Assessment of genetic variation among commercial tomato (Solanum lycopersicum L) varieties using SSR markers and morphological characteristics

Simple sequence repeats (SSR) is one of the most suitable markers for variety identification as it has great discrimination power for varieties with limited genetic variation. Genetic characterization of commercial tomato varieties was investigated using 33 SSR markers and 22 morphological traits. Thirty three SSR primer pairs were screened for 63 tomato varieties. A total of 132 polymorphic amplified fragments were obtained by using 33 SSR markers. The average polymorphism information content (PIC) was 0.628 ranging from 0.210 to 0.880. One hundred thirty two SSR loci were used to calculate Jaccard's distance coefficients for UPGMA cluster analysis. A clustering group of varieties, based on the results of SSR analysis, were categorized into cherry and classic fruit type varieties. Almost all of the varieties were discriminated by SSR marker genotypes. The relationship between morphological and molecular data for 33 varieties out of 63 varieties was analyzed using Mantel matrix correspondence test. The correlation value between two methods was 0.644. However, SSR based dendrogram topology showed some similar form with morphological traits at the two main groups. Therefore, these markers may be used wide range of practical application in variety identification and pre-screening for distinctiveness test of tomato varieties.     

Ectopic expression of apple fruit homogentisate phytyltransferase gene (MdHPT1) increases tocopherol in transgenic tomato (Solanum lycopersicum cv. Micro-Tom) leaves and fruits

Homogentisate phytyltransferase (HPT) is an important enzyme in the biosynthesis of tocopherols (vitamin E). Herein, an HPT homolog (MdHPT1) was isolated from apple (Malus domestica Borkh. cv. Fuji) fruits, whose gene expression level gradually decreased during fruit ripening, reaching a background level in ripened apple fruits. The amounts of α- and γ-tocopherols, two major tocopherols in plant organs, were 5- to 14-fold lower in the fruits than in the leaves and flowers of apple plants. Transgenic tomato plants (Solanum lycopersicum cv. Micro-Tom) overexpressing MdHPT1 were next constructed. Transgenic independent T(1) leaves contained ～1.8- to 3.6-fold and ～1.6- to 2.9-fold higher levels of α-tocopherol and γ-tocopherol, respectively, than those in control plants. In addition, the levels of α-tocopherol and γ-tocopherol in 35S:MdHPT1 T(1) fruits increased up to 1.7-fold and 3.1-fold, respectively, as compared to the control fruits, indicating that an increase in α-tocopherol in fruits (maximal 1.7-fold) was less evident than that in leaves (maximal 3.6-fold). This finding suggests that the apple MdHPT1 plays a role in tocopherol production in transgenic tomatoes.     

Characterization of the O-acetylserine(thiol)lyase gene family in Solanum lycopersicum L.

Key message

This research demonstrated the conservation and diversification of the functions of the O-acetylserine-(thiol) lyase gene family genes in Solanum lycopersicum L.

Abstract

Cysteine is the first sulfur-containing organic molecule generated by plants and is the precursor of many important biomolecules and defense compounds. Cysteine and its derivatives are also essential in various redox signaling-related processes. O-acetylserine(thiol)lyase (OASTL) proteins catalyze the last step of cysteine biosynthesis. Previously, researches focused mainly on OASTL proteins which were the most abundant or possessed the authentic OASTL activity, whereas few studies have ever given a comprehensive view of the functions of all the OASTL members in one specific species. Here, we characterized 8 genes belonging to the OASTL gene family from tomato genome (SlOAS2 to SlOAS9), including the sequence analyses, subcellular localization, enzymatic activity assays, expression patterns, as well as the interaction property with SATs. Apart from SlOAS3, all the other genes encoded OASTL-like proteins. Tomato OASTLs were differentially expressed during the development of tomato plants, and their encoded proteins had diverse compartmental distributions and functions. SlOAS5 and SlOAS6 catalyzed the biogenesis of cysteine in chloroplasts and in the cytosol, respectively, and this was in consistent with their interaction abilities with SlSATs. SlOAS4 catalyzed the generation of hydrogen sulfide, similar to its Arabidopsis ortholog, DES1. SlOAS2 also functioned as an L-cysteine desulfhydrase, but its expression pattern was very different from that of SlOAS4. Additionally, SlOAS8 might be a β-cyanoalanine synthase in mitochondria, and the S-sulfocysteine synthase activity appeared lost in tomato plants. SlOAS7 exhibited a transactivational ability in yeast; while the subcellular localization of SlOAS9 was in the peroxisome and correlated with the process of leaf senescence, indicating that these two genes might have novel roles.

     

Suitability of mycorrhiza-defective mutant/wildtype plant pairs (Solanum lycopersicum L. cv Micro-Tom) to address questions in mycorrhizal soil ecology

The ectomycorrhizal (ECM) fungi associated with Pinus thunbergii seedlings grown on sand dune were identified by molecular method, and the diversity of bacteria associated with ECM and Extraradical mycelium were examined by Denaturing Gradient Gel Electrophoresis (DGGE) of PCR-amplified 16S rDNA. The mycorrhizal formation rate of 1-year old P. thunbergii seedlings was more than 95%. Cenococcum geophilum was the most dominant ECM fungus, followed by T01, RFLP-8, Russula spp., and Suillus sp. Bacterial community was most diverse with C. geophilum- and RFLP-8-mycorrhiza. Sequencing analysis showed that Burkholderia spp. and Bradyrhizobium spp. were on the surface of ECM short root of seven ECM. The fungi detected as extraradical mycelium using DGGE of 18S rDNA were Suillus bovinus and RFLP-8-mycorrhiza. Bacterial community on the extraradical mycelium was more diverse than those on ECM root tip. Burkholderia spp. and Bradyrhizobium spp. were found also on extraradical mycelium.     

Mineral and Trace Elements Content in 30 Accessions of Tomato Fruits (Solanum lycopersicum L.,) and Wild Relatives (Solanum pimpinellifolium L., Solanum cheesmaniae L. Riley, and Solanum habrochaites S. Knapp & D.M. Spooner)

Tomato quality and its potential health benefits are directly related to its chemical composition. The characterization of nutritional properties of Solanum germplasm is essential to choose suitable donor parents for breeding programs. In this sense, wild species could be very useful for tomato fruit quality genetic improvement. With this objective, in this work, we characterize micronutrients content in Eulycopersicon germplasm (20 cultivars of S. lycopersicum L. and 10 accessions of wild relatives) analyzing mineral (Na, K, Ca, Mg) and trace elements (Cu, Fe, Zn, Mn) and applying multidimensional analysis (principal component and cluster analysis). The classification obtained and the comparison of cultivars performance showed that wild accessions belonging to S. cheesmaniae (L. Riley), S. pimpinellifolium L., and S. habrochaites S. Knapp & D.M. Spooner can be of great usefulness in breeding programs to improve mineral content characteristics of conventional S. lycopersicum varieties due to its higher mineral content.     

花生分子标记的研究进展

国内外对花生的研究特别是在分子水平上的研究相对水稻、油菜等农作物比较薄弱。近些年,分子标记技术迅速发展,在花生上也得到广泛的应用。本文从花生属起源、种质资源的遗传多样性、抗性基因的标记和指纹图谱等方面,综述了国内外花生分子标记的研究进展。     

Proteome-Wide Identification of Lysine Succinylation in the Proteins of Tomato (Solanum lycopersicum)

Post-translational modification of proteins through lysine succinylation plays important regulatory roles in living cells. Lysine succinylation was recently identified as a novel post-translational modification in Escherichia coli, yeast, Toxoplasma gondii, HeLa cells, and mouse liver. Interestingly, only a few sites of lysine succinylation have been detected in plants to date. In this study, we identified 347 sites of lysine succinylation in 202 proteins in tomato by using high-resolution mass spectrometry. Succinylated proteins are implicated in the regulation of diverse metabolic processes, including chloroplast and mitochondrial metabolism. Bioinformatic analysis showed that succinylated proteins are evolutionarily conserved and involved in various cellular functions such as metabolism and epigenetic regulation. Moreover, succinylated proteins exhibit diverse subcellular localizations. We also defined six types of definitively conserved succinylation motifs. These results provide the first in-depth analysis of the lysine succinylome and novel insights into the role of succinylation in tomato, thereby elucidating lysine succinylation in the context of cellular physiology and metabolite biosynthesis in plants.     

番茄(Solanum lycopersicum)类胡萝卜素降解关键基因筛选

类胡萝卜素衍生挥发物对提升番茄风味至关重要。为筛选调控类胡萝卜素衍生挥发物合成的关键基因,以90个番茄自交系中香气寡淡的TI4001和香气浓郁的CI1005为材料,分析了番茄类胡萝卜素裂解双加氧酶(SlCCDs)基因在不同组织及不同发育期果实中的表达量,果实不同成熟期类胡萝卜素及其衍生挥发物的含量。发现在7个SlCCDs基因中,SlCCD1A和SlCCD1B基因在番茄果实中表达量最高,且随着果实发育成熟表达量显著升高。果实中类胡萝卜素及其衍生挥发物含量也显著升高。SlCCD1A和SlCCD1B基因表达量与类胡萝卜素及其衍生挥发物含量之间极显著正相关。推测SlCCD1A和SlCCD1B基因是裂解类胡萝卜素合成挥发物的关键基因。     

Metabolic engineering of flavonoids in tomato (Solanum lycopersicum): the potential for metabolomics

Flavonoids comprise a large and diverse group of polyphenolic plant secondary metabolites. In plants, flavonoids play important roles in many biological processes such as pigmentation of flowers, fruits and vegetables, plant-pathogen interactions, fertility and protection against UV light. Being natural plant compounds, flavonoids are an integral part of the human diet and there is increasing evidence that dietary polyphenols are likely candidates for the observed beneficial effects of a diet rich in fruits and vegetables on the prevention of several chronic diseases. Within the plant kingdom, and even within a single plant species, there is a large variation in the levels and composition of flavonoids. This variation is often due to specific mutations in flavonoid-related genes leading to quantitative and qualitative differences in metabolic profiles. The use of such specific flavonoid mutants with easily scorable, visible phenotypes has led to the isolation and characterisation of many structural and regulatory genes involved in the flavonoid biosynthetic pathway from different plant species. These genes have been used to engineer the flavonoid biosynthetic pathway in both model and crop plant species, not only from a fundamental perspective, but also in order to alter important agronomic traits, such as flower and fruit colour, resistance, nutritional value. This review describes the advances made in engineering the flavonoid pathway in tomato (Solanum lycopersicum). Three different approaches will be described; (I) Increasing endogenous tomato flavonoids using structural or regulatory genes; (II) Blocking specific steps in the flavonoid pathway by RNA interference strategies; and (III) Production of novel tomato flavonoids by introducing novel branches of the flavonoid pathway. Metabolite profiling is an essential tool to analyse the effects of pathway engineering approaches, not only to analyse the effect on the flavonoid composition itself, but also on other related or unrelated metabolic pathways. Metabolomics will therefore play an increasingly important role in revealing a more complete picture of metabolic perturbation and will provide additional novel insights into the effect of the introduced genes and the role of flavonoids in plant physiology and development.     

Multivariate Statistical Analysis of Low-Light Tolerance in Tomato (Solanum lycopersicum Mill.) Cultivars and Their Ultrastructural Observations

This research used multivariate statistical analysis to evaluate the tolerance of 11 tomato cultivars to low light at the seedling stage. The low-light condition (200–420 μmol/m² s) was simulated by a shade net. It was found that 11 of 16 character indices of different cultivars, such as dropping angle, bend degree, and accumulation of leaf area, showed a significant difference by using multiple variance analysis. After factor analysis, the 11 character indices could be summarized into 5 main factors with a cumulative contribution rate of 84.968 %. According to the factor scores after varimax rotation, the 11 tomato cultivars could be classified into three categories by using cluster analysis. The severely low-light-sensitive cultivars were T1, T5, T6, T10, and T11 and the moderately low-light-sensitive cultivars were T4, T7, and T9. Cultivars T2, T3, and T8 were resistant to low light. In accordance with the appraisal result, the light-sensitive cultivars T5 and T10, the moderately low-light-sensitive cultivar T4, and the low-light-tolerant cultivar T8 were randomly selected to observe the variation in the ultrastructure of leaves of different tomato cultivars with the aid of a transmission electron microscope (TEM). In chloroplasts of T5 and T10, membranes were heavily damaged and mitochondria were vacuolated, whereas the chloroplast structure of T4 was slightly damaged and its mitochondria grew normally. In the chloroplasts of T8, the organelle membranes were intact, the degree of thylakoid stacking was high, and mitochondria grew normally. Our results showed that multivariate statistical analysis of low-light tolerance in tomatoes has certain scientific applicability.     

Expression of the IL-2 gene in the potato (Solanum tuberosum cv. Superior)

We intended to examine the expression of the T-cell growth factor (human interleukin-2) so that a binary vector, pSSK-1, carrying the IL-2 gene was constructed and transferred intoA. tumefaciens for the purpose of the transformation of the potato (Solanum tuberosum cv. Superior). All of theAgrobacterium-infected potato explants were regenerated to shoots in modified MS medium and 81% of them rooted on the medium containing kanamycin (200 mg/L). Southern and Northern analysis were performed to verify the transformation events. EL-ISA test indicated that IL-2 protein was produced from IL-2-transformed potatoes. These results suggested expression and production of the IL-2 protein from the transgenic potato.     

Organ-dependent oxylipin signature in leaves and roots of salinized tomato plants (Solanum lycopersicum)

Oxylipins have been extensively studied in plant defense mechanisms or as signal molecules. Depending on the stress origin (e.g. wounding, insect, pathogen), and also on the plant species or organ, a specific oxylipin signature can be generated. Salt stress is frequently associated with secondary stress such as oxidative damage. Little is known about the damage caused to lipids under salt stress conditions, especially with respect to oxylipins. In order to determine if an organ-specific oxylipin signature could be observed during salt stress, tomato (Solanum lycopersicum cv. Money Maker) plants were submitted to salt stress (100 mM of NaCl) for a 30-d period. A complete oxylipin profiling and LOX related-gene expression measurement were achieved in leaves and roots. As expected, salt stress provoked premature senescence in leaves, as revealed by a decrease in photosystem II efficiency (F(v)/F(m) ratio) and sodium accumulation in leaves. In roots, a significant decrease in several oxylipins (9- and 13-hydro(pero)xy linole(n)ic acids, keto and divinyl ether derivatives) was initiated at day 5 and intensified at day 21 after salt treatment, whereas jasmonic acid content increased. In leaves, the main changes in oxylipins were observed later (at day 30), with an increase in some 9- and 13-hydro(pero)xy linole(n)ic acids and a decrease in some keto-derivatives and in jasmonic acid. Oxylipin enantiomeric characterization revealed that almost all compounds were formed enzymatically, and therefore a massive auto-oxidation of lipids that can be encountered in abscission processes can be excluded here.     

Genetic interactions in the control of flowering time and reproductive structure development in tomato (Solanum lycopersicum)

Different tomato (Solanum lycopersicum) mutants, affected in flowering time, reproductive structure or plant architecture, were crossed to produce double mutants in order to investigate gene interactions in flowering regulation in this autonomous species with a sympodial growth habit. The compound inflorescence: uniflora, uniflora: self pruning, uniflora: blind, and jointless: uniflora double mutants all produced solitary flowers like their uniflora parent, instead of inflorescences. All double mutants were late flowering. uniflora: blind and uniflora: self pruning had flowering times intermediate between those of their two parents. jointless: uniflora and compound inflorescence: uniflora flowered later than uniflora, the mutant with the most delayed flowering. All double mutants developed strong lateral shoots at node levels approximately corresponding to the level at which their parent cultivars initiated their first reproductive structure, which is a typical trait of uniflora. These results suggest that the UNIFLORA gene acts upstream of the other investigated genes in controlling flowering in tomato, and that floral transition of the primary shoot and floral transition of sympodial segments are regulated differently.     

Identification and localization of a lipase-like acyltransferase in phenylpropanoid metabolism of tomato (Solanum lycopersicum)

We have isolated an enzyme classified as chlorogenate: glucarate caffeoyltransferase (CGT) from seedlings of tomato (Solanum lycopersicum) that catalyzes the formation of caffeoylglucarate and caffeoylgalactarate using chlorogenate (5-O-caffeoylquinate) as acyl donor. Peptide sequences obtained by trypsin digestion and spectrometric sequencing were used to isolate the SlCGT cDNA encoding a protein of 380 amino acids with a putative targeting signal of 24 amino acids indicating an entry of the SlCGT into the secretory pathway. Immunogold electron microscopy revealed the localization of the enzyme in the apoplastic space of tomato leaves. Southern blot analysis of genomic cDNA suggests that SlCGT is encoded by a single-copy gene. The SlCGT cDNA was functionally expressed in Nicotiana benthamiana leaves and proved to confer chlorogenate-dependent caffeoyltransferase activity in the presence of glucarate. Sequence comparison of the deduced amino acid sequence identified the protein unexpectedly as a GDSL lipase-like protein, representing a new member of the SGNH protein superfamily. Lipases of this family employ a catalytic triad of Ser-Asp-His with Ser as nucleophile of the GDSL motif. Site-directed mutagenesis of each residue of the assumed respective SlCGT catalytic triad, however, indicated that the catalytic triad of the GDSL lipase is not essential for SlCGT enzymatic activity. SlCGT is therefore the first example of a GDSL lipase-like protein that lost hydrolytic activity and has acquired a completely new function in plant metabolism, functioning in secondary metabolism as acyltransferase in synthesis of hydroxycinnamate esters by employing amino acid residues different from the lipase catalytic triad.     

番茄COBRA基因克隆、表达模式及生物信息学分析

COBRA作为一种重要的胞外糖基磷脂酰肌醇(GP-I)锚定蛋白,影响植物细胞壁中纤维素含量及细胞的定向伸长。目前已有多个拟南芥、玉米及水稻的COBRA基因的突变体被研究。而有关番茄COBRA基因克隆的研究尚未见报道。本研究利用RT-PCR技术克隆了一个假定编码番茄COBRA蛋白的SlCOBRA基因,并在GenBank注册(JN398667)。序列测定和分析表明,该序列由6个外显子组成,编码444个氨基酸残基;氨基酸序列中存在COBRA蛋白的CCVS保守基序,N端的跨膜信号肽及C-末端的疏水性尾部和GPI锚定ω-位点。系统进化分析表明番茄SlCOBRA与拟南芥AtCOB具有80%氨基酸序列同源性,聚在一个分支上。Real-time PCR分析番茄各个组织中COBRA基因的表达结果表明番茄COBRA为组成型表达,在营养器官(根、茎、叶)中的表达量高于花和果实,尤其在成熟的果实中(从转色期到红熟期)表达量明显减少。