ArticleBMC genomics2014
Transcriptome sequencing of two parental lines of cabbage (Brassica oleracea L. var. capitata L.) and construction of an EST-based genetic map.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 52 citations in OpenAlex.
- Genetic dissection of morphological variation between cauliflower and a rapid cycling Brassica oleracea line.G3 (Bethesda, Md.) · 2023Article
- Genome-wide analysis-based single nucleotide polymorphism marker sets to identify diverse genotypes in cabbage cultivars (Brassica oleracea var. capitata).Scientific reports · 2022Article
- Development of a new set of genic SSR markers in the genus3 Biotech · 2021Article
- Advances in Multi-Omics Approaches for Molecular Breeding of Black Rot Resistance inFrontiers in plant science · 2021Review
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- Article
- Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome.Plant biotechnology journal · 2019Article
- Identification of NBS-encoding genes linked to black rot resistance in cabbage (Brassica oleracea var. capitata).Molecular biology reports · 2018Article
- Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants.Molecules (Basel, Switzerland) · 2018Review
- Development of SSR markers from transcriptomes forApplications in plant sciences · 2017Article
- De novo transcriptome analysis in radish (Raphanus sativus L.) and identification of critical genes involved in bolting and flowering.BMC genomics · 2016Article
- De novo assembly and characterization of the leaf, bud, and fruit transcriptome from the vulnerable tree Juglans mandshurica for the development of 20 new microsatellite markers using Illumina sequencing.Molecular genetics and genomics : MGG · 2016Article
- Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae).Molecules (Basel, Switzerland) · 2016Article
- Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.).DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- De novo Assembly and Characterization of the Transcriptome of Broomcorn Millet (Panicum miliaceum L.) for Gene Discovery and Marker Development.Frontiers in plant science · 2016Article
- Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage.BMC plant biology · 2015Article
- Recent progress in the use of 'omics technologies in brassicaceous vegetables.Frontiers in plant science · 2015Review
- Gleditsia sinensis: transcriptome sequencing, construction, and application of its protein-protein interaction network.BioMed research international · 2014Article
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundExpressed sequence tag (EST)-based markers are preferred because they reflect transcribed portions of the genome. We report the development of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers derived from transcriptome sequences in cabbage, and their utility for map construction.
resultsTranscriptome sequences were obtained from two cabbage parental lines, C1184 and C1234, which are susceptible and resistant to black rot disease, respectively, using the 454 platform. A total of 92,255 and 127,522 reads were generated and clustered into 34,688 and 40,947 unigenes, respectively. We identified 2,405 SSR motifs from the unigenes of the black rot-resistant parent C1234. Trinucleotide motifs were the most abundant (66.15%) among the repeat motifs. In addition, 1,167 SNPs were detected between the two parental lines. A total of 937 EST-based SSR and 97 SNP-based dCAPS markers were designed and used for detection of polymorphism between parents. Using an F2 population, we built a genetic map comprising 265 loci, and consisting of 98 EST-based SSRs, 21 SNP-based dCAPS, 55 IBP markers derived from B. rapa genome sequence and 91 public SSRs, distributed on nine linkage groups spanning a total of 1,331.88 cM with an average distance of 5.03 cM between adjacent loci. The parental lines used in this study are elite breeding lines with little genetic diversity; therefore, the markers that mapped in our genetic map will have broad spectrum utility.
conclusionsThis genetic map provides additional genetic information to the existing B. oleracea map. Moreover, the new set of EST-based SSR and dCAPS markers developed herein is a valuable resource for genetic studies and will facilitate cabbage breeding. Additionally, this study demonstrates the usefulness of NGS transcriptomes for the development of genetic maps even with little genetic diversity in the mapping population.
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