Abstract: To develop the fine and reliable molecular markers in Arabidopsis thaliana, this work analyzed the whole genome sequence of Columbia and Landsberg erecta with comparative genomics. From total 10 449 insertion/deletion (INDEL) 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 first-pass mapping molecular markers that are relatively evenly distributed in five chromosomes of Arabidopsis thaliana. When using these molecular markers, we were able to obtain stable polymerase chain reaction (PCR) and agarose gel electrophoresis results under uniform reaction system and amplification conditions. This study will facilitate researchers to find suitable molecular markers, and under the common instrument conditions and lower experimental costs, to quickly locate the mutant gene and improve the efficiency of gene map-based cloning.
Key words: Arabidopsis thaliana; molecular marker; map-based cloning; mutant screening; gene mapping