Genetic Diversity of Landrace Rice Varieties in Lower Northern Thailand Using Chloroplast DNA Markers

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Abstract
In this study, the genetic diversity and evolutionary relationship among 65 Thai rice varieties were classified by the neighbor‐joining (NJ) analysis of DNA sequences, amplified by three cpDNA barcoding markers, namely, mat K , rbc L, and trn H -psb A. Based on DNA sequencing analyses, all studied rice varieties were incorporated with 20 plant accessions by comparison with the rice reference genome available on GenBank. These accessions were categorized into two groups of an ingroup (belonging to 17 accessions of Oryza genus). The findings revealed that the highest species resolution (100%) was achieved by using the mat K gene individually and combination of the mat K and rbc L genes. These markers proved highly effective in distinguishing landrace rice varieties from the outgroup (reference species of rice and grasses), with bootstrap support values ranging from 25% to 100%. Meanwhile, the classification of landrace rice varieties was successfully accomplished using the rbc L gene. However, it was unable to distinguish between the ingroup and outgroup. Additionally, the trn H -psb A marker exhibited a limited effectiveness in distinguishing native rice varieties from either the ingroup or outgroup. In combination with two or three markers, only the combination of mat K and rbc L genes exhibited the capability to distinguish all rice species from grass. However, combining either the mat K or rbc L gene with the trn H -psb A gene trended to enhance the efficacy in classifying native rice varieties. These findings, based on the genetic distance values obtained through various DNA markers using the Kimura two‐parameter model, were proved that the studied Thai rice varieties belong to the Oryza sativa L. species.
Funding Information
  • Pibulsongkram Rajabhat University

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