National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
Plant Cell Rep. 2012 Feb;31(2):323-37. doi: 10.1007/s00299-011-1168-x. Epub 2011 Oct 13.
The unavailability of microsatellite markers and saturated genetic linkage map has restricted the genetic improvement of foxtail millet [Setaria italica (L.) P. Beauv.], despite the fact that in recent times it has been documented as a new model species for biofuel grasses. With the objective to generate a good number of microsatellite markers in foxtail millet cultivar 'Prasad', 690 clones were sequenced which generated 112.95 kb high quality sequences obtained from three genomic libraries each enriched with different microsatellite repeat motifs. Microsatellites were identified in 512 (74.2%) of the 690 positive clones and 172 primer pairs (pp) were successfully designed from 249 (48.6%) unique SSR-containing clones. The efficacies of the microsatellite containing genomic sequences were established by superior primer designing ability (69%), PCR amplification efficiency (85.5%) and polymorphic potential (52%) in the parents of F(2) mapping population. Out of 172 pp, functional 147 markers showed high level of cross-species amplification (74%) in six grass species. Higher polymorphism rate and broad range of genetic diversity (0.30-0.69 averaging 0.58) obtained in constructed phylogenetic tree using 52 microsatellite markers, demonstrated the utility of markers in germplasm characterizations. In silico comparative mapping of 147 foxtail millet microsatellite containing sequences against the mapping data of sorghum (18%), maize (16%) and rice (5%) indicated the presence of orthologous sequences of the foxtail millet in the respective species. The result thus demonstrates the applicability of microsatellite markers in various genotyping applications, determining phylogenetic relationships and comparative mapping in several important grass species.
尽管近年来已将谷子 [Setaria italica (L.) P. Beauv.] 作为生物燃料草的新型模式物种进行了记录，但微卫星标记的不可用性和饱和的遗传连锁图谱限制了谷子的遗传改良。本研究旨在为谷子品种 'Prasad' 生成大量微卫星标记，为此对三个分别富含不同微卫星重复基序的基因组文库中的 690 个克隆进行了测序，共生成了 112.95 kb 的高质量序列。在 690 个阳性克隆中有 512 个（74.2%）克隆中鉴定到了微卫星，从 249 个（48.6%）含有独特 SSR 的克隆中成功设计了 172 对引物。通过在 F2 作图群体的亲本中具有优越的引物设计能力（69%）、PCR 扩增效率（85.5%）和多态性潜力（52%），证实了含有微卫星的基因组序列的有效性。在 172 对引物中，147 个功能标记在 6 种禾本科植物中显示出较高的种间扩增能力（约 74%）。使用 52 个微卫星标记构建的系统发育树显示出较高的多态性率和广泛的遗传多样性（0.30-0.69，平均值为 0.58），证明了这些标记在种质特性分析中的实用性。147 个谷子微卫星标记序列与高粱 (18%)、玉米 (16%)和水稻 (~5%)的图谱数据的比较作图表明，在相应物种中存在谷子的直系同源序列。因此，结果表明微卫星标记可应用于多种基因型分析应用、确定种间进化关系和在几个重要的禾本科植物中的比较作图。
