Sequence Variation and Haplotype Structure in the Lox3 Gene of Oryza sativa L.

For 24 rice (Oryza sativa L.) varieties, genetic variation was studied of the Lox3 gene in samples of the two subspecies, japonica and indica. The genomic DNA was amplified, followed by DNA sequencing to detect sequence variation. A total of 13 single nucleotide polymorphisms (SNPs) was detected in the exon 4 containing lipoxygenase domain. The nucleotide diversity in the Lox3 region of O. sativa was 0.00112, which could be classified into ten haplotypes. Phylogenetic relationships among varieties were inferred using neighbor-joining methods. Cluster analysis showed that all populations could be clustered into five groups. The results also revealed that the haplotype of Oryza sativa ssp.japonica rice is distinctively separated from that of Oryza sativa ssp.indica rice.