Genetic Diversity and Population Structure of Capirona (Calycophyllum spruceanum Benth.) from the Peruvian Amazon Revealed by RAPD Markers

Abstract

Capirona (Calycophyllum spruceanum Benth.) is a tree species of commercial importance widely distributed in South American forests that is traditionally used for its medicinal properties and wood quality. Studies on this tree species have been focused mainly on wood properties, propagation, and growth. However, genetic studies on capirona have been very limited to date. Currently, it is possible to explore genetic diversity and population structure in a fast and reliable manner by using molecular markers. We here used 10 random amplified polymorphic DNA (RAPD) markers to analyze the genetic diversity and population structure of 59 samples of capirona that were sampled from four provinces located in the eastern region of the Peruvian amazon. A total of 186 bands were manually scored, generating a 59 × 186 presence/absence matrix. A dendrogram was generated using the UPGMA clustering algorithm, and, similar to the principal coordinate analysis (PCoA), it showed four groups that correspond to the geographic origin of the capirona samples (LBS, Irazola, Masisea, Iñapari). Similarly, a discriminant analysis of principal components (DAPC) and STRUCTURE analysis confirmed that capirona is grouped into four clusters. However, we also noticed that a few samples were intermingled. Genetic diversity estimation was conducted considering the four groups (populations) identified by STRUCTURE software. AMOVA revealed the greatest variation within populations (71.56%) and indicated that variability among populations is 28.44%. Population divergence (Fst) between clusters 1 and 4 revealed the highest genetic difference (0.269), and the lowest Fst was observed between clusters 3 and 4 (0.123). RAPD markers were successful and effective. However, more studies are needed, employing other molecular tools. To the best of our knowledge, this is the first investigation employing molecular markers in capirona in Peru considering its natural distribution, and as such it is hoped that this helps to pave the way towards its genetic improvement and the urgent sustainable management of forests in Peru.

Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum Spruceanum, Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species

“…Very few molecular studies have been conducted for this forest species. Russell et al [ 3 ], Tauchen et al [ 5 ], and Saldaña et al [ 8 ] determined the genetic variation of capirona using molecular markers, such as amplified fragment length polymorphisms (AFLP), internal transcribed spacer (ITS), and random-amplified polymorphic DNA (RAPD), respectively, in different populations of capirona from the Peruvian Amazon. Their results demonstrated a greater variation within provenances than among them.…”

GENETIC STRUCTURE AND DIVERSITY OF A PERUVIAN COLLECTION OF A HIGH-QUALITY WOOD TREE SPECIES, ULCUMANO (Retrophyllum rospigliosii, PODOCARPACEAE)

“…The use of molecular markers in forest species has increased efficiency of genetic improvement programs (Araya et al, 2005). Specifically, molecular markers are used to (i) estimate the rate of gene migration and (ii) characterize and analyze systems of mating, as well as for (iii) paternity or kinship analysis (Valadez and Kahl, 2000), and (iv) phylogenetic studies and genetic diversity estimation (Saldaña et al, 2021). Unfortunately, the use of molecular markers in the forest genetic resources of Peru has not emerged yet.…”

“…Randomly Amplified Polymorphic DNA (RAPD) markers, which were initially described by Williams et al (1990), are still used for initial research in genetic diversity and population structure of plant species. These baseline studies are crucial for the development of conservation programs, being RAPD markers a useful tool to obtain key information in a short time (Renau-Morata et al, 2005;Tijerino et al, 2016;Saldaña et al, 2021). In fact, the efficacy of the RAPD technique in revealing DNA-level genetic variation has been demonstrated for different species such as capirona (Calycophyllum spruceanum Benth.)…”

“…In fact, the efficacy of the RAPD technique in revealing DNA-level genetic variation has been demonstrated for different species such as capirona (Calycophyllum spruceanum Benth.) (Saldaña et al, 2021). In addition, RAPD markers are inexpensive, easy to use, and require low DNA concentrations to generate genetic profiles in a short time (Saldaña et al, 2021).…”

“…(Saldaña et al, 2021). In addition, RAPD markers are inexpensive, easy to use, and require low DNA concentrations to generate genetic profiles in a short time (Saldaña et al, 2021). In this sense, Gómez et al (1997) have indicated that RAPD markers can be employed for genetic mapping in conifers, and to estimate their genetic diversity.…”