Exploring the genetic diversity and population structure of fenugreek (Trigonella foenum-graecum L.) genotypes through  inter-primer binding site (iPBS)-retrotransposon marker system

• Published in: Genetic resources and crop evolution 2024-10, Vol.71 (7), p.3253-3266
• Main Authors: Haliloğlu, Kamil, Özer, Hakan, Melik, Seda, Çoban, Furkan, Türkoğlu, Aras
• Format: Article
• Language: English
• Subjects: Agriculture; Aromatic compounds; Banded structure; Binding sites; Bioactive compounds; Biomedical and Life Sciences; Cluster analysis; Diabetes mellitus; Effectiveness; Fenugreek; Gene polymorphism; Genetic diversity; Genomic analysis; Genotypes; Heterozygosity; Life Sciences; Medicinal plants; Molecular structure; Nutritive value; Pattern analysis; Phylogeny; Plant Genetics and Genomics; Plant Physiology; Plant Sciences; Plant Systematics/Taxonomy/Biogeography; Polymorphism; Population genetics; Population structure; Population studies; Principal components analysis; Research Article; Subpopulations; Trigonella foenum-graecum
• ISSN: 0925-9864; 1573-5109
• DOI: 10.1007/s10722-023-01849-5

Fenugreek, a key medicinal-aromatic plant, offers rich bioactive compounds and nutritional value. Its diverse applications in cuisine and pharmaceuticals, coupled with health benefits like anti-diabetic and antioxidant properties, underscore its significance. Assessing genetic diversity becomes crucial for effective conservation and utilization. In this study, we examined the molecular diversity and population structure of 34 fenugreek genotypes collected from 18 countries worldwide using 24 inter-primer binding site (iPBS) markers. The iPBS primers produced 499 bands, with the total number of bands per primer ranging from 15 (iPBS-2224) to 26 (iPBS-2077), averaging 20.79. Polymorphism information content (PIC) ranged from 0.03 (iPBS-2374) to 0.34 (iPBS-2237), averaging 0.23. In the molecular analysis, the G1 genotype (Isfahan/Iran) exhibited the maximum effective number of alleles (Ne), Nie’s gene diversity (He), and Shannon’s information index (I) at 1.946, 0.486, and 0.679, respectively. Conversely, the G34 genotype (India/B) displayed the lowest values at 1.539, 0.350, and 0.535, respectively. Utilizing the unweighted pair-group means average (UPGMA) method, the iPBS-based tree revealed three distinct groups corresponding to the genomic constitution of fenugreek genotypes, a pattern partially corroborated by principal component analysis (PCA). Further model-based cluster analysis classified the 34 genotypes into four subpopulations, with expected heterozygosity (He) values of 0.428, 0.390, 0.426, and 0.007, respectively. The F-statistic (Fst) values for these subpopulations were 0.197, 0.210, 0.187, and 0.356, respectively. These findings underscored significant genetic variation among the tested fenugreek genotypes, thereby demonstrating the efficacy of iPBS markers in accurately assessing genetic diversity and phylogenetic relationships within fenugreek populations.