Analysis of the genetic variability of peach palm (Bactris gasipaes) in the Yurimáguas region, Peru, using molecular RAPD markers

Molecular markers were used to verify the existence of one or more primitive peach palm landraces, including Pampa Hermosa, in the microregion near Yurimáguas, Peru. This region provides the highest amount of seeds for peach palm heart agribusinesses in Brazil. In this analysis, we used 120 peach palm plants (Bactris gasipaes var. gasipaes) from four river basins around Yurimáguas. We used six primers, generating 73 RAPD markers. The heterozygosity ranged from 0.29 to 0.31, with a mean of 0.32, and the percentage of polymorphism ranged from 80.8 to 86.6, with a mean of 90.4. The dendrogram, based on Jaccard Similarity, presented eight groups, but it did not present groups formed by the water basins. The average gene flow was high, ranging from 11.41 to 18.89, as expected for populations within a same landrace. The analysis of the genetic diversity in this set of plants showed a common genetic basis among the plants. Nei's Genetic Distances were low, varying between 0.012 and 0.027. This suggests that such populations are very similar to each other, and that there is only one landrace in the region. Therefore, we propose the existence of only one landrace in the Yurimáguas region and the name "Pampa Hermosa" should be adopted. © 2018 Cientifica. All rights reserved

Uso de AFLPS para discriminar raças primitivas de pupunha (Bactris gasipaes) na Amazônia brasileira

Although the first inhabitants of western Amazonia domesticated pejibaye (Bactris gasipaes Kunth, Palmae) or peach palm for its fruits, today it is widely planted for its heart-of-palm. Like other domesticates, pejibaye presents a complex hierarchy of landraces developed before the conquest of the Americas. The existence of three landraces (Pará, Solimões, Putumayo) was proposed along the Amazonas and Solimões Rivers, Brazil, based on morphological characteristics. There are some questions remaining about the intermediate landrace being an artifact of the morphometric analysis. AFLPs were used to evaluate the relationships among samples of these putative landraces. DNA was extracted from 99 plants representing 13 populations maintained in the Pejibaye Germplasm Bank, Manaus, AM; six primer combinations generated 245 markers via PCR, which were scored in an ABI Prism 310 sequencer and analyzed with GeneScan Software; Jaccard similarities were estimated and a dendrogram was generated with UPGMA. Two groups of plants were observed in the dendrogram instead of three, and were similar at 0.795. Each group contained two subgroups, similar at 0.815. One group (n=41) contained 73% Pará landrace plants, with one subgroup (n=22) containing 91% Pará, and the other (n=19) containing 53% Pará. The other group (n=58) contained 53% Solimões and 40% Putumayo landrace plants, with one subgroup (n=21) containing 52% Solimões and 43% Putumayo, and the other (n=35) containing 57% Solimões and 37% Putumayo. The first group confirmed the Pará landrace. The second group suggested that the Solimões landrace does not exist, but that the Putumayo landrace extends along the Solimões River to Central Amazonia.Os primeiros povos da Amazônia ocidental domesticaram a pupunha (Bactris gasipaes Kunth, Palmae) por seu fruto, embora hoje seja muito plantada por seu palmito. Como outros cultivos domesticados, a pupunha apresenta uma hierarquia complexa de raças primitivas criadas antes da conquista das Américas. A existência de três raças (Pará, Solimões, Putumayo) foi proposta ao longo dos rios Amazonas e Solimões, Brasil, com base em características morfológicas. Algumas dúvidas existem sobre a raça intermediária, pois podia ser um artefato da análise morfométrica. AFLPs foram usados para avaliar as relações entre amostras destas raças hipotéticas. DNA foi extraido de 99 plantas representando 13 populações mantidas no Banco de Germoplasma de Pupunha, Manaus, AM; seis combinações de 'primers' geraram 245 marcadores via PCR, que foram codificados num sequenciador ABI Prism 310 e analisados com o programa GeneScan; similaridades de Jaccard foram estimadas e um dendrograma foi criado com UPGMA. Dois grupos de plantas foram observados no dendrograma, em lugar de três, com similaridade de 0,795. Cada grupo continha dois subgrupos, similares a 0,815. Um grupo (n=41) continha 73% de plantas da raça Pará, com um subgrupo (n=22) contendo 91% Pará e o outro (n=19) contendo 53% Pará. O outro grupo (n=58) continha 53% de plantas da raça Solimões e 40% da Putumayo, com um subgrupo (n=21) contendo 52% Solimões e 43% Putumayo, e o outro (n=35) contendo 57% Solimões e 37% Putumayo. O primeiro grupo confirmou a raça Pará, mas o segundo grupo sugeriu que a raça Solimões não existe; em lugar desta raça, a raça Putumayo se extende ao longo do rio Solimões até a Amazônia Central

Conservation implications of the mating system of the Pampa Hermosa landrace of peach palm analyzed with microsatellite markers

Peach palm (Bactris gasipaes) is cultivated by many indigenous and traditional communities from Amazonia to Central America for its edible fruits, and is currently important for its heart-of-palm. The objective of this study was to investigate the mating system of peach palm, as this is important for conservation and breeding. Eight microsatellite loci were used to genotype 24 open-pollinated progenies from three populations of the Pampa Hermosa landrace maintained in a progeny trial for genetic improvement. Both the multi-locus outcrossing rates (0.95 to 0.99) and the progeny level multi-locus outcrossing rates (0.9 to 1.0) were high, indicating that peach palm is predominantly allogamous. The outcrossing rates among relatives were significantly different from zero (0.101 to 0.202), providing evidence for considerable biparental inbreeding within populations, probably due to farmers planting seeds of a small number of open-pollinated progenies in the same plot. The correlations of paternity estimates were low (0.051 to 0.112), suggesting a large number of pollen sources (9 to 20) participating in pollination of individual fruit bunches. Effective population size estimates suggest that current germplasm collections are insufficient for long-term ex situ conservation. As with most underutilized crops, on farm conservation is the most important component of an integrated conservation strategy. © 2015, Sociedade Brasileira de Genética. Printed in Brazil

Method for obtaining high-resolution proteomic analysis from pericarps of guarana

Guarana has great agricultural potential and is largely used therapeutically and in the production of non-alcoholic energy drinks. Genomic and proteomic studies are crucial to identify proteins that play central roles in the maintenance and viability of fruits, as well as to identify proteins related to the main metabolic pathways. However, the success of any protein analysis starts with the protein extract preparation, which needs to offer an extract that is free of contaminants. This study aimed to evaluate different extraction methods to obtain high-quantity and high-quality extracts that are compatible with analysis by 2-dimensional electrophoresis and tandem mass spectrometry protein identification. Three different methods were tested: trichloroacetic acid (TCA)/acetone, sodium dodecyl sulfate (SDS)/phenol, and polyvinylpolypyrrolidone (PVPP)/SDS/phenol. The extract obtained from the TCA/acetone precipitation presented low solubility and contamination with lipids and carbohydrates. On the other hand, the quality of the extract gradually improved after using phenol and PVPP/phenol, enabling a yield up to 2 mg/g macerated tissues and the detection of 457 spots by 2-dimensional electrophoresis. The effectiveness of the procedure used was validated by identification of 10 randomly selected proteins by mass spectrometry. The procedure described here can be a starting point for applications using tissues of other organs of guarana or tissues of species that are similar to guarana. © FUNPEC-RP

Electrophoresis and spectrometric analyses of adaptation-related proteins in thermally stressed Chromobacterium violaceum

Chromobacterium violaceum is a Gram-negative proteobacteria found in water and soil; it is widely distributed in tropical and subtropical regions, such as the Amazon rainforest. We examined protein expression changes that occur in C. violaceum at different growth temperatures using electrophoresis and mass spectrometry. The total number of spots detected was 1985; the number ranged from 99 to 380 in each assay. The proteins that were identified spectrometrically were categorized as chaperones, proteins expressed exclusively under heat stress, enzymes involved in the respiratory and fermentation cycles, ribosomal proteins, and proteins related to transport and secretion. Controlling inverted repeat of chaperone expression and inverted repeat DNA binding sequences, as well as regions recognized by sigma factor 32, elements involved in the genetic regulation of the bacterial stress response, were identified in the promoter regions of several of the genes coding proteins, involved in the C. violaceum stress response. We found that 30°C is the optimal growth temperature for C. violaceum, whereas 25, 35, and 40°C are stressful temperatures that trigger the expression of chaperones, superoxide dismutase, a probable small heat shock protein, a probable phasing, ferrichrome-iron receptor protein, elongation factor P, and an ornithine carbamoyltransferase catabolite. This information improves our comprehension of the mechanisms involved in stress adaptation by C. violaceum. © FUNPEC-RP

The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability

Chromobacterium violaceum is one of millions of species of free-living microorganisms that populate the soil and water in the extant areas of tropical biodiversity around the world. Its complete genome sequence reveals (i) extensive alternative pathways for energy generation, (ii) ≈500 ORFs for transport-related proteins, (iii) complex and extensive systems for stress adaptation and motility, and (iv) wide-spread utilization of quorum sensing for control of inducible systems, all of which underpin the versatility and adaptability of the organism. The genome also contains extensive but incomplete arrays of ORFs coding for proteins associated with mammalian pathogenicity, possibly involved in the occasional but often fatal cases of human C. violaceum infection. There is, in addition, a series of previously unknown but important enzymes and secondary metabolites including paraquat-inducible proteins, drug and heavy-metal-resistance proteins, multiple chitinases, and proteins for the detoxification of xenobiotics that may have biotechnological applications

Analysis of the genetic variability of peach palm (Bactris gasipaes) in the Yurimáguas region, Peru, using molecular RAPD markers

Molecular markers were used to verify the existence of one or more primitive peach palm landraces, including Pampa Hermosa, in the microregion near Yurimáguas, Peru. This region provides the highest amount of seeds for peach palm heart agribusinesses in Brazil. In this analysis, we used 120 peach palm plants (Bactris gasipaes var. gasipaes) from four river basins around Yurimáguas. We used six primers, generating 73 RAPD markers. The heterozygosity ranged from 0.29 to 0.31, with a mean of 0.32, and the percentage of polymorphism ranged from 80.8 to 86.6, with a mean of 90.4. The dendrogram, based on Jaccard Similarity, presented eight groups, but it did not present groups formed by the water basins. The average gene flow was high, ranging from 11.41 to 18.89, as expected for populations within a same landrace. The analysis of the genetic diversity in this set of plants showed a common genetic basis among the plants. Nei's Genetic Distances were low, varying between 0.012 and 0.027. This suggests that such populations are very similar to each other, and that there is only one landrace in the region. Therefore, we propose the existence of only one landrace in the Yurimáguas region and the name "Pampa Hermosa" should be adopted. © 2018 Cientifica. All rights reserved

Molecular-genetic analysis for validation of peach palm (Bactris gasipaes Kunt) landraces using RAPD markers

Numerous landraces of peach palm (Bactris gasipaes var. gasipaes) have been described in the Neotropics and are conserved in a genebank of INPA. We used RAPD markers to analyze the genetic diversity of eight peach palm landraces and two wild populations. Eight primers generated 124 markers; 101 markers were polymorphic (81.5 %). Observed heterozygosity was 0.38 and polymorphism was 93 %, both slightly higher than in previous studies. Amazonian landraces presented high heterozygosity (0.30) and a percentage of polymorphism (87,8 %) similar to Central American landraces (0.29 and 83,5 %, respectively), different from previous studies, which found Central American landraces to have lower values than Amazonian landraces. The structure of the dendrogram with Nei s genetic distance was similar to that of previous studies, with minor differences. The two wild populations were grouped far from the landraces, suggesting that they did not participate in the domestication of the cultivated populations. © 2019 Universidade Estadual Paulista - UNESP. All rights reserved

Uma coleção nuclear de pupunha na Amazônia Brasileira

The Peach palm Active Germplasm Bank has abundant genetic diversity in its holdings. Because it is a live collection, maintenance, characterization and evaluation are expensive, restricting its use. One way to promote more efficient use is to create a Core Collection, a set of accessions with at least 70% of the genetic diversity of the full collection with minimal repetition. The available geographic, molecular marker (RAPD) and morphometric information was systematized and the populations were stratified into wild and domesticated. The Core Collection consists of 10% of the entire collection: 31 accessions of landraces, 5 accessions of non-designated populations and 4 accessions of wild populations. The Core has 92% of the molecular polymorphism and 95% of the heterozygosity of the full collection, with minimal divergence between them by molecular variance. The Core is already receiving priority maintenance, which will contribute to long term conservation. © 2015, Crop Breeding and Applied Biotechnology. All rights reserved

Microsatellite loci for population and parentage analysis in the Amazon River dolphin (Inia geoffrensis de Blainville, 1817)

We developed specific primers for microsatellite DNA regions for the Amazon River dolphin or boto Inia geoffrensis, for use in population and conservation genetic studies. We also tested their transferability for two other species, Pontoporia blainvillei (sister taxon of I. geoffrensis) and Sotalia guianensis. A total of 12 microsatellite loci were polymorphic for the boto. An additional 25 microsatellite loci previously isolated from other cetacean species were also tested in the boto. The 26 polymorphic microsatellite loci indicate they will be excellent markers for studies of population structure and kinship relations of the boto. © 2009 Blackwell Publishing Ltd