ArticleBMC genomics2013
Development and validation of microsatellite markers for Brachiaria ruziziensis obtained by partial genome assembly of Illumina single-end reads.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
- Simple Sequence Repeat-Based Genetic Diversity Analysis of Alfalfa Varieties.International journal of molecular sciences · 2025Article
- An Overview of the Genetics and Genomics of theFrontiers in plant science · 2021Review
- Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Frontiers in plant science · 2021Article
- Genetic diversity of leafy amaranth (Breeding science · 2019Article
- Expected Genotype Quality and Diploidized Marker Data from Genotyping-by-Sequencing of Urochloa spp. Tetraploids.The plant genome · 2019Article
- SSR identification and marker development for sago palm based on NGS genome data.Breeding science · 2019Article
- Location of low copy genes in chromosomes of Brachiaria spp.Molecular biology reports · 2018Article
- Genetic diversity and population structure ofRevista brasileira de botanica : Brazilian journal of botany · 2018Article
- Transcriptome Analysis and Microsatellite Markers Development of a Traditional Chinese Medicinal HerbEvolutionary bioinformatics online · 2018Article
- Microsatellite marker development by partial sequencing of the sour passion fruit genome (Passiflora edulis Sims).BMC genomics · 2017Article
- Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes.BMC genomics · 2017Article
- Molecular Characterizations of Kenyan Brachiaria Grass Ecotypes with Microsatellite (SSR) Markers.Agronomy (Basel, Switzerland) · 2017Article
- Article
- Microsatellite loci for Urochloa decumbens (Stapf) R.D. Webster and cross-amplification in other Urochloa species.BMC research notes · 2016Article
- Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae).Molecules (Basel, Switzerland) · 2016Article
- Development and characterization of polymorphic genic-SSR markers in Larix kaempferi.Molecules (Basel, Switzerland) · 2015Article
- De novo assembly and discovery of genes that are involved in drought tolerance in Tibetan Sophora moorcroftiana.PloS one · 2015Article
- De Novo Transcriptome Assembly and Development of Novel Microsatellite Markers for the Traditional Chinese Medicinal Herb, Veratrilla baillonii Franch (Gentianaceae).Evolutionary bioinformatics online · 2015Article
- iMSAT: a novel approach to the development of microsatellite loci using barcoded Illumina libraries.BMC genomics · 2014Article
- Whole genome shotgun sequences for microsatellite discovery and application in cultivated and wild Macadamia (Proteaceae).Applications in plant sciences · 2014Article
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5 authors.
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Abstract
backgroundBrachiaria ruziziensis is one of the most important forage species planted in the tropics. The application of genomic tools to aid the selection of superior genotypes can provide support to B. ruziziensis breeding programs. However, there is a complete lack of information about the B. ruziziensis genome. Also, the availability of genomic tools, such as molecular markers, to support B. ruziziensis breeding programs is rather limited. Recently, next-generation sequencing technologies have been applied to generate sequence data for the identification of microsatellite regions and primer design. In this study, we present a first validated set of SSR markers for Brachiaria ruziziensis, selected from a de novo partial genome assembly of single-end Illumina reads.
resultsA total of 85,567 perfect microsatellite loci were detected in contigs with a minimum 10X coverage. We selected a set of 500 microsatellite loci identified in contigs with minimum 100X coverage for primer design and synthesis, and tested a subset of 269 primer pairs, 198 of which were polymorphic on 11 representative B. ruziziensis accessions. Descriptive statistics for these primer pairs are presented, as well as estimates of marker transferability to other relevant brachiaria species. Finally, a set of 11 multiplex panels containing the 30 most informative markers was validated and proposed for B. ruziziensis genetic analysis.
conclusionsWe show that the detection and development of microsatellite markers from genome assembled Illumina single-end DNA sequences is highly efficient. The developed markers are readily suitable for genetic analysis and marker assisted selection of Brachiaria ruziziensis. The use of this approach for microsatellite marker development is promising for species with limited genomic information, whose breeding programs would benefit from the use of genomic tools. To our knowledge, this is the first set of microsatellite markers developed for this important species.
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