Development and validation of microsatellite markers for Brachiaria ruziziensis obtained by partial genome assembly of Illumina single-end reads.
Development and validation of microsatellite markers for Brachiaria ruziziensis obtained by partial genome assembly of Illumina single-end reads.
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通过 Illumina 单端读数的部分基因组组装获得的 Brachiaria ruziziensis 微卫星标记的开发和验证。
DOI：
10.1186/1471-2164-14-17
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发表时间：
2013-01-16
期刊：
影响因子：
4.4
通讯作者：
Ferreira ME
中科院分区：
文献类型：
--
作者：
Silva PI;Martins AM;Gouvea EG;Pessoa-Filho M;Ferreira ME
鲁孜臂尾草（Brachiaria ruziziensis）是热带地区最重要的牧草之一。应用基因组学工具帮助筛选优良基因型，可为白螺旋藻育种提供支持。然而，关于ruziziensis基因组的信息完全缺乏。此外，基因组工具的可用性，如分子标记，以支持白僵菌育种计划是相当有限的。近年来，新一代测序技术已被应用于微卫星区域识别和引物设计中。在这项研究中，我们提出了一组经过验证的ruziziensis Brachiaria SSR标记，这些标记是从单端Illumina reads的从头部分基因组组装中选择的。总共检测到85,567个完美微卫星位点，覆盖范围至少为10倍。我们选择了500个微卫星位点进行引物设计和合成，并测试了269个引物对，其中198个引物对在11个有代表性的ruziziensis材料上具有多态性。介绍了这些引物对的描述性统计数据，以及对其他相关臂鱼物种的标记可转移性的估计。最后，验证了包含30个最具信息量标记的11个多重标记，并提出了一套用于ruziziensis遗传分析的方法。研究表明，从基因组组装的Illumina单端DNA序列中检测和开发微卫星标记是高效的。所开发的标记易于进行遗传分析和标记辅助选择。使用这种方法开发微卫星标记对于基因组信息有限的物种是有希望的，它们的育种计划将受益于基因组工具的使用。据我们所知，这是为这一重要物种开发的第一套微卫星标记。
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. 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. 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 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. 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 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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