Abstract: In order to understand the DNA polymorphism of the waxy genes in waxy maize and flint maize landraces from Southwest China, the 25 sequences from the ninth exon to the fourteenth exon of waxy gene were cloned and sequenced. The sampled landraces included 16 waxy maize cultivars (Zea mays L. ceratina Kulesh.) and seven flint maize cultivars from Southwest China, and tow waxy maize cultivars from Argentina. Additionally we downloaded 16 homologous sequences from six Z. mays subsp. parviglimis individuals, five Z. luxurians individuals and five American landraces from NCBI. The sequences were aligned and DNA variations among them were analyzed. We found waxy maize, flint maize, and parviglumis had 14, 19, and 40 polymorphic sites, respectively. Within the Z. taxa samples, Chinese waxy maize contained 30% of the genetic diversity in Chinese flint maize and 14% of the genetic diversity in Z. mays subsp. parviglimis, respectively. The statistical Tajima’D significance was only found in Chinese waxy maize population. Seventy five percent of the Chinese waxy maize landraces contained one deletion of fifteen nucleotides, which encodes the amino acid sequence NKEAL and is located at the start site of the glycosyl transferases group 1 of waxy gene. Chinese waxy maize might be originated from one special mutant of flint maize and experienced one domestication bottleneck in the process of evolution. The founder effect made the nucleotide diversity of waxy gene in waxy maize lower than that in its relatives. To improve the quality and quantity of starch in maize different alleles from its relatives should be introduced into maize genome.

Key words: Waxy maize, waxy gene, Nucleotide polymorphism, Landrace