Abstract:Drought tolerance is a comprehensive quantitative trait being understood further at the molecular genetic level. Abscisic acid (ABA) is the main drought induced hormone which regulates the expression of many genes related to drought responses. Nine-cis-epoxycarotenoid dioxygenase (NCED3) is thought to be a key enzyme in ABA biosynthesis. In this paper, we measured the times of ABA content increase under drought stress, and sequenced and compared the sequence of AtNCED3 among 22 Arabidopsis thaliana accessions. The results showed that the times of ABA content increase under drought stress was highly variable among these accessions. High density of single nucleotide polymorphism (SNP) and insertion/deletion (Indel) were found in AtNCED3 region, on average 1 SNP per 87.4bp and 1 indel per 502 bp. Nucleotide diversity was significantly lower in coding region than that in non-coding region. The results of association study with ANOVA analysis suggested that the 274th site (PnS) and the 327th site (P nR) amino acid variations might be the cause of ABA content increase of 163av accession under drought stress.