Development and validation of microsatellite markers for <it>Brachiaria ruziziensis</it> obtained by partial genome assembly of Illumina single-end reads

• Main Authors: Silva Pedro IT, Martins Alexandre M, Gouvea Ediene G, Pessoa-Filho Marco, Ferreira Márcio E
• Format: Article
• Language: English
• Published: BMC 2013-01-01
• Series: BMC Genomics
• Online Access: http://www.biomedcentral.com/1471-2164/14/17

<p>Abstract</p> <p>Background</p> <p><it>Brachiaria ruziziensis</it> 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 <it>B. ruziziensis</it> breeding programs. However, there is a complete lack of information about the <it>B. ruziziensis</it> genome. Also, the availability of genomic tools, such as molecular markers, to support <it>B. ruziziensis</it> 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 <it>Brachiaria ruziziensis</it>, selected from a <it>de novo</it> partial genome assembly of single-end Illumina reads.</p> <p>Results</p> <p>A 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 <it>B. ruziziensis</it> 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 <it>B. ruziziensis</it> genetic analysis.</p> <p>Conclusions</p> <p>We 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 <it>Brachiaria ruziziensis</it>. 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.</p>