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.
Highlights
Brachiaria ruziziensis is one of the most important forage species planted in the tropics
We present a first set of 500 SSR markers developed for Brachiaria ruziziensis, selected from a de novo partial genome assembly of single-end Illumina reads
In order to select loci for subsequent primer design, we looked for perfect microsatellites in contigs >200 pb with a minimum 10X coverage
Summary
Brachiaria 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. The availability of genomic tools, such as molecular markers, to support B. ruziziensis breeding programs is rather limited. A few apomictic brachiaria clones occupy tens of millions of hectares in the country [3], what represents a high risk of genetic vulnerability for forage production. This risk could be reduced with the increased use of genetic diversity conserved in germplasm banks in order to generate recombinant genotypes in breeding programs. The development of new cultivars must be a dynamic process, providing the pasture production sector with increasing genetic diversity
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