Genetic diversity and population structure of endangered rosewood from the Peruvian Amazon using ISSR markers

Abstract

Rosewood, Aniba rosaeodora is an endangered species in Amazon forests and its natural stands have been heavily depleted due to over-exploitation for the cosmetic industry. This study aimed to investigate the genetic diversity and population structure of 90 rosewood accessions from eight localities in the Peruvian Amazon through 11 Inter Simple Sequence Repeats (ISSR) primers. The ISSR primers produced a sum of 378 bands, of which 375 (99.2%) were polymorphic, with an average polymorphism information content (PIC) value of 0.774. The mean effective number of alleles (Ne), Shannon informative index (I), gene diversity (He) and total gene diversity (Ht) were 1.485, 0.294, 0.453 and 0.252, respectively. Analysis of molecular variance (AMOVA) showed the presence of maximum variability within populations (88%). The Structure algorithm, neighbor joining and principal coordinate analysis (PCoA) grouped the 90 rosewood accessions into three main populations (A, B and C). Diversity indices at the inter-population level revealed a greater genetic diversity in population A, due to higher gene flow. The neighbor-joining analysis grouped populations A and B, while population C was found to be divergent at the inter population level. We concluded that population A reflects higher genetic diversity and should be prioritized for future management and conservation plans.

In-Depth Genetic Diversity and Population Structure of Endangered Peruvian Amazon Rosewood Germplasm Using Genotyping by Sequencing (GBS) Technology

“…The analysis of molecular variance (AMOVA) is performed to investigate the level of genetic differentiation among studied populations. The AMOVA results revealed that higher genetic variations in rosewood germplasm were due to differences within the populations and these results were found in line with previous reports [29][30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45]. Santos et al [46] used RAPD markers for the characterization of central Brazilian Amazon germplasm and found higher genetic variations (76.6%) within populations than among (23.4%) populations.…”

“…All of these accessions were considered unclassified accessions as they revealed membership coefficients Q < 75%. Grouping of rosewood accession in this study was also supported by our very recent study in which Peruvian rosewood germplasm was characterized with an ISSR marker [29]. The neighbor-joining analysis also supported the clustering of STRUC-TURE software and grouped the whole germplasm into three populations on the basis of their collection points ( Figure 5).…”

“…Very recent studies confirmed genetic distance as a valuable criterion for the selection of parents that can be used in breeding activities [49,50]. Germplasm resources proposing the highest level of genetic distance must be properly conserved and utilize in future breeding programs for their improvement [29]. During this study, the maximum Jaccard coefficient of genetic dissimilarity was present between Tamshiyacu-2 and Mairiricay-15.…”

“…Santos et al [46] used RAPD markers for the characterization of central Brazilian Amazon germplasm and found higher genetic variations (76.6%) within populations than among (23.4%) populations. Very recently, Guizado et al [29] characterized the Peruvian rosewood using ISSR markers and found higher variations within populations (98.1%) than among (1.9%) populations. A previous study concluded that long-term natural selection and geographical isolation allowed the local population to conserve a specific genotype, thereby increasing the genetic variations between populations [51].…”

“…Previous studies explored the genetic diversity of Brazilian rosewood germplasm through RAPD markers [27] and SSR markers [28]. Very recently, Guizado et al [29] for the first time reported the characterization of Peruvian rosewood germplasm with molecular markers (ISSR markers) and confirmed the existence of a good level of genetic diversity in their germplasm. Genotyping by Sequencing (GBS) resulted in SNP and DArTseq markers have been found robust, high throughput and more informative compared to PCR-based markers [30,31].…”