE COWPEA,VIGNA UNGUICULATA (LEGUMINOSAE)

Twenty-one independent chloroplast DNA polymorphisms were identified in Vigna unguiculata defining 19 different chloroplast DNA molecules (plastome types). Two plastome types, differing by a single character, were found among 32 accessions of cultivated cowpea (Vigna unguiculata ssp. unguiculata). Eighteen different plastome types were found among 26 accessions of wild cowpea (V. unguiculata ssp. dekindtiana). The very low level of chloroplast DNA diversity found in cultivated accessions relative to wild cowpea suggests that 1) the domesticated form was derived from a narrow selection of the wild germplasm and 2) chloroplast gene flow between wild and cultivated types has been very limited. Cladistic analysis of the cpDNA data generated a robust tree completely lacking homoplasy. Three wild accessions from Nigeria possessed a plastome type indistinguishable from one present in cultivated accessions, suggesting that Nigeria represents one center of domestication of the cowpea. The other plastome type within the cultivated germplasm was not found among wild accessions.     

Light signaling genes and their manipulation towards modulation of phytonutrient content in tomato fruits

Due to its economic importance, ease of genetic manipulation, cultivation and processing, the tomato plant has been a target for increasing and diversifying content of fruit phytonutrients by transgenic and non-transgenic approaches. The tomato high pigment (hp) mutations exemplify the latter alternative and due to their positive effect on fruit lycopene content, they were introgressed into elite tomato germplasm for cost effective extraction of this important carotenoid. Interestingly, hp mutant fruits are also characterized by higher fruit levels of other functional metabolites, phenotypes caused by mutations in central genes regulating light signal-transduction. This gene identification suggests that modulation of light signaling machinery in plants may be highly effective towards manipulation of fruit phytonutrients but has never been thoroughly reviewed. This review therefore summarizes the progress which has been made on this valuable approach, emphasizing the consequences of transgenic modulation of light signaling components on the functional properties of the tomato fruit.     

Integration of tomato reproductive developmental landmarks and expression profiles, and the effect of SUN on fruit shape

Background  

Universally accepted landmark stages are necessary to highlight key events in plant reproductive development and to facilitate comparisons among species. Domestication and selection of tomato resulted in many varieties that differ in fruit shape and size. This diversity is useful to unravel underlying molecular and developmental mechanisms that control organ morphology and patterning. The tomato fruit shape gene SUN controls fruit elongation. The most dramatic effect of SUN on fruit shape occurs after pollination and fertilization although a detailed investigation into the timing of the fruit shape change as well as gene expression profiles during critical developmental stages has not been conducted.