LEARNING The objectives of BIOS 781 are to present: OBJECTIVES: 1. basic population and quantitative genetic principles, including classical genetics, chromosomal theory of inheritance, and meiotic recombination 2. an exposure to QTL mapping methods of complex quantitative traits and linkage methods to detect co-segregation with disease 3. methods for assessing marker-disease linkage disequilibrium, including case-control approaches 4. methods for genome-wide association and stratification control.

Genetic Data Analysis

Molecular analyses are providing new elements to decipher the origin, domestication and dispersal of native Amazonian crops in an expanding archaeological context. Solid molecular data are available for manioc (Manihot esculenta), cacao (Theobroma cacao), pineapple (Ananas comosus), peach palm (Bactris gasipaes) and guarana (Paullinia cupana), while hot peppers (Capsicum spp.), inga (Inga edulis), Brazil nut (Bertholletia excelsa) and cupuassu (Theobroma grandiflorum) are being studied. Emergent patterns include the relationships among domestication, antiquity (terminal Pleistocene to early Holocene), origin in the periphery, ample pre-Columbian dispersal and clear phylogeographic population structure for manioc, pineapple, peach palm and, perhaps, Capsicum peppers. Cacao represents the special case of an Amazonian species possibly brought into domestication in Mesoamerica, but close scrutiny of molecular data suggests that it may also have some incipiently domesticated populations in Amazonia. Another pattern includes the relationships among species with incipiently domesticated populations or very recently domesticated populations, rapid pre- or post-conquest dispersal and lack of phylogeographic population structure, e.g., Brazil nut, cupuassu and guarana. These patterns contrast the peripheral origin of most species with domesticated populations with the subsequent concentration of their genetic resources in the center of the basin, along the major white water rivers where high pre-conquest population densities developed. Additional molecular genetic analyses on these and other species will allow better examination of these processes and will enable us to relate them to other historical ecological patterns in Amazonia.

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Origin and domestication of native Amazonian crops.

S & BIBLIOGRAPHIES Bibliography of Agriculture Biological Abstracts Botany Subject Index (U. S. Dept. of Agriculture) Chemical Abstracts Craker, L. E., A. F. Chadwick, & J. E. Simon. 1986. An introduction to the scientific literature on herbs, spices, and medicinal plants. Recent Adv. Bot. Hort. Pharm. 1: 1-9. Excerpta Botanica Index Medicus Index to American Botanical Literature Simon, J. E., A. F. Chadwick, & L. E. Craker. 1984. Herbs: an indexed bibliography, 1971-1980: the scientific literature on selected herbs, and aromatic and medicinal plants of the temperate zone. Shoe String Press. 770 pp.

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Plants & Civilization; An Introduction to the Interrelationships of Plants and People

Occurrence of intervarietal or interspecific natural crosses has been reported for many crop plants in traditional farming systems, underlining the potential importance of this source of genetic exchange for the dynamics of genetic diversity of crop plants. In this study, we use microsatellite loci to investigate the role of volunteer seedlings (plants originating from unmanaged sexual reproduction) in the dynamics of genetic diversity of cassava (Manihot esculenta Crantz), a vegetatively propagated crop, in a traditional farming system in Guyana. A previous field study showed that farmers incorporate such plants into the germplasm for vegetative propagation, and that many of them are likely to be assigned by farmers to recognized varieties. Under strict vegetative propagation clonality of varieties is expected. The high proportion of polyclonal varieties observed suggests that incorporation of seedlings into the germplasm for propagation is a frequent event. The molecular variability assessed with microsatellite markers shows that there is high differentiation among heterozygous varieties, whereas populations of seedlings do not depart from the proportions expected under Hardy–Weinberg assumptions. Assignment of seedlings to a recognized variety on the basis of morphological similarity greatly increases genetic diversity within the variety. We argue that recombination and gene flow play a major role in the dynamics of genetic diversity of cassava in traditional farming systems. Documenting unmanaged sexual reproduction and its genetic consequences is a prerequisite for defining strategies of in situ conservation of crop plant genetic resources.

Unmanaged sexual reproduction and the dynamics of genetic diversity of a vegetatively propagated crop plant, cassava (Manihot esculenta Crantz), in a traditional farming system

The emergence of sedentism and agriculture in Amazonia continues to sit uncomfortably within accounts of South American pre-Columbian history. This is partially because deep-seated models were formulated when only ceramic evidence was known, partly because newer data continue to defy simple explanations, and partially because many discussions continue to ignore evidence of pre-Columbian anthropogenic landscape transformations. This paper presents the results of recent geoarchaeological research on Amazonian anthropogenic soils. It advances the argument that properties of two different types of soils, terras pretas and terras mulatas, support their interpretation as correlates of, respectively, past settlement areas and fields where spatially-intensive, organic amendment-reliant cultivation took place. This assessment identifies anthropogenic soil formation as a hallmark of the Amazonian Formative and prompts questions about when similar forms of enrichment first appear in the Amazon basin. The paper reviews evidence for embryonic anthrosol formation to highlight its significance for understanding the domestication of a key Amazonian crop: manioc (Manihot esculenta ssp. esculenta). A model for manioc domestication that incorporates anthropogenic soils outlines some scenarios which link the distribution of its two broader varieties—sweet and bitter manioc—with the widespread appearance of Amazonian anthropogenic dark earths during the first millennium AD.

https://www.mdpi.com/1424-2818/2/4/473/pdf

The Amazonian Formative: Crop Domestication and Anthropogenic Soils

A survey was conducted of Caicara farmers from Ubatuba in the Brazilian coastland between Sao Paulo and Rio de Janeiro States regarding the folk-taxonomy for cassava (Manihot esculenta Crantz) landraces they cultivate and cassava evolutionary dynamics in swidden cultivation The accuracy of their folk taxonomy was assessed Cluster analysis was used to make comparisons between names given by the farmers to sampled individuals and their isozyme phenotypes obtained with four isozyme systems Interviews with farmers were done and ethnobiological data collected These farmers possess a loose taxonomic system and tend to underestimate cassava genetic diversity in their gardens However, classification skills vary considerably among them The accuracy of their taxonomy along with the results of interviews with farmers and ethnobiological data are discussed in light of a proposed evolutionary dynamics model for cultivated cassava and its ecology in tropical swidden cultivation

Folk taxonomy and evolutionary dynamics of cassava: a case study in Ubatuba, Brazil

The objective of this work was to quantify the genetic diversity among cassava folk varieties as well as to examine the distribution of the genetic diversity among varieties of different origin and type. Fifty-four cassava varieties were chosen from 4 Brasilian regions: 45 of the Amazon basin (23 from River Negro, 6 of the River Branco and 16 of the River Solimoes) and 9 of the south coast of the Sao Paulo State, Brazil. The modern variety Mantiqueira was also included as a reference. Among these, 38 were bitter varieties and 17 sweet. Three different types of DNA markers were used: RAPD (randomly amplified polymorphic DNA), AFLP (amplified fragment length polymorphism) and microsatellites. Analysis of the results consisted of a description of band patterns, a calculation of similarity indexes (Nei & Li) and a principal coordinate analysis (PCoA) for each marker type. Heterozygosity, diversity indexes (DI, Weir) and genetic differentiation coefficients (GST) were calculated for the microsatellite loci.Genetic variability was more concentrated within regions, then among regions (GST = 0.07). Mean heterozygosity was 56%. Mean similarity indexes were dependent on the marker used: S = 0.89 for RAPD, S = 0.85 for AFLP and S = 0.59 for microsatellites. PCoA analysis revealed groups, distinguishing bitter from sweet varieties.

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Variabilidade genética de etnovariedades de mandioca, avaliada por marcadores de DNA

The management practices used in authoctonous agriculture with landraces of cassava (Manihot esculenta Crantz) play an important role in the in situ conservation of genetic resources The objective of this work was to analyze the genetic variability present in 141 landraces of cassava, collected in gardens of different geographical regions of Brazil using isozyme techniques visualized by starch gel electrophoresis Eleven enzymatic systems were analised Of the 15 polymorphic loci evaluated the observed mean heterozigosity was 0354 GST estimates presented a value of 880% for the genetic variability between regions In cluster analysis, three distinct groups were observed: the first group was formed by the gardens of the Amazon; the second group consisted of gardens of Sao Paulo State; and the third group was formed by the gardens of the Xingu region Most of the genetic variability of cassava landraces was restricted within the geographical regions, which confirmed the evolutionary dynamic model for this species

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Variabilidade genética de etnovariedades de mandioca em regiões geográficas do Brasil

A agricultura itinerante, caracterizada por ciclos de uso e pousio, e uma tecnica utilizada por muitos agricultores no mundo, assim como por agricultores tradicionais da regiao de Cananeia (SP). Estes agricultores herdaram toda um gama de conhecimentos transmitidos oralmente sobre a agricultura praticada por povos indigenas desde o periodo pre colonial. A mandioca e o principal cultivo neste sistema, o que a torna um organismo chave para entender as especificidades do sistema agricola itinerante. Foram obtidas informacoes sobre as especies cultivadas no sistema itinerante, e mais especificamente sobre as etnovariedades de mandioca. Entrevistas com os agricultores permitiram caracterizar o sistema utilizado, demonstrando que na propriedade estudada podem ser cultivadas ate 62 etnovariedades pertencentes a 15 especies diferentes, mostrando a grande diversidade tanto inter como intra especifica. O objetivo principal foi aferir a identificacao feita pelo agricultor das etnovariedades de mandioca (Manihot esculenta Crantz) cultivadas intra-roca e a divergencia morfologica entre elas. Atraves da avaliacao de 21 caracteres morfologicos avaliados in situ, em uma roca de agricultores tradicionais da comunidade de Ariri (Cananeia), e utilizando analise de componentes principais (PCA) e analise de agrupamento, foi possivel agrupar as etnovariedades em grupos coerentes com a classificacao local. Alem disso a metodologia empregada mostrou grande eficiencia com dados tomados em condicoes nao experimentais.

Akihiko Ando

Papers

Folk taxonomy and evolutionary dynamics of cassava: a case study in Ubatuba, Brazil

Variabilidade genética de etnovariedades de mandioca, avaliada por marcadores de DNA

Variabilidade genética de etnovariedades de mandioca em regiões geográficas do Brasil

Diversidade inter- e intra-específica e uso de análise multivariada para morfologia da mandioca (Manihot esculenta Crantz): um estudo de caso