Doriane Picanço Rodrigues

Molecular marker-mediated validation of morphologically defined landraces of Pejibaye (Bactris gasipaes) and their phylogenetic relationships

RAPD markers were used to evaluate the genetic variability and structure of seven morphologically defined landraces of pejibaye (Bactris gasipaes Kunth, Palmae) to determine their validity and phylogenetic relationships. Two hundred and twenty plants of four Amazonian and three Central American landraces of var.gasipaes (the domesticate) and 30 plants of var.chichagui (H. Karsten) Henderson (the crop ancestor) maintained at the National Research Institute for Amazonia, Manaus, Amazonas, Brazil, were utilized. Eight RAPD primers yielded 113 markers, with good reproducibility, of which 97 were polymorphic. The four Amazonian landraces had an average heterozygosity of 0.30, with 86% polymorphism, greater than the Central American landraces (0.25; 74.3%) and var.chichagui (0.27; 80%). Among landrace genetic diversity (GST) was 15%, while within (Hs) was 85%, essentially equivalent to the AMOVA within (82.2%) and among (17.8%) variances. The Jaccard similarities, PCA, gene flow coefficients and Exact tests suggested that only one landrace exists in Central America, called Utilis after the first taxon described there, and that the Solimões landrace is part of the Putumayo landrace, rather than a separate entity. The Pará and Pampa Hermosa landraces were validated in accordance with their morphometric interpretations. The dendrogram of Nei’s genetic distances among valid landraces and var.chichagui supported the hypothesis of a single origin for pejibaye in southwestern Amazonia, with two migration routes: one to the northeast, becoming the Pará landrace, and another to the northwest along the Andes, spreading into western Amazonia (Pampa Hermosa and Putumayo landraces) and across the Andes, reaching Central America (Utilis landrace).

Discriminação de raças primitivas de Pupunha (Bactris Gasipaes) na Amazônia brasileira por meio de marcadores moleculares (RAPDs)

The pejibaye (Bactris gasipaes Kunth, Palmae) was domesticated for it fruits by the first peoples of western Amazonia. Consequently it exhibits a landrace complex that has been partially characterized morphologically and mapped. Along the Amazonas and Solimoes Rivers, in Brazil, three landraces have been proposed [Para (Amazonas River), Solimoes (lower and middle Solimoes River), Putumayo (upper Solimoes River)], with indications that the Solimoes landrace could be an artifact of the morphometric analysis. RAPD markers were used to evaluate the three landrace hypothesis. DNA was extracted from 30 plants of each landrace maintained in the Pejibaye germplasm bank, Manaus, AM, Brazil. During PCR amplification, 8 primers generated 80 markers, Jaccard similarities were estimated, the plants were grouped with UPGMA. The dendrogram contained 2 large groups that joined at a similarity of 0.535: the group of the Para landrace contained 26 plants of this race, 5 of the Putumayo and 1 of the Solimoes; the group of the Solimoes River contained 29 plants of the Solimoes race, 19 of the Putumayo and 1 of the Para. The structure of the second group suggested that there is only one landrace along the Solimoes River, since the plants were mixed in sub-groups without apparent order. This marker-based genetic analysis did not support the three landrace hypothesis and suggests that the Putumayo landrace extends along the Solimoes River to central Amazonia. Genetic and morphological data must now be used to evaluate this new hypothesis.

Chloroplast Sequence of Treegourd (Crescentia cujete, Bignoniaceae) to Study Phylogeography and Domestication

Premise of the study: Crescentia cujete (Bignoniaceae) fruit rinds are traditionally used for storage vessels and handicrafts. We assembled its chloroplast genome and identified single-nucleotide polymorphisms (SNPs). Methods and Results: Using a genome skimming approach, the whole chloroplast of C. cujete was assembled using 3,106,928 sequence reads of 150 bp. The chloroplast is 154,662 bp in length, structurally divided into a large single copy region (84,788 bp), a small single copy region (18,299 bp), and two inverted repeat regions (51,575 bp) with 88 genes annotated. By resequencing the whole chloroplast, we identified 66 SNPs in C. cujete (N = 30) and 68 SNPs in C. amazonica (N = 6). Nucleotide diversity was estimated at 1.1 × 10-3 and 3.5 × 10-3 for C. cujete and C. amazonica, respectively. Conclusions: This broadened C. cujete genetic toolkit will be important to study the origin, domestication, diversity, and phylogeography of treegourds in the Neotropics.

Human management and hybridization shape treegourd fruits in the Brazilian Amazon Basin

Local peoples perceptions of cultivated and wild agrobiodiversity, as well as their management of hybridization are still understudied in Amazonia. Here we analyze domesticated treegourd (Crescentia cujete), whose versatile fruits have technological, symbolic, and medicinal uses. A wild relative (C. amazonica) of the cultivated species grows spontaneously in Amazonian flooded forests. We demonstrated, using whole chloroplast sequences and nuclear microsatellites, that the two species are strongly differentiated. Nonetheless, they hybridize readily throughout Amazonia and the proportions of admixture correlate with fruit size variation of cultivated trees. New morphotypes arise from hybridization, which are recognized by people and named as local varieties. Small hybrid fruits are used to make the important symbolic rattle (maracá), suggesting that management of hybrid trees is an ancient human practice in Amazonia. Effective conservation of Amazonian agrobiodiversity needs to incorporate this interaction between wild and cultivated populations that is managed by smallholder families. Beyond treegourd, our study clearly shows that hybridization plays an important role in tree crop phenotypic diversification and that the integration of molecular analyses and farmers’ perceptions of diversity help disentangle crop domestication history.

Crop domestication in the upper Madeira River basin

Most native Amazonian crops were domesticated in the periphery of the basin. The upper Madeira River basin is an important part of this periphery where several important crops were domesticated and others are suspected to have been domesticated or arrived early. Some of these crops have been reasonably well studied, such as manioc, peanut, peach palm, coca and tobacco, while others are not as well known, such as the hot peppers Capsicum baccatum and C. frutescens, and still others need confirmation, such as cocoyam and annatto. We review the information available for manioc, peach palm, Capsicum, peanut, annatto and cocoyam. The state-of-the-art for Capsicum frutescens, annatto and cocoyam is insufficient to conclude definitively that they were domesticated in the upper Madeira, while all the others have at least one of their origins or centers of diversity in the upper Madeira.

Diversity of Treegourd (Crescentia cujete) Suggests Introduction and Prehistoric Dispersal Routes into Amazonia

The use and dispersal of domesticated plants may reflect patterns of early human diffusion of technologies and lifestyles. Treegourd (Crescentia cujete) has fruits with ancient utilitarian and symbolic value in the Neotropics. We assessed diversity based on chloroplast (SNPs), nuclear (SSR) markers and fruit shapes of cultivated treegourds and wild relatives across Amazonia and Mesoamerica in order to discuss hypothesis of dispersal routes and diversification of fruits along its distribution. The haplotype network showed three distinct groups: Crescentia amazonica, wild Mesoamerican Crescentia cujete, and cultivated Crescentia cujete from Brazilian Amazonia and Mexico. Mexico and Brazil shared two haplotypes, with slightly different distributions in Amazonia. The most divergent haplotype is well represented in Eastern Amazonia. Nuclear differentiation between Mesoamerican wild and cultivated C. cujete is relatively low (FST = 0.35), compared with Amazonian cultivated (FST = 0.45 to 0.61). Differentiation is also higher between wild C. amazonica and cultivated C. cujete (FST = 0.57), but modest within cultivated C. cujete from Amazonia and Mexico (FST = 0.04), with higher genetic similarity in northwestern Amazonia. Mexico and Amazonia showed similar chloroplast nucleotide diversity (4.66 x 10-2 and 5.31 x 10-2, respectively), although sample sizes are very different. Except in Northwestern and Eastern Amazonia, we found ample genetic homogeneity of cultivated C. cujete across Amazonia, but highest morphological diversity in the Northwest, with fruit shapes that are absent in Mexico. We conclude that treegourds introduced into the Amazon Basin and Mexico share a common ancestry with a currently unknown origin. The patterns of genetic diversity across Amazonia allow two hypotheses of the routes of introduction: a northwestern introduction into the Negro and Solimoes Rivers, and an eastern introduction from the coastal Guianas into the Amazonas River. The dispersal into Amazonia followed previously proposed routes of human and plant migrations. The contrasting fruit shape diversity suggests different utilitarian demands and cultural preferences for treegourd fruits between Mexico and Amazonia.