• Touchkanin Jongjitvimol
  • Sittichai Urtgam
Keywords: Landrace rice, Phitsanulok, Identification, DNA barcode, trnH-psbA


Landrace rice identification is generally based on morphological characters, which is costly, labor-intensive including time-consuming process. This study was aimed to improve the identification of Phitsanulok’s Landrace rice assay using DNA barcoding based on nucleotide sequence diversity at trnH-psbA locus. The PCR product was amplified corresponding to ~650 bp long which could classify Phitsanulok’s landrace rice into 2 groups. Ton Dip and Lao is the farthest evolution from the ancestor. Individual sequence among 35 landrace-rice cultivars had a high genetic divergence (%K2P) approximately 19%, compared to Oryza sativa L. and 1.3% within group of the Phitsanulok’s landrace rice. Thirty out of Phitsanulok’s landrace rice cultivated varieties was able to be identified by using DNA barcode at trnH-psbA locus with the high efficient of 85.71%. This finding is the first report of implemented DNA barcode at trnH-psbA locus to identify Thai landrace rice’s subspecies using trnH-psbA DNA barcode . However, the combinations of more two DNA barcodes with different loci would be further experimental for increasing efficiency of identification in landrace rice cultivated varieties.


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Aiumsumang S, Phimphan S. Assessment of genetic relationship of rice using SSR markers. Khon Kaen Agriculture Journal. 2019; 47(1): 603-610.

Aiumsumang S, Srisuvoramas B, Koomsab K. Genetic relationship of some rice varieties in Phetchabun province using nucleotide sequence of rbcl genes. Journal of Science & Technology Phetchabun Rajabhat University. 2018; 3(1): 32-39.

Chase MW, Cowan RS, Hollingsworth PM. et al. A proposal for a standardised protocol to barcode all land plants. Taxon. 2007; 56: 295-299.

Costion C, Ford A, Cross H. et al. Plant DNA barcodes can accurately estimate species richness in poorly known floras. PLoS ONE. 2011; 6(11): e26841.

Hollingsworth PM. DNA barcoding plants in biodiversity hot spots: Progress and outstanding questions. Heredity. 2008; 101(1): 1-2.

Kim HM, Oh SH, Bhandari GS. et al. DNA barcoding of Orchidaceae in Korea. Molecular Ecology Resources. 2014; 14: 499–507.

Kress WJ, Erickson DL. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE. 2007; 2: e508.

Kress WJ, Wurdack KJ, Zimmer EA. et al. Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences. 2005; 102: 8369-8374.

Kumar S, Stecher G, Li M. et al. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution. 2018; 35: 1547-1549.

Ladpala S, Boonkorn P, Thaisuchat H. Genetic diversity of black sticky rice in Lampang province by RAPD technique. Khon Kaen Agriculture Journal. 2018; 46(1): 468-474.

Lahaye R, van der Bank M, Bogarin D. et al. DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences. 2008; 105(8): 2923-2928.

Liu Z, Zeng X, Yang D. et al. Applying DNA barcodes for identification of plant species in the family Araliaceae. Gene. 2012; 499: 76–80.

Ma X, Xie C, Liu C. et al. Species identification of medicinal pterdophytes by a DNA barcode marker, the chloroplast psbA-trnH intergenic region. Biological and Pharmaceutical Bulletin. 2010; 33: 1919–1924.

Maneenet T, Thanananta T, Thanananta N. Assessment of genetic relationship and Identification of Dendrobium section callista using nucleotide sequences of rbcL gene and trnH-psbA intergenic spacer region. Thai Journal of Science and Technology. 2018; 7(2): 181-190.

Monkheang P, Chaveerach A, Tanee T. et al. DNA Barcode for Identification of Processed Medicinal Senna Species. KKU Research Journal (Graduate Studies). 2013; 13(2): 18-30.

Mullis K, Faloona F, Scharf S. Specific enzymatic amplification of DNA in vitro: The polymerase chain reaction. Cold Spring Harbor Symposia on Quantitative Biology. 1986; 51(1): 263-273.

Osathanunkul M, Ounja S, Osathanunku R. et al. Evaluation of a DNA-based method for spice/herb authentication, so you do not have to worry about what is in your curry, buon appetite. PLoS ONE. 2017; 12(10): e0186283.

Phosiri P, Sreewongchai T, Chowpongpang S. Genetic relationship analysis of rice using AFLP marker. Proceedings of The 54th Kasetsart University Annual Conference. 2017; 285-292.

Phungsombat W, Hutsadang K, Bodeerat SC. et al. The validation of DNA markers for landrace rice varieties discrimination. Proceeding of 12th Rajamangala University of Technology Tawan-ok Research Conference. 2019; 1101-1111.

Ribeiro PL, Rapini A, Silva UCS, Berg C. Using multiple analytical methods to improve phylogenetic hypotheses in Minaria (Apocynaceae). Molecular Phylogenetics and Evolution. 2012; 65(3): 915-925.

Sang T, Crawford DJ, Stuessy TF. Chloroplast DNA phylogeny, reticulate evolution and biogeography of Paeonia (Paeoniaceae). American Journal of Botany. 1997; 84: 1120-1136.

Soltis PS & Soltis DE. Applying the bootstrap in phylogeny reconstruction. Statistical Science. 2003; 18(2): 256–267.

Somjai O, Nualsri C, Laosuwan P. Genetic diversity of indigenous rice in Nathawi basin of Songkhla province by seed morphology and microsatellite markers. Agricultural Science Journal. 2010; 41(1): 89-97.

Tajima F & Nei M. Estimation of evolutionary distance between nucleotide sequences. Molecular Biology and Evolution. 1984; 1: 269-285.

Tamura K & Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution. 1993; 10: 512-526.

Tate JA, Simpson BB. Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploid species. Systematic Botany. 2003; 28: 723-737.

Techen N, Parveen I, Pan Z. et al. DNA barcoding of medicinal plant material for identification. Current Opinion in Biotechnology. 2014; 25C: 103-110.

Urtgam S & Jongjitvimol T. Landrace rice in Phitsanulok province. PSRU Journal of Science and Technology. 2019; 4(1): 19-27.

Waugh J. DNA barcoding in animal species: progress, potential and pitfalls. BioEssays. 2018; 29: 188–197.

Zuo Y, Chen C, Kondo K. et al. DNA barcoding of Panax species. Planta Medica. 2011; 77(2): 182-187.

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