Applicability of inter-primer binding site iPBS- retrotransposon marker system for the assessment of genetic diversity and population structure of Peruvian rosewood (Aniba rosaeodora Ducke) germplasm.

BACKGROUND: Rosewood (Aniba rosaeodora Ducke), which has a great demand due to its essential oil globally, is an evergreen tree of the Amazon forests. Rosewood natural stands have been depleted through deforestation and the destruction of habitat. Currently, rosewood is included in the ICUN red list of endangered species. METHODS AND RESULTS: The 11 highly polymorphic primers amplified total 305 bands of which 301 (98.69%) were polymorphic. The number of effective alleles (Ne), Shannon's information index (I), overall gene diversity (Ht), gene diversity (h), and polymorphism information content (PIC) were (1.562), (0.505), (0.330), (0.337) and (0.343), respectively. These diversity indices explored high genetic diversity in rosewood germplasm. Among studied germplasm, the Santa Marta population was found most diverse by reflecting higher values of diversity indices while the Zungarococha population was found least diverse. The analysis of molecular variance (AMOVA) revealed that 79% of the genetic variation was within the populations. The STRUCTURE algorithm, unweighted pair group with arithmetic mean (UPGMA), and principal coordinate's analysis (PCoA) separated all germplasms into different population groups according to their geographic locations. Santa Marta population was found more diverse by reflecting higher values of diversity indices. The maximum genetic distance (0.868) was found between the Huajoya-10 and Nanay-3. In this investigation, iPBS- retrotransposon marker system was used to explore the genetic diversity of Peruvian rosewood germplasm. CONCLUSIONS: The results in this study such as higher genetic diversity indices, AMOVA (79%) within population and PIC value (0.343) showed the utility and reproducibility of iPBS-retrotransposons in this species successfully. The STRUCTURE algorithm separated the germplasms into six population groups according to their geographic locations. These results have valuable information for the conservation, management strategies and future breeding activities of rosewood.

Exploring the genetic diversity and population structure of scarlet eggplant germplasm from Rwanda through iPBS-retrotransposon markers.

BACKGROUND: Scarlet eggplant (Solanum aethiopicum gr. gilo) is a part of African indigenous vegetables and acknowledged as a source of variations in the breeding of Brinjal. Since its genetic diversity is still largely unexplored, therefore genetic diversity and population structure of this plant were investigated in this study. METHODS AND RESULTS: Scarlet eggplant germplasm made of fifty-two accessions originated from two districts of Rwanda was assessed by employing the iPBS-retrotransposon markers system. Twelve most polymorphic primers were employed for molecular characterization and they yielded 329 total bands whereupon 85.03% were polymorphic. The recorded mean polymorphism information content was 0.363 and other diversity indices such as; mean the effective number of alleles, mean Shannon's information index and gene diversity with the following values; 1.298, 0.300 and 0.187 respectively. A superior level of diversity was noticed among accessions from Musanze district. The model-based structure, neighbor-joining, and principal coordinate analysis (PCoA) gathered scarlet germplasm in a divergence manner to their collection district. Analysis of molecular variance (AMOVA) displayed that the utmost variations (81%) in scarlet eggplant germplasm are resulting in differences within populations. CONCLUSIONS: The extensive diversity of scarlet eggplant in Rwanda might be used to form the base and genetic resource of an exhaustive breeding program of this economically important African indigenous vegetable. For instance, accessions MZE53 and GKE11 might be proposed as parent candidates due to their high relative genetic distance (0.6781).