Development of Microsatellite Markers to Assess Genetic Diversity and Population Structure in Mitragyna Parvifolia (Roxb.) Korth
Revathy R.1, Manikandan S.2, Haritha S.3, Soosai Raj J.4, Shanthi A.5, Rajasugunasekar D6
1Revathy R., Scholar, Department of Genetics and Tree Improvement, ICFRE- Institute of Forest Genetics and Tree Breeding, Coimbatore (Tamil Nadu), India.
2Manikandan S., Department of Genetics and Tree Improvement, ICFRE- Institute of Forest Genetics and Tree Breeding, Coimbatore (Tamil Nadu), India.
3Haritha S., Department of Genetics and Tree Improvement, ICFRE- Institute of Forest Genetics and Tree Breeding, Coimbatore (Tamil Nadu), India.
4Dr Soosai Raj J., Department of Genetics and Tree Improvement, ICFRE- Institute of Forest Genetics and Tree Breeding, Coimbatore (Tamil Nadu), India.
5Dr Shanthi A., Department of Genetics and Tree Improvement, ICFRE- Institute of Forest Genetics and Tree Breeding, Coimbatore (Tamil Nadu), India.
6Dr Rajasugunasekar D, Department of Genetics and Tree Improvement, ICFRE- Institute of Forest Genetics and Tree Breeding, Coimbatore (Tamil Nadu), India.
Manuscript received on 04 February 2026 | First Revised Manuscript received on 09 February 2026 | Second Revised Manuscript received on 19 March 2026 | Manuscript Accepted on 15 April 2026 | Manuscript published on 30 April 2026 | PP: 13-21 | Volume-6 Issue-1, April 2026 | Retrieval Number: 100.1/ijb.A107206010426 | DOI: 10.54105/ijab.A1072.06010426
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© The Authors. Published by Lattice Science Publication (LSP). This is an open-access article under the CC-BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Abstract: Mitragyna parvifolia (Roxb.) Korth., Rubiaceae, is an economically important timber tree species. To meet the increasing market demand for M. parvifolia, it is necessary to assess genetic diversity within individuals to accelerate genetic improvement. Microsatellites, or simple sequence repeats (SSRs), are the most widely used molecular markers in population genetic studies. The present study estimated genetic variation in M. parvifolia among 20 individuals collected from wild populations using 10 polymorphic SSR markers. Allelic data were used to calculate genetic diversity parameters, including genotype distance, the Shannon index, and pairwise relatedness. The Analysis of molecular variance (AMOVA) was also performed to assess the distribution of genetic variation within and among the individuals. Further genotypic distance analysis revealed a wide range of divergence (6–30), indicating both close kinship and distinct lineages among individuals. The Principal Coordinates Analysis (PCoA) explained 45.97% of the total variation across the first three axes, with clear clustering patterns among populations. Another observation from the Analysis of Molecular Variance (AMOVA) showed that most genetic diversity resides within individuals (72%), followed by among individuals within populations (16%) and among populations (12%). Further, the analysis indicated moderate genetic differentiation (FST = 0.124, p < 0.001), with gene flow estimated at Nm = 1.768, suggesting substantial interpopulation connectivity. Shannon’s diversity index further supported high within-population diversity (sH = 0.559) compared to among-population variation (sH = 0.155). Pairwise relatedness estimates indicated that most individuals were genetically unrelated, confirming a broad and heterogeneous genetic base. The presence of population-specific alleles and moderate structuring highlights the importance of conserving diverse populations. The genetic diversity of M. parvifolia provides valuable insight for conservation strategies and future genetic improvement programs.
Keywords: Mitragyna Parvifolia, SSR Markers, Genetic Diversity, Genetic Improvement.
Scope of the Article: Plant Morphology