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

Authors

  • Nongnat Phoka Interdisciplinary Graduate Program in Genetic Engineering, Faculty of Graduate School, Kasetsart University, Bangkok 10900, Thailand.
  • Somvong Tragoonrung DNA Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, P.O.BOX 7, Thailand.
  • Apichart Vanavichit Rice Gene Discovery unit, National Center for Genetic Engineering and Biotechnology, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, P.O.BOX 7, Thailand.

Keywords:

genetic variation, nucleotide diversity, haplotypes, lipoxygenase, Oryza sativa

Abstract

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. 

Downloads

Published

2010-06-30

How to Cite

Nongnat Phoka, Somvong Tragoonrung, and Apichart Vanavichit. 2010. “Sequence Variation and Haplotype Structure in the Lox3 Gene of Oryza Sativa L”. Agriculture and Natural Resources 44 (3). Bangkok, Thailand:372-80. https://li01.tci-thaijo.org/index.php/anres/article/view/244942.

Issue

Vol. 44 No. 3 (2010): May-June

Section

Research Article

License

online 2452-316X print 2468-1458/Copyright © 2022. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/),
production and hosting by Kasetsart University of Research and Development Institute on behalf of Kasetsart University.