基于名优谷子品种晋谷21全基因组重测序的分子标记开发

Genome-wide Identification of Molecular Markers Based on Genomic Re-sequencing of Foxtail Millet Elite Cultivar Jingu 21

小米因其营养丰富日益受到重视,而小米的品质是民众选择小米时最为关注的指标。晋谷21米质优异,但由于缺少基因组信息,严重阻碍了其优异米质形成机制的研究。本研究利用高通量测序技术,对晋谷21全基因组进行重测序,获得了14.95 Gb高质量测序数据。进一步将其与豫谷1号参考基因组比较,发掘了169 037个In Del位点和1 167 555个SNP位点,其中长度在13~50 bp之间适于琼脂糖凝胶电泳检测的In Del位点为14 578个。选择其中1个SNP位点和68个In Del位点验证,表明利用二代测序技术开发的In Del和SNP标记真实可靠。基于名优谷子晋谷21重测序数据开发的In Del和SNP分子标记具有通用性,可用于其他谷子、狗尾草和谷莠子等种质资源的相关研究。同时,开发了一个晋谷21特异的In Del标记2G5501976,利用该标记即可快速鉴定待测材料是否为晋谷21及其衍生品种。本研究初步揭示了晋谷21的基因组特征,不仅为深入解析其优异米质形成的分子机制奠定了基础,而且为相关分子标记辅助育种、遗传分析和基因克隆提供了分子标记资源。

Foxtail millet becomes more and more popular for its rich nutrients, and the grain quality is the key concern that consumers would consider when selecting millet brand. Jingu 21 is an elite cultivar with high edible quality. However, the lack of genomic information impedes studies on the molecular mechanisms of millet quality formation. Here, we re-sequenced the whole genome of Jingu 21 using high-throughput sequencing technology, and obtained 14.95 Gb high quality data. By comparing sequence of Jingu 21 with the reference genome of Yugu 1, we identified 169 037 InDels and 1 167 555 SNPs. Of these InDels, 14 578 could be detected easily by agarose gel electrophoresis. One SNP and 68 InDel markers were selected to verify the polymorphism between Jingu 21 and Yugu 1, showing that the InDel and SNP markers developed by using next generation sequencing technology were reliable. Although the InDel and SNP markers were generated based on genome re-sequencing data of the elite cultivar Jingu 21, they could also be used for research on other foxtail millet, green foxtail, and giant foxtail. Moreover, a specific InDel marker 2G5501976 for Jingu 21 was developed, which could be used to identify Jingu 21 and its derivative varieties. Taken all together, the genomic characterization of Jingu 21 not only lays a foundation for elucidating the molecular mechanisms of high quality formation, but also provides a large number of molecular markers for marker-assisted selection of high qua-lity millet, genetic analysis and map-based cloning.