Genome-Wide SNP Genotyping to Infer the Effects on Gene Functions in Tomato

Hirakawa, Hideki; Shirasawa, Kenta; Ohyama, Akio; Fukuoka, Hiroyuki; Aoki, Koh; Rothan, Christophe; Sato, Shusei; Isobe, Sachiko; Tabata, Satoshi

doi:10.1093/dnares/dst005

Cited by 58 publications

(48 citation statements)

References 29 publications

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“…SNP markers constitute the most abundant type of DNA polymorphism in genomic sequences and are thought to play major roles in the induction of phenotypic variations [68]. RNA-seq, together with SNP discovery, can be applied to develop new markers in candidate genes for genetic breeding and to investigate the variability of these genes in rubber tree, which has been performed in other tree species.…”

Section: Resultsmentioning

confidence: 99%

De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways

et al. 2014

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Hevea brasiliensis (Willd. Ex Adr. Juss.) Muell.-Arg. is the primary source of natural rubber that is native to the Amazon rainforest. The singular properties of natural rubber make it superior to and competitive with synthetic rubber for use in several applications. Here, we performed RNA sequencing (RNA-seq) of H. brasiliensis bark on the Illumina GAIIx platform, which generated 179,326,804 raw reads on the Illumina GAIIx platform. A total of 50,384 contigs that were over 400 bp in size were obtained and subjected to further analyses. A similarity search against the non-redundant (nr) protein database returned 32,018 (63%) positive BLASTx hits. The transcriptome analysis was annotated using the clusters of orthologous groups (COG), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Pfam databases. A search for putative molecular marker was performed to identify simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). In total, 17,927 SSRs and 404,114 SNPs were detected. Finally, we selected sequences that were identified as belonging to the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways, which are involved in rubber biosynthesis, to validate the SNP markers. A total of 78 SNPs were validated in 36 genotypes of H. brasiliensis. This new dataset represents a powerful information source for rubber tree bark genes and will be an important tool for the development of microsatellites and SNP markers for use in future genetic analyses such as genetic linkage mapping, quantitative trait loci identification, investigations of linkage disequilibrium and marker-assisted selection.Citation: Mantello CC, Cardoso-Silva CB, da Silva CC, de Souza LM, Scaloppi Junior EJ, et al. (2014) De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways. PLoS ONE 9(7): e102665.

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Section: Resultsmentioning

confidence: 99%

De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways

et al. 2014

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“…The KatomicsDB contains links to the marker database described above, a functional SNP database (Hirakawa et al 2013a: http://plant1.kazusa.or.jp/tomato/), and a database for genome sequences of selected BAC clone mixtures in gene-rich regions (http://www.kazusa.or.jp/tomato_sbm/). …”

Section: Plant Species Registered In the Kazusa Marker Databasementioning

confidence: 99%

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

et al. 2014

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In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops.

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“…SNPs have been widely used in studies of gene function, phenotypes, evolution, and species diversity, because of their high density and convenience (Li et al, 2009;Hirakawa et al, 2013;Qi et al, 2013). An increasing number of high-density genetic linkage maps have been constructed in the peach (Martínez-García et al, 2013), oilseed rape (Delourme et al, 2013), and the cucumber (Qi et al, 2013), based on SNP mining from sequences or arrays.…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, SNPs have been used to distinguish between similar taxonomic groups and to investigate evolutionary relationships between plants ( Lu et al, 2013;Wang et al, 2014). Because of their wide distribution in genomes, SNPs can be used to infer gene function (Hirakawa et al, 2013;Guimaraes et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Large-scale detection and application of expressed sequence tag single nucleotide polymorphisms in Nicotiana

Wang¹,

Zhou²,

Wang³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Single nucleotide polymorphisms (SNPs) are widespread in the Nicotiana genome. Using an alignment and variation detection method, we developed 20,607,973 SNPs, based on the expressed sequence tag sequences of 10 Nicotiana species. The replacement rate was much higher than the transversion rate in the SNPs, and SNPs widely exist in the Nicotiana. In vitro verification indicated that all of the SNPs were high quality and accurate. Evolutionary relationships between 15 varieties were investigated by polymerase chain reaction with a special primer; the specific 302 locus of these sequence results clearly indicated the origin of Zhongyan 100. A database of Nicotiana SNPs (NSNP) was developed to store and search for SNPs in Nicotiana. NSNP is a tool for researchers to develop SNP markers of sequence data.

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Genome-Wide SNP Genotyping to Infer the Effects on Gene Functions in Tomato

Cited by 58 publications

References 29 publications

De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways

De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

Large-scale detection and application of expressed sequence tag single nucleotide polymorphisms in Nicotiana

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