ArticleBMC plant biology2016
High-throughput development of simple sequence repeat markers for genetic diversity research in Crambe abyssinica.
Article in BMC plant biology, 2016. 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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18 citing papers in PubMed.
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- Systematic Analysis of Survival-Associated Alternative Splicing Signatures in Thyroid Carcinoma.Frontiers in oncology · 2021Article
- Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences fromPeerJ · 2021Article
- Development of nuclear SSR and chloroplast genome markers in diverse Liriodendron chinense germplasm based on low-coverage whole genome sequencing.Biological research · 2020Article
- Complete Chloroplast Genomes ofPlants (Basel, Switzerland) · 2020Article
- Complete Chloroplast Genomes ofPlants (Basel, Switzerland) · 2019Article
- Molecular Characterization of 170 New gDNA-SSR Markers for Genetic Diversity in Button Mushroom (Mycobiology · 2019Article
- Comparative Chloroplast Genomics at Low Taxonomic Levels: A Case Study UsingFrontiers in plant science · 2019Article
- Development of novel EST-SSR markers in the macaúba palm (Acrocomia aculeata) using transcriptome sequencing and cross-species transferability in Arecaceae species.BMC plant biology · 2018Article
- Dynamic evolution and phylogenomic analysis of the chloroplast genome in Schisandraceae.Scientific reports · 2018Article
- Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies.BMC plant biology · 2018Article
- Interspecific Divergence of TwoFrontiers in plant science · 2018Article
- Complete Chloroplast Genome Sequence of Decaisnea insignis: Genome Organization, Genomic Resources and Comparative Analysis.Scientific reports · 2017Article
- Development of EST-SSR markers forApplications in plant sciences · 2017Article
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7 authors.
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Abstract
backgroundThe allohexaploid Crambe abyssinica (crambe) is an oilseed crop that has been recognized for its potential value in the chemical industry, particularly in terms of producing high-erucic acid content vegetable oil. However, as an understudied crop, improvement of crambe has been hampered by the lack of genetic and genomic information to enhance its yield, oil quality and resistance against biotic and abiotic stress. Development of molecular markers is therefore of great significance to facilitate genetic improvement of crambe.
resultsIn this study, high-throughput sequencing was performed to generate sequences for the transcriptome and genome of a widely planted crambe cultivar, Galactica. A total of 186,778 expressed sequence tag (EST) contigs as 8,130,350 genomic contigs were assembled as well. Altogether, 82,523 pairs of primers were designed in the flanking sequences of the simple sequence repeat (SSR) within these contigs. Virtual PCR analysis showed that a fraction of these primers could be mapped onto the genomes of related species of Brassica, including Brassica rapa, B. oleraceae and B. napus. Genetic diversity analysis using a subset of 166 markers on 30 independent C. abyssinica accessions exhibited that 1) 95 % of the designed SSRs were polymorphic among these accessions; 2) the polymorphism information content (PIC) value of the markers ranged from 0.13 to 0.89; 3) the genetic distances (coefficient NEI72) between accessions varied from 0.06 to 0.36. Cluster analysis subsequent on the accessions demonstrated consistency with crambe breeding history. F-statistics analysis revealed a moderate level of genetic differentiation in C. abyssinica (Gst = 0.3934) and a accordingly low estimated gene flow (Nm = 0.7709).
conclusionApplication of high-throughput sequencing technology has facilitated SSR marker development, which was successfully employed in evaluating genetic diversity of C. abyssinica as demonstrated in our study. Results showed these molecular markers were robust and provided powerful tools for assessing genetic diversity and estimating crambe breeding history. Moreover, the SSR primers and sequence information developed in the study are freely available to the research community.
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