应用限制性酶切位点相关DNA测序技术(RAD-seq)检测白洋淀和微山湖野生莲多样性

Genetic Diversity and Structure of Wild Asian Lotus Populations from Baiyangdian Lake and Weishan Lake Using RAD-seq/

采集莲(Nelumbo Adans.)样本共127份,其中:白洋淀野生莲居群样本60份、微山湖居群样本45份、对照样本共22份(黑龙江、吉林、辽宁、内蒙、湖南、四川野生莲样本6份,古代莲样本4份,莲栽培品种样本5份,泰国、印度、越南、澳大利亚的野生莲样本5份,美洲莲、亚美杂交莲样本各1份)。采用限制性酶切位点相关DNA测序技术(RAD-seq)对莲样本单核苷酸多态性(SNP)检测、遗传多样性和遗传结构分析。结果表明:对116份莲样本简化测序,共得到高质量序列数919915896条、高质量碱基数据128055038010 bp。经单核苷酸多态性检测,共得到535269个单核苷酸多态性标记,构建了邻接法(NJ)系统发育树和群体遗传结构图;系统发育树表明,所有莲样本可分为10个分支,其中48份白洋淀野生莲样本、36份微山湖野生莲样本、6份中国其他地区野生莲样本、4份古代莲样本,泰国、印度等外国野生莲样本共同组成1个伞状分支。遗传结构分析表明,白洋淀和微山湖野生莲居群主体属于同一遗传背景,与系统发育树反映的结果高度一致。说明在大地理范围的外国野生莲作为对照的背景下,白洋淀野生莲居群和微山湖野生莲居群之间未呈现显著遗传分化。

The restriction-site associated DNA sequencing(RAD-seq)was used to sequence a total of 127 lotus germplasm samples,including 60 wild Asian lotus samples from Baiyangdian Lake and Weishan Lake and 22 comparison samples including wild Asian lotus samples from other regions of China,ancient Asian lotus samples,Asian lotus cultivars samples,wild Asian lotus samples from other countries,American lotus and Asian-American hybrid lotus sample,and their genetic diversity and structure were analyzed.All of 919915896 high-quality reads and 128055038010 bp high-quality data were obtained.The 535269 single nucleotide polymorphism(SNP)were obtained by SNP detection.Neighbor-Joinning(NJ)phylogenetic tree were constructed based on these SNP.According to the phylogenetic tree,all lotus samples were divided into 10 branches,of which 48 Baiyangdian Lake wild Asian lotus samples,36 Weishan Lake wild Asian lotus samples,6 wild Asian lotus samples from other regions of China,4 ancient lotus samples and wild Asian lotus samples from other countries including Thailand and India were clustered into one umbrella-shape branch.By genetic structure analysis,Baiyangdian and Weishanhu populations belong to the same genetic pool,which was highly consistent with the result revealed by the phylogenetic tree.Therefore,there was no obvious genetic differentiation between Baiyangdian Lake and Weishan Lake populations in the context of a large geographical range of lotus samples from other countries used as comparison.