Effective Mapping by Sequencing to Isolate Causal Mutations in the Tomato Genome

Abstract A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits an integrated genome map to be stored, retrieved, viewed, and queried in a stand-alone capacity, in a client/server relationship with the Fungal Genome Database (FGDB), and as a web-browsing tool for the FGDB. In that ODS3 is programmed in Java, the tool promotes platform independence and supports export of integrated genome-mapping data in the extensible markup language (XML) for data interchange with other genome information systems. The tool ODS3 is used to create an initial integrated genome map of the AIDS-related fungal pathogen, Pneumocystis carinii. Contig dynamics would indicate that this physical map is ∼50% complete with ∼200 contigs. A total of 10 putative multigene families were found. Two of these putative families were previously characterized in P. carinii, namely the major surface glycoproteins (MSGs) and HSP70 proteins; three of these putative families (not previously characterized in P. carinii) were found to be similar to families encoding the HSP60 in Schizosaccharomyces pombe, the heat-shock Ψ protein in S. pombe, and the RNA synthetase family (i.e., MES1) in Saccharomyces cerevisiae. Physical mapping data are consistent with the 16S, 5.8S, and 26S rDNA genes being single copy in P. carinii. No other fungus outside this genus is known to have the rDNA genes in single copy.

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Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice

Plants ◽

10.3390/plants10040705 ◽

2021 ◽

Vol 10 (4) ◽

pp. 705

Author(s):

John Carlos I. Ignacio ◽

Maricris Zaidem ◽

Carlos Casal ◽

Shalabh Dixit ◽

Tobias Kretzschmar ◽

...

Keyword(s):

Genetic Basis ◽

Snp Markers ◽

Nucleotide Polymorphism ◽

Rice Varieties ◽

Single Nucleotide ◽

Genotyping Platform ◽

Anaerobic Germination ◽

Direct Seeded ◽

Mapping By Sequencing ◽

Simple Sequence

Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germination (AG). To map the genetic basis of its tolerance, we examined a population of 200 F2:3 families derived from a cross between IR64 and ASD1 using the restriction site-associated DNA sequencing (RAD-seq) technology. This genotyping platform enabled the identification of 1921 single nucleotide polymorphism (SNP) markers to construct a high-resolution genetic linkage map with an average interval of 0.9 cM. Two significant quantitative trait loci (QTLs) were detected on chromosomes 7 and 9, qAG7 and qAG9, with LOD scores of 7.1 and 15.0 and R2 values of 15.1 and 29.4, respectively. Here, we obtained more precise locations of the QTLs than traditional simple sequence repeat and low-density SNP genotyping methods and may help further dissect the genetic factors of these QTLs.

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Development of Capsicum EST–SSR markers for species identification and in silico mapping onto the tomato genome sequence

Molecular Breeding ◽

10.1007/s11032-012-9774-z ◽

2012 ◽

Vol 31 (1) ◽

pp. 101-110 ◽

Cited By ~ 37

Author(s):

Kenta Shirasawa ◽

Kohei Ishii ◽

Cholgwang Kim ◽

Tomohiro Ban ◽

Munenori Suzuki ◽

...

Keyword(s):

Species Identification ◽

Ssr Markers ◽

Genome Sequence ◽

In Silico ◽

Tomato Genome ◽

In Silico Mapping

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Genome-wide identification and analyses of tomato (Solanum lycopersicum L.) high-affinity nitrate transporter 2 (NRT2) family genes and their responses to drought and salinity

10.1101/2021.12.08.471831 ◽

2021 ◽

Author(s):

M. AYDIN AKBUDAK ◽

Ertugrul Filiz ◽

Durmus Cetin

Keyword(s):

Solanum Lycopersicum ◽

Expression Profiles ◽

Gene Families ◽

Major Facilitator Superfamily ◽

Nitrate Transporter ◽

Tomato Genome ◽

High Affinity ◽

Solanum Lycopersicum L ◽

Major Facilitator ◽

Systematic Identification

High-affinity nitrate transporter 2 (NRT2) proteins have vital roles in nitrate (NO3-) uptake and translocation in plants. The gene families coding NRT2 proteins have been identified and functionally characterized in many plant species. However, no systematic identification of NRT2 family members have been reported in tomato (Solanum lycopersicum). There is also little known about their expression profiles under environmental stresses. Accordingly, the present study aimed to identify NRT2 gene family in the tomato genome; then, investigate them in detail through bioinformatics, physiological and expression analyses. As a result, four novel NRT2 genes were identified in the tomato genome, all of which contain the same domain belonging to the Major Facilitator Superfamily (PF07690). The co-expression network of SlNRT genes revealed that they were co-expressed with several other genes in many different molecular pathways including transport, photosynthesis, fatty acid metabolism and amino acid catabolism. Programming many crucial physiological and metabolic pathways, various numbers of phosphorylation sites were predicted in the NRT2 proteins.

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A Solanum lycopersicoides reference genome facilitates biological discovery in tomato

10.1101/2020.04.16.039636 ◽

2020 ◽

Author(s):

Adrian F. Powell ◽

Lance E. Courtney ◽

Maximilian H.-W. Schmidt ◽

Ari Feder ◽

Alexander Vogel ◽

...

Keyword(s):

Pathogen Resistance ◽

Wild Relatives ◽

Introgression Lines ◽

Tomato Genome ◽

Nutrient Quality ◽

Solanum Lycopersicoides ◽

Genomic Studies ◽

Biological Discovery ◽

Cultivated Species ◽

Tomato Breeding

SummaryWild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs). Despite the utility of these wild relatives and their associated ILs, limited finished genomes have been produced to aid genetic and genomic studies. We have generated a chromosome-scale genome assembly for Solanum lycopersicoides LA2951 using PacBio sequencing, Illumina, and Hi-C. We identified 37,938 genes based on Illumina and Isoseq and compared gene function to the available cultivated tomato genome resources, in addition to mapping the boundaries of the S. lycopersicoides introgressions in a set of cv. VF36 x LA2951 introgression lines (IL). The genome sequence and IL map will support the development of S. lycopersicoides as a model for studying fruit nutrient/quality, pathogen resistance, and environmental stress tolerance traits that we have identified in the IL population and are known to exist in S. lycopersicoides.

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Concomitant phytonutrient and transcriptome analysis of mature fruit and leaf tissues of tomato (Solanum lycopersicum L. cv. Oregon Spring) grown using organic and conventional fertilizer

10.1101/755769 ◽

2019 ◽

Cited By ~ 2

Author(s):

Richard M Sharpe ◽

Luke Gustafson ◽

Seanna Hewitt ◽

Benjamin Kilian ◽

James Crabb ◽

...

Keyword(s):

Secondary Metabolites ◽

Solanum Lycopersicum ◽

Organic Fertilizer ◽

Agricultural Practices ◽

Organic Soil ◽

Fertilizer Treatment ◽

Tomato Genome ◽

Mature Fruit ◽

Solanum Lycopersicum L ◽

Leaf Tissues

ABSTRACTEnhanced levels of antioxidants, phenolic compounds, carotenoids and vitamin C have been reported for several crops grown under organic fertilizer, albeit with yield penalties. As organic agricultural practices continue to grow and find favor it is critical to gain an understanding of the molecular underpinnings of the factors that limit the yields in organically farmed crops. Concomitant phytochemical and transcriptomic analysis was performed on mature fruit and leaf tissues derived from Solanum lycopersicum L. ‘Oregon Spring’ grown under organic and conventional fertilizer conditions to evaluate the following hypotheses. 1. Organic soil fertilizer management results in greater allocation of photosynthetically derived resources to the synthesis of secondary metabolites than to plant growth, and 2. Genes involved in changes in the accumulation of phytonutrients under organic fertilizer regime will exhibit differential expression, and that the growth under different fertilizer treatments will elicit a differential response from the tomato genome. Both these hypotheses were supported, suggesting an adjustment of the metabolic and genomic activity of the plant in response to different fertilizers. Organic fertilizer treatment showed an activation of photoinhibitory processes through differential activation of nitrogen transport and assimilation genes resulting in higher accumulation of phytonutrients. This information can be used to identify alleles for breeding crops that allow for efficient utilization of organic inputs.Significance statementOrganic fertilizer changes the expression of the tomato genome, induces photosynthetic stress which elicits higher production of secondary metabolites.

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Introduksi Gen DefH9-iaaM dan DefH9-RI-iaaM ke dalam Genom Tanaman Tomat Menggunakan Vektor Agrobacterium tumefaciens

Jurnal AgroBiogen ◽

10.21082/jbio.v6n1.2010.p18-25 ◽

2016 ◽

Vol 6 (1) ◽

pp. 18

Author(s):

Ragapadmi S Purnamaningsih

Keyword(s):

Acetic Acid ◽

Agrobacterium Tumefaciens ◽

Genetic Improvement ◽

Plant Cells ◽

Fruit Production ◽

Total Efficiency ◽

Parthenocarpic Fruit ◽

Tomato Genome ◽

Tomato Cultivars ◽

Indole 3 Acetic Acid

Introduction of DefH9-iaaM and DefH9-RI-iaaM Gene Into Tomato Genome Using Agrobacterium tumefaciens. Ragapadmi Purnamaningsih. Plant genetic improvement can be conducted through genetic engineering. Parthenocarpic fruit production could increase fruit production and its qulities. IAA genes were introduced into three tomato cultivars Ratna, Opal and LV 6117 using two constract genes DefH9-iaaM and DefH9-RI-iaaM. The iaaM gene is able to increase auxin biosynthesis in transgenic plant cells and organs because indol-eacetamide, synthesized by the product of the iaaM gene, is converted either chemically or enzimatically to indole-3-acetic acid (IAA), while the promotor DefH9 enable IAA gene expressed specifically in the ovules. The objectives of this experiment was to identify gene introduction into plant genom of three tomato cultivars. The factors tested were two constract of IAA genes (DefH9-iaaM or DefH9-RI-iaaM), tomato cultivars (Ratna, Opal, and LV 6117) and time of explant inoculation (5, 15, 30 minute). The result showed that the best time inoculation was 5 minute. Otherwise three tomato cultivars response better to DefH9-RI-iaaM than DefH9-iaaM. The total efficiency of regeneration and total efficiency of transformation of both genes were 25.38% and 20.32%. PCR analysis showed that 10 plant have positive PCR, were 1 plant carried (Opal) DefH9-iaaM gene and 9 plant (Ratna, Opal, LV 6117) carried DefH9-RI-iaaM gene.

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Annotation of the Tomato Genome

Compendium of Plant Genomes - The Tomato Genome ◽

10.1007/978-3-662-53389-5_9 ◽

2016 ◽

pp. 159-171

Author(s):

Stephane Rombauts

Keyword(s):

Tomato Genome

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Light and ripening-regulated BBX protein-encoding genes in Solanum lycopersicum

Scientific Reports ◽

10.1038/s41598-020-76131-0 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Bruno Silvestre Lira ◽

Maria José Oliveira ◽

Lumi Shiose ◽

Raquel Tsu Ay Wu ◽

Daniele Rosado ◽

...

Keyword(s):

Tomato Fruit ◽

Protein Family ◽

Tomato Genome ◽

Physiological Processes ◽

Fruit Development And Ripening ◽

Protein Encoding ◽

Ripening Inhibitor ◽

Encoding Genes ◽

Signalling Cascade

Abstract Light controls several aspects of plant development through a complex signalling cascade. Several B-box domain containing proteins (BBX) were identified as regulators of Arabidopsis thaliana seedling photomorphogenesis. However, the knowledge about the role of this protein family in other physiological processes and species remains scarce. To fill this gap, here BBX protein encoding genes in tomato genome were characterised. The robust phylogeny obtained revealed how the domain diversity in this protein family evolved in Viridiplantae and allowed the precise identification of 31 tomato SlBBX proteins. The mRNA profiling in different organs revealed that SlBBX genes are regulated by light and their transcripts accumulation is directly affected by the chloroplast maturation status in both vegetative and fruit tissues. As tomato fruits develops, three SlBBXs were found to be upregulated in the early stages, controlled by the proper chloroplast differentiation and by the PHYTOCHROME (PHY)-dependent light perception. Upon ripening, other three SlBBXs were transcriptionally induced by RIPENING INHIBITOR master transcriptional factor, as well as by PHY-mediated signalling and proper plastid biogenesis. Altogether, the results obtained revealed a conserved role of SlBBX gene family in the light signalling cascade and identified putative members affecting tomato fruit development and ripening.

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Basal differences in the transcriptional profiles of tomato leaves associated with the presence/absence of the resistance gene Mi-1 and changes in these differences after infestation by the whitefly Bemisia tabaci

Bulletin of Entomological Research ◽

10.1017/s0007485319000828 ◽

2019 ◽

Vol 110 (4) ◽

pp. 463-479

Author(s):

Clara I. Rodríguez-Alvarez ◽

Irene López-Vidriero ◽

José M. Franco-Zorrilla ◽

Gloria Nombela

Keyword(s):

Differential Expression ◽

Resistance Gene ◽

Bemisia Tabaci ◽

Plant Resistance ◽

Tomato Genome ◽

Transcriptional Profiles ◽

Resistance To Insects ◽

Before And After ◽

Genome Array ◽

Microarray Analyses

AbstractThe tomato Mi-1 gene mediates plant resistance to whitefly Bemisia tabaci, nematodes, and aphids. Other genes are also required for this resistance, and a model of interaction between the proteins encoded by these genes was proposed. Microarray analyses were used previously to identify genes involved in plant resistance to pests or pathogens, but scarcely in resistance to insects. In the present work, the GeneChip™ Tomato Genome Array (Affymetrix®) was used to compare the transcriptional profiles of Motelle (bearing Mi-1) and Moneymaker (lacking Mi-1) cultivars, both before and after B. tabaci infestation. Ten transcripts were expressed at least twofold in uninfested Motelle than in Moneymaker, while other eight were expressed half or less. After whitefly infestation, differences between cultivars increased to 14 transcripts expressed more in Motelle than in Moneymaker and 14 transcripts less expressed. Half of these transcripts showed no differential expression before infestation. These results show the baseline differences in the tomato transcriptomic profile associated with the presence or absence of the Mi-1 gene and provide us with valuable information on candidate genes to intervene in either compatible or incompatible tomato–whitefly interactions.

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