Morphological and genetic diversity of camu-camu [Myrciaria dubia (Kunth) McVaugh] in the Peruvian Amazon

Research Highlights: This study assesses the genetic diversity and structure of the ice-cream-bean (Inga edulis Mart.; Fabaceae) in wild and cultivated populations from the Peruvian Amazon. This research also highlights the importance of protecting the biodiversity of the forest in the Peruvian Amazon, to preserve the genetic resources of species and allow further genetic improvement. Background and Objectives: Ice-cream-bean is one of the most commonly used species in the Amazon region for its fruits and for shading protection of other species (e.g., cocoa and coffee plantations). Comprehensive studies about the impact of domestication on this species’ genetic diversity are needed, to find the best conservation and improvement strategies. Materials and Methods: In the current study, the genetic structure and diversity were assessed by genotyping 259 trees, sampled in five wild and 22 cultivated I. edulis populations in the Peruvian Amazon, with microsatellite markers. Pod length was measured in wild and cultivated trees. Results: The average pod length in cultivated trees was significantly higher than that in wild trees. The expected genetic diversity and the average number of alleles was higher in the wild compared to the cultivated populations; thus, a loss of genetic diversity was confirmed in the cultivated populations. The cultivated trees in the Loreto region had the highest pod length and lowest allelic richness; nevertheless, the wild populations’ genetic structure was not clearly differentiated (significantly different) from that of the cultivated populations. Conclusions: A loss of genetic diversity was confirmed in the cultivated populations. The species could have been simultaneously domesticated in multiple locations, usually from local origin. The original I. edulis Amazonian germplasm should be maintained. Cultivated populations’ new germplasm influx from wild populations should be undertaken to increase genetic diversity.

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THE CULTIVATION OF CAMU CAMU (MYRCIARIA DUBIA): A TREE PLANTING PROGRAMME IN THE PERUVIAN AMAZON

Forests Trees and Livelihoods ◽

10.1080/14728028.2006.9752547 ◽

2006 ◽

Vol 16 (1) ◽

pp. 85-101 ◽

Cited By ~ 11

Author(s):

JAMES W. PENN

Keyword(s):

Tree Planting ◽

Peruvian Amazon ◽

Myrciaria Dubia

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

Acta Amazonica ◽

10.1590/1809-4392201902203 ◽

2020 ◽

Vol 50 (3) ◽

pp. 204-212

Author(s):

Stalin Juan Vasquez GUIZADO ◽

Muhammad Azhar NADEEM ◽

Fawad ALI ◽

Muzaffer BARUT ◽

Ephrem HABYARIMANA ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Diversity ◽

Population Level ◽

Diversity Indices ◽

Issr Markers ◽

Neighbor Joining ◽

Peruvian Amazon ◽

Over Exploitation ◽

Issr Primers

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.

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Individual selection in a genetic test with 43 advanced progenies of camu-camu Myrciaria dubia Kunth (McVaugh) in floodable plot near Iquitos, Peruvian Amazon

Scientia Agropecuaria ◽

10.17268/sci.agropecu.2020.03.06 ◽

2020 ◽

Vol 11 (3) ◽

pp. 345-355

Author(s):

Mario Pinedo-Panduro ◽

Edvan Alves-Chagas ◽

Elvis Paredes-Davila ◽

Carlos Abanto-Rodriguez ◽

Ricardo Bardales-Lozano ◽

...

Keyword(s):

Genetic Test ◽

Individual Selection ◽

Peruvian Amazon ◽

Myrciaria Dubia

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Preliminary Evidence for Domestication Effects on the Genetic Diversity of Guazuma crinita in the Peruvian Amazon

Forests ◽

10.3390/f11080795 ◽

2020 ◽

Vol 11 (8) ◽

pp. 795

Author(s):

Lady Laura Tuisima-Coral ◽

Petra Hlásná Čepková ◽

John C. Weber ◽

Bohdan Lojka

Keyword(s):

Genetic Diversity ◽

Early Stage ◽

Geographic Distance ◽

Preliminary Evidence ◽

Group Method ◽

Peruvian Amazon ◽

Information Index ◽

Pair Group ◽

Timber Tree ◽

The Impact

Guazuma crinita, a fast-growing timber tree species, was chosen for domestication in the Peruvian Amazon because it can be harvested at an early age and it contributes to the livelihood of local farmers. Although it is in an early stage of domestication, we do not know the impact of the domestication process on its genetic resources. Amplified fragment length polymorphic (AFLP) fingerprints were used to estimate the genetic diversity of G. crinita populations in different stages of domestication. Our objectives were (i) to estimate the level of genetic diversity in G. crinita using AFLP markers, (ii) to describe how the genetic diversity is distributed within and among populations and provenances, and (iii) to assess the genetic diversity in naturally regenerated, cultivated and semi-domesticated populations. We generated fingerprints for 58 leaf samples representing eight provenances and the three population types. We used seven selective primer combinations. A total of 171 fragments were amplified with 99.4% polymorphism at the species level. Nei’s genetic diversity and Shannon information index were slightly higher in the naturally regenerated population than in the cultivated and semi-domesticated populations (He = 0.10, 0.09 and 0.09; I = 0.19, 0.15 and 0.16, respectively). The analysis of molecular variation showed higher genetic diversity within rather than among provenances (84% and 4%, respectively). Cluster analysis (unweighted pair group method with arithmetic mean) and principal coordinate analysis did not show correspondence between genetic and geographic distance. There was significant genetic differentiation among population types (Fst = 0.12 at p ˂ 0.001). The sample size was small, so the results are considered as preliminary, pending further research with larger sample sizes. Nevertheless, these results suggest that domestication has a slight but significant effect on the diversity levels of G. crinita and this should be considered when planning a domestication program.

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Genetic diversity and hybridization in the two species Inga ingoides and Inga edulis: potential applications for agroforestry in the Peruvian Amazon

Annals of Forest Science ◽

10.1007/s13595-015-0535-0 ◽

2016 ◽

Vol 73 (2) ◽

pp. 425-435 ◽

Cited By ~ 3

Author(s):

Alexandr Rollo ◽

Bohdan Lojka ◽

David Honys ◽

Bohumil Mandák ◽

Julio A. Chia Wong ◽

...

Keyword(s):

Genetic Diversity ◽

Peruvian Amazon ◽

Inga Edulis ◽

Potential Applications

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Diversidade genética em acessos do banco de germoplasma de camu-camu (Myrciaria dúbia [H.B.K.] McVaugh) do INPA usando marcadores microssatélites (EST-SSR).

Ciencia y Tecnología Agropecuaria ◽

10.21930/rcta.vol12_num1_art:215 ◽

2010 ◽

Vol 12 (1) ◽

pp. 51 ◽

Cited By ~ 8

Author(s):

Salvador Rojas ◽

Yuyama K. Clement Ch. ◽

Eduardo Ossamu Nagao

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Germplasm Conservation ◽

Great Difficulty ◽

Genetic Distances ◽

Great Distance ◽

Lack Of Information ◽

Myrciaria Dubia ◽

High Level ◽

Diversity Studies

O conhecimento da diversidade genética das espécies amazônicas é de grande importância para a domesticação e melhoramento das culturas. Uma das grandes dificuldades em espécies não domesticadas como o camu-camu é a falta de informação sobre a sua variabilidade genética. Devido ao potencial econômico do camu-camu por sua alta produção de vitamina C, foi realizado o presente trabalho, o qual tem como objetivo estimar a variabilidade genética de 139 acessos de camu-camu oriundos de 17 populações de diferentes rios da Amazônia brasileira, conservados no banco de germoplasma (BAG) de camu-camu do Instituto Nacional de Pesquisa da Amazônia INPA na cidade de Manaus, utilizando marcadores EST-SSR. Oito loci de EST-SSR detectaram um total de 102 alelos com uma média de 12,87 alelos por loco. Os resultados mostram altos níveis de diversidade para todos os locicom uma média de heterozigosidade esperada (He) de 0,797 e heterozigosidade total (Ht) de 0,502. As populações apresentaram altos valores de endogamia, o que sugere déficit de heterozigotos como observado pelos baixos valores de Heterozigosidade observada (H0), provavelmente devido ao isolamento das populações e as distâncias entre elas, o que limita o fluxo gênico favorecendo a endogamia. O valor de diferenciação genética (FST) foi alto 0,21 indicando uma alta variabilidade entre as populações. As medidas baseadas nas freqüências alélicas, amostraram uma maior variabilidade dentro das populações (80,3%) que entre as populações (19,7%). Através das distâncias genéticas entre as populações foi encontrada uma grande variação entre os acessos provenientes de populações de Rondônia (Jarú) e os provenientes de Amazonas (Pirarucu e Tarumã) e Roraima (Urubu). No ordenamento pelo método UPGMA, observou-se a formação de dois grupos principais e cinco sub-grupos os quais estão relacionados geograficamente. Os resultados revelaram a utilidade dos marcadores EST-SSR nos estudos de diversidade genética entre acessos do camu-camu. Estes resultados serão úteis no planejamento de novas coletas e conservação do BAG, no analise de variabilidade de populações, assim como no direcionamento de cruzamentos através da escolha de genótipos geneticamente divergentes, o que contribuirá às atividades de melhoramento de camu-camu nos paises amazônicos. Genetic diversity of the INPA germoplasm bank of camu-camu (Myrciaria dubia [H.B.K.] McVaugh) using microsatellites markers (EST-SSR).The knowledge of genetic diversity in Amazonian species is of great importance for domestication and breeding purposes. A great difficulty with non-domesticated species such as “camu-camu” is the lack of information about their genetic variability. Due to the economic potential of camu-camu, a fruit with a high level of vitamin C production, the aim of this study was to estimate the genetic diversity using the molecular markers EST-SSR, to study the genetic variability of 139 accessions from 17 “camu-camu” materiales from different rivers in the Brazilian's Amazon region, preserved at the INPA (Instituto Nacional de Pesquisas da Amazônia Brasilera) Active Germoplasm Bank (BAG) of “camu-camu” in Manaus. Eight of the EST-SSR polimorfic loci used had 102 alleles detected with an average of 12.87 alleles per locus. The results show high levels of diversity for all loci with an average expected heterocygocity (He) of 0.797 and a total heterocygocity (Ht) value of 0.502. Populations had high inbreeding values, suggesting a heterocigotes deficiency as observed by the heterocigocity (H0), perhaps as result of the great distance and isolation among populations, which limits gene flow and favors inbreeding. A high genetic differentiation value (FST) of 0.21, indicates high variability among populations. Measures based on the alleles frequency, showed a larger variability within populations (80.3%) than among populations (19.7%). Genetic distances between populations showed high differences within accessions coming from Rondonia (Jaru) and those from Amazonas (and Pirarucu Tarumã) and Roraima (Urubu). The dendogram made by the UPGMA method, showed two major groups and five subgroups related geographically. Results proved EST-SSR marker's utility in genetic diversity studies among BAG of camu-camu. These results will be useful in planning new collections, germplasm conservation and population variability analysis, as well as directional crossover using divergent genotypes; which will contribute to camu-camu breeding in Amazonian countries.

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Genetic monogamy and mate choice in a pair-living primate

Scientific Reports ◽

10.1038/s41598-020-77132-9 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Sofya Dolotovskaya ◽

Christian Roos ◽

Eckhard W. Heymann

Keyword(s):

Genetic Diversity ◽

Mate Choice ◽

Microsatellite Loci ◽

Inbreeding Avoidance ◽

Peruvian Amazon ◽

Extra Pair Paternity ◽

Genetic Monogamy ◽

Titi Monkeys ◽

Socially Monogamous ◽

Study Population

AbstractIn pair-living mammals, genetic monogamy is extremely rare. One possible reason is that in socially monogamous animals, mate choice can be severely constrained, increasing the risk of inbreeding or pairing with an incompatible or low-quality partner. To escape these constraints, individuals might engage in extra-pair copulations. Alternatively, inbreeding can be avoided by dispersal. However, little is known about the interactions between mating system, mate choice, and dispersal in pair-living mammals. Here we genotyped 41 wild individuals from 14 groups of coppery titi monkeys (Plecturocebus cupreus) in Peruvian Amazon using 18 microsatellite loci. Parentage analyses of 18 young revealed no cases of extra-pair paternity, indicating that the study population is mostly genetically monogamous. We did not find evidence for relatedness- or heterozygosity-based mate choice. Despite the lack of evidence for active inbreeding avoidance via mate choice, mating partners were on average not related. We further found that dispersal was not sex-biased, with both sexes dispersing opportunistically over varying distances. Our findings suggest that even opportunistic dispersal, as long as it is not constrained, can generate sufficient genetic diversity to prevent inbreeding. This, in turn, can render active inbreeding avoidance via mate choice and extra-pair copulations less necessary, helping to maintain genetic monogamy.

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

Forests ◽

10.3390/f12020197 ◽

2021 ◽

Vol 12 (2) ◽

pp. 197

Author(s):

Muhammad Azhar Nadeem ◽

Stalin Juan Vasquez Guizado ◽

Muhammad Qasim Shahid ◽

Muhammad Amjad Nawaz ◽

Ephrem Habyarimana ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Characterization ◽

Clustering Algorithms ◽

Genotyping By Sequencing ◽

Diversity Indices ◽

Peruvian Amazon ◽

Mean Values ◽

Management Plans

Research studies on conservative genetics of endangered plants are very important to establish the management plans for the conservation of biodiversity. Rosewood is an evergreen tree of the Amazon region and its essential oil has great acceptance in the medical and cosmetic industry. The present study aimed to explore the genetic diversity and population structure of 90 rosewood accessions collected from eight localities of Peruvian Amazon territory through DArTseq markers. A total of 7485 informative markers resulted from genotyping by sequencing (GBS) analysis were used for the molecular characterization of rosewood germplasm. Mean values of various calculated diversity parameters like observed number of alleles (1.962), the effective number of alleles (1.669), unbiased expected heterozygosity (0.411), and percent polymorphism (93.51%) over the entire germplasm showed the existence of a good level of genetic variations. Our results showed that the Mairiricay population was more diverse compared to the rest of the populations. Tamshiyacu-2 and Mairiricay-15 accessions were found genetically distinct accessions. The analysis of molecular variance (AMOVA) reflected maximum variations (75%) are due to differences within populations. The implemented clustering algorithms, i.e., STRUCTURE, neighbor-joining analysis and principal coordinate analysis (PCoA) separated the studied germplasm on the basis of their geographical locations. Diversity indices for STRUCTURE-based populations showed that subpopulation A is more diverse population than the rest of the populations, for such reason, individuals belonging to this subpopulation should be used for reintroduction or reinforcement plans of rosewood conservation. We envisage that molecular characterization of Peruvian rosewood germplasm with DArTseq markers will provide a platform for the conservation, management and restoration of endangered rosewood in upcoming years.

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

Forests ◽

10.3390/f12081125 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1125

Author(s):

Carla L. Saldaña ◽

Johan D. Cancan ◽

Wilbert Cruz ◽

Mirian Y. Correa ◽

Miriam Ramos ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Markers ◽

Tree Species ◽

Rapd Markers ◽

Clustering Algorithm ◽

Random Amplified Polymorphic Dna ◽

Population Divergence ◽

Eastern Region ◽

Peruvian Amazon

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.

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