为了开发精细可靠且易用的拟南芥(Arabidopsis thaliana)分子标记，通过比较基因组学，分析拟南芥哥伦比亚(Columbia)和兰兹伯格(Landsberg erecta)2个生态型的全基因组序列，从 10 449个不小于 6个碱基的插入 /缺失(INDEL)DNA片段中筛选得到 2 321个新的 INDEL标记。针对每个标记位点，设计一对或多对引物序列(共计 4 764对)。在此基础上选择相对均匀分布在拟南芥 5条染色体的 20个初定位分子标记，它们能够在统一的反应体系和扩增条件下获得稳定的聚合酶链式反应(PCR)和琼脂糖凝胶电泳结果。该研究能够方便研究者找到合适的分子标记，在常规的仪器条件和较低的试验成本下，快速进行突变体基因定位，提高基因图位克隆效率。

To develop the.ne and reliable molecular markers in Arabidopsis thaliana, this work analyzed the whole ge-nome sequence of Columbia and Landsberg erecta with comparative genomics. From total 10 449 insertion/deletion (IN-DEL) DNA fragments that have no less than six bases, we screened 2 321 INDEL molecular markers. For each marker, at least one pair of primers (a total of 4 764) were designed. Based on this, we randomly selected 20.rst-pass mapping molecular markers that are relatively evenly distributed in.ve chromosomes of Arabidopsis thaliana. When using these molecu-lar markers, we were able to obtain stable polymerase chain reaction (PCR) and agarose gel electrophoresis results under uni-form reaction system and ampli.cation conditions. This study will facilitate researchers to.nd suitable molecular markers, and under the common instrument conditions and lower experimental costs, to quickly locate the mutant gene and improve the e.ciency of gene map-based cloning.