Genotyping selection for resistance against tomato yellow leaf curl virus (TYLCV) conferred by Ty-1 and Ty-3 genes in tomato

The tomato yellow leaf curl virus (TYLCV), transmitted by whitefly, causes major disease losses to tomato crops in tropical and subtropical regions of the world. Several genes conferring resistance to TYLCV, mainly Ty-1 and Ty-3 genes, have been introgressed to cultivated tomato (Solanum lycopersicum) from the wild relative species Solanum chilense. By combining bulked segregant analysis and amplified fragment length polymorphisms (AFLP), several AFLP markers closely linked to Ty-1 and Ty-3 genes were identified from the resistant breeding line TZ841-4. Cloning and sequencing of the selected AFLP fragments allowed us to develop codominant cleaved amplified polymorphic sequence and dominant sequence characterized amplified region markers closely linked to Ty-1. In addition, Ty-3-linked allelic-specific markers have been discriminated by a quantitative real-time PCR protocol. Taken together, these markers constitute useful tools for marker-assisted selection breeding programs to improve genetic resistance to TYLCV, and also to initiate map-based cloning approaches to isolate the resistance genes.     

Genetic characterization of the Pto locus of tomato: semi-dominance and cosegregation of resistance to Pseadomonas syringae pathovar tomato and sensitivity to the insecticide Fenthion

The Pto locus governs resistance to bacterial speck disease in tomato caused by race 0 strains of Pseudomonas syringae pathovar tomato (Pst). Large populations segregating for the Pto locus were generated and genetically characterized. Analysis of the locus has revealed that Pto acts in a semi-dominant manner and cosegegrates with sensitivity to an organophosphorous insecticide, Fenthion, suggesting that Pto may be a complex locus responsible for both phenotypes. We have redefined its map position on chromosome five of the classical genetic map and assigned its position on the molecular map, thus facilitating the alignment of the two genetic maps of the short arm of chromosome five of tomato. Furthermore, we have screened random amplified polymorphic (RAPD) markers for their ability to differentiate near-isogenic lines that differ only with respect to Pto and have identified and mapped seven of these markers. Our results suggest that Pto may be located in a euchromatic region on chromosome five which will be advantageous for the cloning of this locus by one of several molecular strategies.     

Identification, Phylogeny, and Expression Analysis of Pto-like Genes in Pepper

The Pto gene from the wild tomato (Solanum pimpinellifolium Mill.) encodes a serine/threonine kinase that plays an important role in bacterial speck resistance in the cultivated tomato (Solanum lycopersicum Mill.). In this paper, 10 classes of Pto-like genes are identified using degenerate polymerase chain reaction (PCR) primers and database mining in pepper. Sequences alignment reveals that many features of the gene family, such as subdomains, autophosphorylation sites, and important amino acid residues for tomato Pto, are well conserved in pepper. A phylogenetic tree of pepper Pto-like genes along with those of other plant species, including tomato Pto genes, suggests that these genes share a common evolutionary origin, and they may have evolved prior to the divergence of monocotyledonous and dicotyledonous plants. Expression analysis has revealed that nine selected Pto-like genes can be detected in at least one of the tissues grown under normal growth conditions; however, these genes are differentially expressed. In addition, some of these genes are regulated by at least one of the subjected treatments, including hormones, abiotic stress, and pathogen infection. These findings will contribute to expanding our knowledge of the roles of Pto-like genes in growth, development, and stress tolerance in pepper.     

Cuticular wax variation in the tomato (Solanum lycopersicum L.), related wild species and their interspecific hybrids

The tomato (Solanum lycopersicum L.) is one of the world's most important vegetable crop species. Among the many tomato accessions available, only a few are tolerant to abiotic stresses, which are responsible for the majority of the crop losses worldwide. Wild tomato species are then secondary gene pool in the breeding of more resistant tomato cultivars. In the current study, the composition of leaf cuticular waxes from fourteen tomato accessions, including S. lycopersicum, Solanum pennellii, Solanum pimpinellifolium, and their interspecific hybrids was studied in order to select the most adequate chemotaxonomic markers. Total cuticular wax load of S. pennellii plants was much higher than in the other plant species. Hydrocarbons were usually the most abundant wax components, followed by minor quantities of triterpenes and other compounds. Interspecific hybrids showed intermediate wax characteristics. The amount and composition of surface waxes were not correlated with the abiotic stress tolerance in S. lycopersicum. The composition of the hydrocarbon fraction was the least variable both within a single accession and between all the plants studied. Based on the results, cuticular hydrocarbons are proposed as potential chemotaxonomic markers in the classification of tomato and related species.     

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.Key Words: Solanum lycopersicum, genetic and genomic resources, molecular markers, microarray, resistance to pathogens, fruit quality.     

Natural Variation for Responsiveness to flg22, flgII-28, and csp22 and Pseudomonas syringae pv. tomato in Heirloom Tomatoes

Tomato (Solanum lycopersicum L.) is susceptible to many diseases including bacterial speck caused by Pseudomonas syringae pv. tomato. Bacterial speck disease is a serious problem worldwide in tomato production areas where moist conditions and cool temperatures occur. To enhance breeding of speck resistant fresh-market tomato cultivars we identified a race 0 field isolate, NC-C3, of P. s. pv. tomato in North Carolina and used it to screen a collection of heirloom tomato lines for speck resistance in the field. We observed statistically significant variation among the heirloom tomatoes for their response to P. s. pv. tomato NC-C3 with two lines showing resistance approaching a cultivar that expresses the Pto resistance gene, although none of the heirloom lines have Pto. Using an assay that measures microbe-associated molecular pattern (MAMP)-induced production of reactive oxygen species (ROS), we investigated whether the heirloom lines showed differential responsiveness to three bacterial-derived peptide MAMPs: flg22 and flgII-28 (from flagellin) and csp22 (from cold shock protein). Significant differences were observed for MAMP responsiveness among the lines, although these differences did not correlate strongly with resistance or susceptibility to bacterial speck disease. The identification of natural variation for MAMP responsiveness opens up the possibility of using a genetic approach to identify the underlying loci and to facilitate breeding of cultivars with enhanced disease resistance. Towards this goal, we discovered that responsiveness to csp22 segregates as a single locus in an F₂ population of tomato.     

Genetic characterization of the Pto locus of tomato: semi-dominance and cosegregation of resistance to Pseadomonas syringae pathovar tomato and sensitivity to the insecticide Fenthion

The Pto locus governs resistance to bacterial speck disease in tomato caused by race 0 strains of Pseudomonas syringae pathovar tomato (Pst). Large populations segregating for the Pto locus were generated and genetically characterized. Analysis of the locus has revealed that Pto acts in a semi-dominant manner and cosegegrates with sensitivity to an organophosphorous insecticide, Fenthion, suggesting that Pto may be a complex locus responsible for both phenotypes. We have redefined its map position on chromosome five of the classical genetic map and assigned its position on the molecular map, thus facilitating the alignment of the two genetic maps of the short arm of chromosome five of tomato. Furthermore, we have screened random amplified polymorphic (RAPD) markers for their ability to differentiate near-isogenic lines that differ only with respect to Pto and have identified and mapped seven of these markers. Our results suggest that Pto may be located in a euchromatic region on chromosome five which will be advantageous for the cloning of this locus by one of several molecular strategies.     

SNP Discovery and Linkage Map Construction in Cultivated Tomato

Few intraspecific genetic linkage maps have been reported for cultivated tomato, mainly because genetic diversity within Solanum lycopersicum is much less than that between tomato species. Single nucleotide polymorphisms (SNPs), the most abundant source of genomic variation, are the most promising source of polymorphisms for the construction of linkage maps for closely related intraspecific lines. In this study, we developed SNP markers based on expressed sequence tags for the construction of intraspecific linkage maps in tomato. Out of the 5607 SNP positions detected through in silico analysis, 1536 were selected for high-throughput genotyping of two mapping populations derived from crosses between ‘Micro-Tom’ and either ‘Ailsa Craig’ or ‘M82’. A total of 1137 markers, including 793 out of the 1338 successfully genotyped SNPs, along with 344 simple sequence repeat and intronic polymorphism markers, were mapped onto two linkage maps, which covered 1467.8 and 1422.7 cM, respectively. The SNP markers developed were then screened against cultivated tomato lines in order to estimate the transferability of these SNPs to other breeding materials. The molecular markers and linkage maps represent a milestone in the genomics and genetics, and are the first step toward molecular breeding of cultivated tomato. Information on the DNA markers, linkage maps, and SNP genotypes for these tomato lines is available at http://www.kazusa.or.jp/tomato/.     

A novel tomato mutant,Solanum lycopersicum elongated fruit1 (Slelf1), exhibits an elongated fruit shape caused by increased cell layers in the proximal region of the ovary

Genes controlling fruit morphology offer important insights into patterns and mechanisms determining organ shape and size. In cultivated tomato (Solanum lycopersicum L.), a variety of fruit shapes are displayed, including round-, bell pepper-, pear-, and elongate-shaped forms. In this study, we characterized a tomato mutant possessing elongated fruit morphology by histologically analyzing its fruit structure and genetically analyzing and mapping the genetic locus. The mutant line, Solanum lycopersicum elongated fruit 1 (Slelf1), was selected in a previous study from an ethylmethane sulfonate-mutagenized population generated in the background of Micro-Tom, a dwarf and rapid-growth variety. Histological analysis of the Slelf1 mutant revealed dramatically increased elongation of ovary and fruit. Until 6 days before flowering, ovaries were round and they began to elongate afterward. We also determined pericarp thickness and the number of cell layers in three designated fruit regions. We found that mesocarp thickness, as well as the number of cell layers, was increased in the proximal region of immature green fruits, making this the key sector of fruit elongation. Using 262 F₂ individuals derived from a cross between Slelf1 and the cultivar Ailsa Craig, we constructed a genetic map, simple sequence repeat (SSR), cleaved amplified polymorphism sequence (CAPS), and derived CAPS (dCAPS) markers and mapped to the 12 tomato chromosomes. Genetic mapping placed the candidate gene locus within a 0.2?Mbp interval on the long arm of chromosome 8 and was likely different from previously known loci affecting fruit shape.     

Molecular dissection of Tomato leaf curl virus resistance in tomato line TY172 derived from Solanum peruvianum

Tomato yellow leaf curl virus (TYLCV) is devastating to tomato (Solanum lycopersicum) crops and resistant cultivars are highly effective in controlling the disease. The breeding line TY172, originating from Solanum peruvianum, is highly resistant to TYLCV. To map quantitative trait loci (QTLs) controlling TYLCV resistance in TY172, appropriate segregating populations were analyzed using 69 polymorphic DNA markers spanning the entire tomato genome. Results show that TYLCV resistance in TY172 is controlled by a previously unknown major QTL, originating from the resistant line, and four additional minor QTLs. The major QTL, we term Ty-5, maps to chromosome 4 and accounts for 39.7–46.6% of the variation in symptom severity among segregating plants (LOD score 33–35). The minor QTLs, originated either from the resistant or susceptible parents, were mapped to chromosomes 1, 7, 9 and 11, and contributed 12% to the variation in symptom severity in addition to Ty-5.     

Fine-mapping of the <Emphasis Type="Italic">woolly</Emphasis> gene controlling multicellular trichome formation and embryonic development in tomato

Trichomes are small hairs that originate from the epidermal cells of nearly all land plants, and they exist in unicellular and multicellular forms. The regulatory pathway of unicellular trichomes in Arabidopsis is well characterized. However, little is known about the multicellular trichome formation in tomato (Solanum lycopersicum). The woolly (Wo) gene controls multicellular trichome initiation and leads to embryonic lethality when homozygous in tomato. To clone and characterize Wo, the gene was fine-mapped to a DNA fragment of ~200 kb using the map-based cloning strategy. A series of sequence-based molecular markers, including simple sequence repeat, sequence characterized amplified region, and cleaved amplified polymorphic sequence were utilized in this study. Analysis of the sequence indicated that this region carries 19 putative open reading frames. These results will provide not only the important information for the isolation and characterization of Wo but also the starting point for studying the regulatory pathway responsible for trichome formation and embryonic lethality in tomato.     

Marker assisted gene pyramiding for enhanced Tomato leaf curl virus disease resistance in tomato cultivars

The present research is aimed towards molecular marker assisted pyramiding Tomato leaf curl virus (ToLCV) disease resistance genes into two ToLCV susceptible tomato (Solanum lycopersicum L.) cvs. Pbc and H-86 (resistance genes recipient parents). Resistance gene donors were EC-538408 (Solanum chilense) and EC-520061 (S. peruvianum) in the case of cv. Pbc, and EC-520061 (S. peruvianum) and H-24 (S. lycopersicum) in the case of cv. H-86. A ToLCV resistance gene associated co-dominant simple sequence repeat (SSR) marker SSR-218 was used to discriminate between homozygotes and heterozygotes at the seedling stage prior to pollination, which enabled the rejection of nontarget back crosses and pyramiding progenies of the crosses PbcxEC-520061 and H-86xEC-520061, whereas SSR-306 was used for the cross PbcxEC-538408. Ty-2 gene cleaved amplified polymorphic sequences (CAPS) marker was used for the cross H-86xH-24. Out of 279 pyramiding progenies of the cross PbcxEC-538408/PbcxEC-520061, total 91 plants showed the presence of both resistance allele 1 and 2 along with both susceptibility alleles, and in 243 pyramiding progenies of the cross H-86xEC-520061/H-86xH-24, total 82 plants showed the presence of both resistance allele 1 and Ty-2 along with both susceptible alleles. The pyramiding lines that carried both pyramided resistance genes were resistant to tomato leaf curl disease throughout its life cycle.     

Comprehensive Resources for Tomato Functional Genomics Based on the Miniature Model Tomato Micro-Tom

Tomato (Solanum lycopersicum L., Solanaceae) is an excellent model plant for genomic research of solanaceous plants, as well as for studying the development, ripening, and metabolism of fruit. In 2003, the International Solanaceae Project (SOL, www.sgn.cornell.edu ) was initiated by members from more than 30 countries, and the tomato genome-sequencing project is currently underway. Genome sequence of tomato obtained by this project will provide a firm foundation for forthcoming genomic studies such as the comparative analysis of genes conserved among the Solanaceae species and the elucidation of the functions of unknown tomato genes. To exploit the wealth of the genome sequence information, there is an urgent need for novel resources and analytical tools for tomato functional genomics. Here, we present an overview of the development of genetic and genomic resources of tomato in the last decade, with a special focus on the activities of Japan SOL and the National Bio-Resource Project in the development of functional genomic resources of a model cultivar, Micro-Tom.Key Words: Expressed sequence tag, full-length cDNA, genome sequence, mutant resource, Micro-Tom, JSOL, Solanum lycopersicum, tomato.     

巴西橡胶Pto类抗病同源序列的克隆与系统发育重建

番茄Pto基因是一类可以编码丝氨酸/苏氨酸激酶(STK)序列的广谱抗性候选基因,其序列克隆与鉴定为深入了解番茄的抗病机制奠定了基础.在该研究中,一对依据Pto基因的保守序列设计的简并引物被用来扩增巴西橡胶中Pto基因抗病同源序列,扩增得到了一个约550 bp的基因片段,其随后被克隆并测序.序列分析发现,其中的7个抗病同源序列与Pto基因高度同源(BLASTX E value <3e-53),所以其被认为是Pto基因抗病同源序列(Pto-RGCs).通过巴西橡胶的Pto-RGCs多序列比对表明,这些序列包含了多个STKs保守的次级结构域.此外,系统发育分析也表明,巴西橡胶的Pto-RGCs属于Pto基因同源的R基因.该研究结果中Pto-RGCs可为巴西橡胶抗病的发展提供一个有效的基因资源.     

Multi-environment QTL mapping reveals genetic architecture of fruit cracking in a tomato RIL <Emphasis Type="Italic">Solanum lycopersicum</Emphasis> × <Emphasis Type="Italic">S. pimpinellifolium</Emphasis> population

Key message

QTL and codominant genetic markers for fruit cracking have been identified in a tomato genetic map derived from a RIL population, providing molecular tools for marker-assisted breeding of this trait.

Abstract

In tomato, as well as in other fleshy fruits, one of the main disorders that widely limit quality and production is fruit cracking or splitting of the epidermis that is observed on the fruit skin and flesh at any stage of fruit growth and maturation. To elucidate the genetic basis of fruit cracking, a quantitative trait loci (QTL) analysis was conducted in a recombinant inbred line (RIL) population derived from a cross between tomato (Solanum lycopersicum) and the wild-relative species S. pimpinellifolium. The RIL population was evaluated for fruit cracking during three consecutive growing seasons. Construction of a high-density linkage map based on codominant markers, covering more than 1000 cM of the whole genome, led to the identification of both main and epistatic QTL controlling fruit cracking on the basis of a single-environment as well as multiple-environment analysis. This information will enhance molecular breeding for novel cracking resistant varieties and simultaneously assist the identification of genes underlying these QTL, helping to reveal the genetic basis of fruit cracking in tomato.

     

Domestication and Breeding of Tomatoes: What have We Gained and What Can We Gain in the Future?

Background

It has been shown that a large variation is present and exploitable from wild Solanum species but most of it is still untapped. Considering the thousands of Solanum accessions in different gene banks and probably even more that are still untouched in the Andes, it is a challenge to exploit the diversity of tomato. What have we gained from tomato domestication and breeding and what can we gain in the future?

Scope

This review summarizes progress on tomato domestication and breeding and current efforts in tomato genome research. Also, it points out potential challenges in exploiting tomato biodiversity and depicts future perspectives in tomato breeding with the emerging knowledge from tomato-omics.

Conclusions

From first domestication to modern breeding, the tomato has been continually subjected to human selection for a wide array of applications in both science and commerce. Current efforts in tomato breeding are focused on discovering and exploiting genes for the most important traits in tomato germplasm. In the future, breeders will design cultivars by a process named ‘breeding by design’ based on the combination of science and technologies from the genomic era as well as their practical skills.Key words: Breeding, domestication, genomics, Solanum lycopersicum     

QTL mapping of fruit mineral contents provides new chances for molecular breeding of tomato nutritional traits

Key message

Agronomical characterization of a RIL population for fruit mineral contents allowed for the identification of QTL controlling these fruit quality traits, flanked by co-dominant markers useful for marker-assisted breeding.

Abstract

Tomato quality is a multi-variant attribute directly depending on fruit chemical composition, which in turn determines the benefits of tomato consumption for human health. Commercially available tomato varieties possess limited variability in fruit quality traits. Wild species, such as Solanum pimpinellifolium, could provide different nutritional advantages and can be used for tomato breeding to improve overall fruit quality. Determining the genetic basis of the inheritance of all the traits that contribute to tomato fruit quality will increase the efficiency of the breeding program necessary to take advantage of the wild species variability. A high-density linkage map has been constructed from a recombinant inbred line (RIL) population derived from a cross between tomato Solanum lycopersicum and the wild-relative species S. pimpinellifolium. The RIL population was evaluated for fruit mineral contents during three consecutive growing seasons. The data obtained allowed for the identification of main QTL and novel epistatic interaction among QTL controlling fruit mineral contents on the basis of a multiple-environment analysis. Most of the QTL were flanked by candidate genes providing valuable information for both tomato breeding for new varieties with novel nutritional properties and the starting point to identify the genes underlying these QTL, which will help to reveal the genetic basis of tomato fruit nutritional properties.