Complex migration history is revealed by genetic diversity of tomato samples collected in Italy during the eighteenth and nineteenth centuries.

Native to South America, the tomato is now grown almost worldwide. During its domestication and improvement, important selection signatures were fixed in certain agronomic and adaption traits. Such traits include fruit morphology, which became a major target for selection over the centuries. However, little is known about precisely when some mutations arose and how they spread through the germplasm. For instance, elongated fruit variants, originating both via mutations in SUN and OVATE genes, may have arisen prior to domestication or during tomato cultivation in Europe. To gain insights into the tomato admixture and selection pattern, the genome of two tomato herbarium specimens conserved in the Herbarium Porticense (PORUN) was sequenced. Comparison of the DNA of herbarium samples collected in Italy between 1750 and 1890 with that of living tomato accessions yielded insights into the history of tomato loci selection. Interestingly, the genotype of the more recent sample (LEO90), classified in 1890 as the oblungum variety, shows several private variants in loci implicated in fruit shape determination, also present also in wild tomato samples. In addition, LEO90, sampled in the nineteenth century, is genetically more distant from cultivated varieties than the SET17 genotype, collected in the eighteenth century, suggesting that elongated tomato varieties may originate from a cross between a landrace and a wild ancestor. Findings from our study have major implications for the understanding of tomato migration patterns and for the conservation of allelic diversity and loci recovery.

Exploring tomato Solanum pennellii introgression lines for residual biomass and enzymatic digestibility traits.

BACKGROUND: Residual biomass production for fuel conversion represents a unique opportunity to avoid concerns about compromising food supply by using dedicated feedstock crops. Developing tomato varieties suitable for both food consumption and fuel conversion requires the establishment of new selection methods. RESULTS: A tomato Solanum pennellii introgression population was assessed for fruit yield, biomass phenotypic diversity, and for saccharification potential. Introgression lines 2-5, 2-6, 6-3, 7-2, 10-2 and 12-4 showed the best combination of fruit and residual biomass production. Lignin, cellulose, hemicellulose content and saccharification rate showed a wide variation in the tested lines. Within hemicellulose, xylose value was high in IL 6-3, IL 7-2 and IL 6-2, whereas arabinose showed a low content in IL 10-2, IL 6-3 and IL 2-6. The latter line showed also the highest ethanol potential production. Alkali pre-treatment resulted in the highest values of saccharification in most of lines tested, suggesting that chemical pretreatment is an important factor for improving biomass processability. Interestingly, extreme genotypes for more than one single trait were found, allowing the identification of better genotypes. Cell wall related genes mapping in genomic regions involved into tomato biomass production and digestibility variation highlighted potential candidate genes. Molecular expression profile of few of them provided useful information about challenged pathways. CONCLUSIONS: The screening of S. pennellii introgression population resulted very useful for delving into complex traits such as biomass production and digestibility. The extreme genotypes identified could be fruitfully employed for both genetic studies and breeding.

Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics.

To investigate the genome-wide spatial arrangement of R loci, a complete catalogue of tomato (Solanum lycopersicum) and potato (Solanum tuberosum) nucleotide-binding site (NBS) NBS, receptor-like protein (RLP) and receptor-like kinase (RLK) gene repertories was generated. Candidate pathogen recognition genes were characterized with respect to structural diversity, phylogenetic relationships and chromosomal distribution. NBS genes frequently occur in clusters of related gene copies that also include RLP or RLK genes. This scenario is compatible with the existence of selective pressures optimizing coordinated transcription. A number of duplication events associated with lineage-specific evolution were discovered. These findings suggest that different evolutionary mechanisms shaped pathogen recognition gene cluster architecture to expand and to modulate the defence repertoire. Analysis of pathogen recognition gene clusters associated with documented resistance function allowed the identification of adaptive divergence events and the reconstruction of the evolution history of these loci. Differences in candidate pathogen recognition gene number and organization were found between tomato and potato. Most candidate pathogen recognition gene orthologues were distributed at less than perfectly matching positions, suggesting an ongoing lineage-specific rearrangement. Indeed, a local expansion of Toll/Interleukin-1 receptor (TIR)-NBS-leucine-rich repeat (LRR) (TNL) genes in the potato genome was evident. Taken together, these findings have implications for improved understanding of the mechanisms of molecular adaptive selection at Solanum R loci.

A novel synthetic peptide from a tomato defensin exhibits antibacterial activities against Helicobacter pylori.

Defensins are a class of cysteine-rich proteins, which exert broad spectrum antimicrobial activity. In this work, we used a bioinformatic approach to identify putative defensins in the tomato genome. Fifteen proteins had a mature peptide that includes the well-conserved tetradisulfide array. We selected a representative member of the tomato defensin family; we chemically synthesized its γ-motif and tested its antimicrobial activity. Here, we demonstrate that the synthetic peptide exhibits potent antibacterial activity against Gram-positive bacteria, such as Staphylococcus aureus A170, Staphylococcus epidermidis, and Listeria monocytogenes, and Gram-negative bacteria, including Salmonella enterica serovar Paratyphi, Escherichia coli, and Helicobacter pylori. In addition, the synthetic peptide shows minimal (<5%) hemolytic activity and absence of cytotoxic effects against THP-1 cells. Finally, SolyC exerts an anti-inflammatory activity in vitro, as it downregulates the level of the proinflammatory cytokines TNF-α and IFN-γ.

Genetic and genomic approaches for R-gene mediated disease resistance in tomato: retrospects and prospects.

Tomato (Solanum lycopersicum) is one of the world's most important vegetable crops. Managing the health of this crop can be particularly challenging; crop resistance may be overcome by new pathogen races while new pathogens have been introduced by global agricultural markets. Tomato is extensively used as a model plant for resistance studies and much has been attained through both genetic and biotechnological approaches. In this paper, we illustrate genomic methods currently employed to preserve resistant germplasm and to facilitate the study and transfer of resistance genes, and we describe the genomic organization of R-genes. Patterns of gene activation during disease resistance response, identified through functional approaches, are depicted. We also describe the opportunities offered by the use of new genomic technologies, including high-throughput DNA sequencing, large-scale expression data production and the comparative hybridization technique, whilst reporting multifaceted approaches to achieve genetic tomato disease control. Future strategies combining the huge amount of genomic and genetic data will be able to accelerate development of novel resistance varieties sustainably on a worldwide basis. Such strategies are discussed in the context of the latest insights obtained in this field.

High-throughput genomics enhances tomato breeding efficiency.

Tomato (Solanum lycopersicum) is considered a model plant species for a group of economically important crops, such as potato, pepper, eggplant, since it exhibits a reduced genomic size (950 Mb), a short generation time, and routine transformation technologies. Moreover, it shares with the other Solanaceous plants the same haploid chromosome number and a high level of conserved genomic organization. Finally, many genomic and genetic resources are actually available for tomato, and the sequencing of its genome is in progress. These features make tomato an ideal species for theoretical studies and practical applications in the genomics field. The present review describes how structural genomics assist the selection of new varieties resistant to pathogens that cause damage to this crop. Many molecular markers highly linked to resistance genes and cloned resistance genes are available and could be used for a high-throughput screening of multiresistant varieties. Moreover, a new genomics-assisted breeding approach for improving fruit quality is presented and discussed. It relies on the identification of genetic mechanisms controlling the trait of interest through functional genomics tools. Following this approach, polymorphisms in major gene sequences responsible for variability in the expression of the trait under study are then exploited for tracking simultaneously favourable allele combinations in breeding programs using high-throughput genomic technologies. This aims at pyramiding in the genetic background of commercial cultivars alleles that increase their performances. In conclusion, tomato breeding strategies supported by advanced technologies are expected to target increased productivity and lower costs of improved genotypes even for complex traits.

Assessment of genetic variability of haploids extracted from tetraploid (2n = 4x = 48) Solanum tuberosum.

The objectives of this study were to assess the genetic variability of haploids (2n = 2x = 24) extracted from tetraploid Solanum tuberosum through 4x x 2x crosses with Solanum phureja. Molecular and phenotypic analyses were performed to fingerprint the genotypes used and to evaluate their potential use in breeding programs. AFLP analysis revealed the presence of specific bands derived from the tetraploid seed parent S. phureja, as well as ex novo originated bands. On average, 210 bands were visualized per genotype, 149 (70%) of which were common to both parental genotypes. The percentage of S. tuberosum specific bands ranged from 25.1% to 18.6%, with an average of 22%. The fraction of genome coming from S. phureja ranged from 1.9% to 6.5%, with an average value of 4%. The percentage of ex novo bands varied from 1.9% to 9.0%. The presence of S. phureja DNA is very interesting because it indicated that S. phureja pollinator is involved in the mechanism of haploid formation. The characterization for resistance to Erwinia carotovora subsp. carotovora and potato virus X (PVX) provided evidence that haploids may express traits that are lacking in the tetraploids they come from, which can be useful for both genetic studies and breeding purposes. It is noteworthy that genotypes combining resistance to both diseases and good pollen stainability were identified. Other possible breeding implications owing to the presence of S. phureja genome in the haploids analyzed are discussed.

Selection for aneuploid potato hybrids combining a low wild genome content and resistance traits from Solanum commersonii.

A breeding scheme based on the production of progenies with odd ploidy was followed to introduce useful genes from the wild Solanum commersonii (cmm) into S. tuberosum (tbr) genome. Hybrids from 5 x x 4 x crosses were characterized for traits of interest, and selection was assisted by amplified fragment length polymorphism (AFLP) analysis. As expected, most of the hybrids were aneuploids, with a trend towards a low degree of aneuploidy. Despite the fact that aneuploidy has often been associated with a reduction in male and female fertility, most of the hybrids were fertile following crosses with tbr, making it possible to produce viable offspring. A screening for resistance traits deriving from cmm was also carried out. With respect to freezing resistance, the killing temperatures of cold-acclimated genotypes were distributed between the wild and cultivated parental values, with some hybrids displaying an acclimation capacity higher than 3 degrees C. A wide variability was also found for tuber soft rot resistance, and hybrids with high levels of resistance were identified. Selection of hybrids was based on a two-stage scheme that consisted of conventional phenotypic selection followed by an estimation of the wild genome content still present in order to identify hybrids combining noteworthy traits with a low wild genome content. Previously selected cmm-specific AFLPs were used to monitor the degree of wild genome content still present in each hybrid. The percentage of cmm-specific markers ranged from 59% to 91%, with an average value of 75%. AFLP analysis was employed to assist in the selection of valuable hybrids for further breeding efforts.

Glycoalkaloids and acclimation capacity of hybrids between Solanum tuberosum and the incongruent hardy species Solanum commersonii.

F(1) and backcross hybrids between sexually incompatible species Solanum commersonii and Solanum tuberosum were characterized for glycoalkaloid content and capacity to cold acclimate. Glycoalkaloid (GA) analysis revealed that F(1) triploids and BC(1) pentaploids contained the glycoalkaloids of both parents. In BC(2) (near) tetraploids the situation was different, in that some hybrids produced the GAs of both parents, whereas others contained only the GAs of S. tuberosum. This suggested that the GAs from S. commersonii may be lost rapidly, and that they may have a simple genetic control. The total tuber GA content of BC(1) and BC(2) groups averaged quite acceptable levels (165.9 mg/kg in BC(1) and 192.8 mg/kg in BC(2)), with six genotypes having a GA content <200 mg/kg fresh weight. The F(1) triploid hybrids expressed a capacity to cold acclimate similar to S. commersonii, whereas BC(1) and BC(2) genotypes generally displayed an acclimation capacity higher than the sensitive parent but lower than S. commersonii. However, one BC(1) and two BC(2) genotypes with an acclimation capacity as high as S. commersonii were identified. The polar lipid fatty acid composition in S. commersonii and its hybrid derivatives showed that, following acclimation, there was a significant increase in 18:3. Correlation analysis between the capacity to cold acclimate and the increase in 18:3 was significant, suggesting that the increase in 18:3 can be used as a biochemical marker for the assisted selection of cold-acclimating genotypes in segregating populations.

Evidence for tetrasomic inheritance in a tetraploid Solanum commersonii (+) S. tuberosum somatic hybrid through the use of molecular markers.

In order to assess the potential for interspecific recombination between the cultivated Solanum tuberosum (tbr) and the sexually isolated wild species Solanum commersonii(cmm), genetic analysis of a F(2) progeny obtained by selfing one tetraploid cmm (+) tbr somatic hybrid was performed through molecular markers. For this purpose, the extent of disomic and/or tetrasomic inheritance of species-specific RAPD and AFLP markers was determined by following their segregation in a 90-genotype progeny, and testing all the possible segregation ratios in a selfed tetraploid progeny. The RAPD analysis performed using 16 primers revealed that the cmm-specific RAPDs were mainly (93.7%) duplex markers and were equally distributed between loci with a disomic (46.7%) and tetrasomic (53.3%) inheritance. The AFLP analysis led to the identification of 272 (58%) informative AFLPs, which were either cmm- or tbr-specific markers. About 63% of cmm-specific AFLPs were duplex loci, most of which (92.6%) were inherited as tetrasomic loci. As regards the tbr-specific AFLPs, the percentage of simplex loci (52.9%) was higher than that of duplex loci (32.6%), and among the latter most (88.5%) were inherited as tetrasomic loci. Overall, 130 duplex markers were found, of which 53.1% were cmm-specific and 46.9% were tbr-specific. Out of 130 markers, 18 (13.8%) were inherited as disomic, and 112 (86.2%) as tetrasomic, loci. This implies that the majority of duplex markers were located on chromosomes which at meiosis tend to randomly pair as bivalents or to form tetravalents. The total number of simplex loci was 119, and most of them (82.3%) were tbr-specific loci. In some cases the observed segregation ratios even allowed us to clearly determine whether a random chromosome or chromatid segregation was detected. This was the case of three cmm-specific RAPDs, 19 cmm- and 25 tbr-specific AFLPs, which fit a 20.8:1 or 2.5:1 ratio, both cases for which a clear random chromatid segregation can be assumed, since they represent the limit of segregation expected when the distance between the locus and the centromere always leads to a cross-over event. The percentage of ascertained crossing-over events was around 37% out of the tetrasomically inherited loci clearly identified (128 loci), a value indicating that the flow of genes from the sexually isolated S. commersonii to the cultivated potato is possible, for at least a large proportion of genes.

Evaluation and use of plant biodiversity for food and pharmaceuticals.

Many epidemiological studies have shown the importance of fruit and vegetables in the human diet so as to prevent the onset of cardiovascular disease and several forms of cancer. The use for food and pharmaceuticals of two of the most widely grown and genetically well-known species in the world, the tomato and the potato, is reviewed. Tomatoes are important sources of vitamin C, potassium, folic acid and carotenoids such as lycopene and beta-carotene. It has been demonstrated that lycopene has anti-oxidant properties and interferes with the growth of cancerous cells. At the Department of Agronomy and Plant Genetics in Portici, interesting results have been obtained with the constitution of stable tomato hybrids having a high content of lycopene and vitamin C. Many of the parental lines used in constituting the hybrids come from interspecific crosses. Potato is also very important in the human diet for its content of high quality proteins, mineral salts and vitamins and it has many medicinal properties. The use of diploid wild species to transfer traits such as high content of vitamin C, mineral salts and high quality proteins into the cultivated potato through ploidy manipulation is discussed.

Endosperm balance number manipulation for direct in vivo germplasm introgression to potato from a sexually isolated relative (Solanum commersonii Dun.).

Diploid (2n = 2x = 24) Solanum species with endosperm balance number (EBN) = 1 are sexually isolated from diploid 2EBN species and both tetraploid (2n = 4x = 48, 4EBN) and haploid (2n = 2x = 24, 2EBN) S. tuberosum Group Tuberosum. To sexually overcome these crossing barriers in the diploid species S. commersonii (1EBN), the manipulation of the EBN was accomplished by scaling up and down ploidy levels. Triploid F1 hybrids between an in vitro-doubled clone of S. commersonii (2n = 4x = 48, 2EBN) and diploid 2EBN clones were successfully used in 3x x 4x crosses with S. tuberosum Group Tuberosum, resulting in pentaploid/near pentaploid BC1 progenies. This provided evidence of 2n (3x) egg formation in the triploid female parents. Two selected BC1 pentaploid hybrids were successfully backcrossed both as male and as female parents with S. tuberosum Group Tuberosum. The somatic chromosome number varied greatly among the resulting BC2 progenies, which included hyperaneuploids, but also a number (4.8%) of 48-chromosome plants. The introgression of S. commersonii genomes was confirmed by the presence of S. commersonii-specific randomly amplified polymorphic DNA markers in the BC2 population analyzed. The results clearly demonstrate the feasibility of germplasm introgression from sexually isolated diploid 1EBN species into the 4x (4EBN) gene pool of the cultivated potato using sexual hybridization. Based on the amount and type of genetic variation generated, cumbersomeness, general applicability, costs, and other factors, it would be interesting to compare the approach reported here with other in vitro or in vivo, direct or indirect, approaches previously reported.

Heterozygosity in 2n gametes of potato evaluated by RFLP markers.

The heterozygosity transmitted through 2n gametes in potato was evaluated by following the segregation of RFLP markers in tetraploid progeny from bilateral sexual polyploidization in a cross between two diploid (2x) interspecific hybrids which produce 2n SDR eggs or 2n FDR pollen. Out of 84 probe/enzyme combinations tested, 23 revealed polymorphism between the parents and were heterozygous in at least one of the parents. These probes characterized 13 loci distributed on five different chromosomes of the potato RFLP map. The heterozygosity transmitted through SDR and FDR gametes was estimated to be 31.8% and 71.4%, respectively. Two different indices (LH and RHI) were used to select plants showing a high level of heterozygosity in the tetraploid progeny. The recombination events and the centromere positions were estimated for chromosomes I, VI and VII, following the segregation ratios of SDR or FDR gametes produced by the parents. A different recombination rate was observed between the two interspecific hybrids.

Cytological evidences of SDR-FDR mixture in the formation of 2n eggs in a potato diploid clone.

Macrosporogenesis and microsporogenesis were investigated in a diploid S. tuberosum x S. chacoense potato hybrid, characterized by more than 50% 2n egg formation. Fifty-five percent of dyad formation of 2n macrospores is ascribed to two meiotic abnormalities: omission of the second meiotic division, occurring at a frequency of 38%, and irregular spindle axis orientation at metaphase I at a frequency of 16%: These abnormalities give origin to a mixture of 2n eggs, composed of mostly second division restitution (SDR) and a small portion of first division restitution (FDR). Microsporogenesis showed rare dyads of 2n microspores depending on parallel spindles observed in anaphase II.

The effects of heterozygosity at the af, st and tl loci in peas.

Eight near-isogenic lines of pea representing all the homozygous combinations of three genes af, st and tl, which modify leaf shape and size, were crossed in all possible ways excepting reciprocals. An analysis of the resulting 36 families has shown that homozygous mutant alleles at the tl locus acting with homozygous mutant alleles at the af and st loci increase both seed weight and plant haulm weight. The mutant alleles at the af and st loci seem, when homozygous, to have little effect by themselves upon seed weight but they do increase or decrease haulm weight, respectively. There is clear evidence of heterotic effects resulting from heterozygosity at each one of the three loci which modify seed weight, haulm weight and basal branching. The implications of such heterotic effects in pea breeding programmes are discussed.

The effects of three genes which modify leaves and stipules in the pea plant.

The effects of three genes (af, st and tl) which modify leaf and stipule form and size in peas were investigated in families generated by crossing eight near-isogenic lines in all combinations but excluding the reciprocals. The eight parents and their equivalent phenotypes differed significantly for all characters due to the direct effects of all three genes, with their combined effects being especially influential in some instances. The effects of the recessive allele at any one of the three loci in homozygotes was to reduce plant productivity with stst having the most pronounced effect. The response of characters tended to be similar in direction, if not in magnitude, to any of the three genes. Partial dominance was frequently associated with the tl locus, and was especially obvious in afaf Tltl genotypes.