Hélène Joly

Seed exchange networks for agrobiodiversity conservation. A review.

The circulation of seed among farmers is central to agrobiodiversity conservation and dynamics. Agrobiodiversity, the diversity of agricultural systems from genes to varieties and crop species, from farming methods to landscape composition, is part of humanity’s cultural heritage. Whereas agrobiodiversity conservation has received much attention from researchers and policy makers over the last decades, the methods available to study the role of seed exchange networks in preserving crop biodiversity have only recently begun to be considered. In this overview, we present key concepts, methods, and challenges to better understand seed exchange networks so as to improve the chances that traditional crop varieties (landraces) will be preserved and used sustainably around the world. The available literature suggests that there is insufficient knowledge about the social, cultural, and methodological dimensions of environmental change, including how seed exchange networks will cope with changes in climates, socio-economic factors, and family structures that have supported seed exchange systems to date. Methods available to study the role of seed exchange networks in the preservation and adaptation of crop specific and genetic diversity range from meta-analysis to modelling, from participatory approaches to the development of bio-indicators, from genetic to biogeographical studies, from anthropological and ethnographic research to the use of network theory. We advocate a diversity of approaches, so as to foster the creation of robust and policy-relevant knowledge. Open challenges in the study of the role of seed exchange networks in biodiversity conservation include the development of methods to (i) enhance farmers’ participation to decision-making in agro-ecosystems, (ii) integrate ex situ and in situ approaches, (iii) achieve interdisciplinary research collaboration between social and natural scientists, and (iv) use network analysis as a conceptual framework to bridge boundaries among researchers, farmers and policy makers, as well as other stakeholders.

Evidence of low gene flow in a neotropical clustered tree species in two rainforest stands of French Guiana.

The spatial genetic structure of the neotropical, clustered tree species Vouacapoua americana (Aublet) was studied in two natural forest stands (Paracou and Nouragues) in French Guiana. Using eight microsatellite loci, V. americana is characterized by a marked genetic structure at small spatial distances (under 30–60 m), in agreement with the limited seed dispersal by rodent species. Gene flow through pollen is also shown to be mainly restricted to less than 100 m. This result suggests that most pollination events (mediated through small insects) are probably limited to within‐patches of individuals, which might explain the high genetic differentiation among patches (FST = 0.11) separated by less than 2 km. We also assume that stronger genetic structure in Paracou is likely to be due to lower seed dispersal by rodents, large spatial distances separating patches, or a recent recolonization event.

Chloroplast diversity in Vouacapoua americana (Caesalpiniaceae), a neotropical forest tree

The chloroplast genome has been widely used to describe genetic diversity in plant species. Its maternal inheritance in numerous angiosperm species and low mutation rate are suitable characters when inferring historical events such as possible recolonization routes. Here we have studied chloroplast DNA variation using PCR–RFLP (polymerase chain reaction–restriction fragment length polymorphism) with seven pairs of primers and four restriction enzymes in 14 populations of Vouacapoua americana (Caesalpiniaceae) a neotropical tree sampled throughout French Guiana. Population diversity (Hs), total gene diversity (Ht) and differentiation among populations (GST) were estimated using Nei’s method as 0.09, 0.87 and 0.89, respectively. This is consistent with the limited gene flow associated with synzoochory in this species. The genetic structure observed in the north of French Guiana suggests that historical events such as contractions and recent recolonizations have had a large impact on the distribution of genetic diversity in this species.

High outcrossing rates in fields with mixed sorghum landraces: how are landraces maintained?

The effect of mating system on genetic diversity is a major theme in plant evolutionary genetics, because gene flow plays a large role in structuring the genetic variability within and among populations. Understanding crop mating systems and their consequences for gene flow can aid in managing agricultural systems and conserving genetic resources. We evaluated the extent of pollen flow, its links with farming practices and its impact on the dynamics of diversity of sorghum in fields of Duupa farmers in Cameroon. Duupa farmers grow numerous landraces mixed in a field, a practice that favours extensive pollen flow. We estimated parameters of the mating system of five landraces representative of the genetic diversity cultivated in the study site, using a direct method based on progeny array. The multilocus outcrossing rate calculated from all progenies was 18% and ranged from 0 to 73% among progenies. Outcrossing rates varied greatly among landraces, from 5 to 40%. Our results also showed that individual maternal plants were usually pollinated by more than eight pollen donors, except for one landrace (three pollen donors). Although the biological traits of sorghum (inflorescence morphology, floral traits, phenology) and the spatial planting practices of Duupa farmers led to extensive pollen flow among landraces, selection exerted by farmers appears to be a key parameter affecting the fate of new genetic combinations from outcrossing events. Because both natural and human-mediated factors shape evolution in crop populations, understanding evolutionary processes and designing in situ conservation measures requires that biologists and anthropologists work together.

Gene flow among wild and domesticated almond species: insights from chloroplast and nuclear markers

Hybridization has played a central role in the evolutionary history of domesticated plants. Notably, several breeding programs relying on gene introgression from the wild compartment have been performed in fruit tree species within the genus Prunus but few studies investigated spontaneous gene flow among wild and domesticated Prunus species. Consequently, a comprehensive understanding of genetic relationships and levels of gene flow between domesticated and wild Prunus species is needed. Combining nuclear and chloroplastic microsatellites, we investigated the gene flow and hybridization among two key almond tree species, the cultivated Prunus dulcis and one of the most widespread wild relative Prunus orientalis in the Fertile Crescent. We detected high genetic diversity levels in both species along with substantial and symmetric gene flow between the domesticated P. dulcis and the wild P. orientalis. These results were discussed in light of the cultivated species diversity, by outlining the frequent spontaneous genetic contributions of wild species to the domesticated compartment. In addition, crop‐to‐wild gene flow suggests that ad hoc transgene containment strategies would be required if genetically modified cultivars were introduced in the northwestern Mediterranean.

Tracking a genetic signal of extinction-recolonization events in a neotropical tree species: Vouacapoua americana Aublet in French Guiana.

Abstract Drier periods from the late Pleistocene and early Holocene have been hypothesized to have caused the disappearance of various rainforest species over large geographical areas in South America and restricted the extant populations to mesic sites. Subsequent improvement in climatic conditions has been associated with recolonization. Changes in population size associated with these extinction‐recolonization events should have affected genetic diversity within species. However, these historical hypotheses and their genetic consequences have rarely been tested in South America. Here, we examine the diversity of the chloroplast and nuclear genomes in a Neotropical rainforest tree species, Vouacapoua americana (Leguminosae, Caesalpinioideae) in French Guiana. The chloroplast diversity was analyzed using a polymerase chain reaction‐restriction fragment length polymorphism method (six pairs of primers) in 29 populations distributed over most of French Guiana, and a subset of 17 populations was also analyzed at nine polymorphic microsatellite loci. To determine whether this species has experienced extinction‐recolonization, we sampled populations in areas supposedly not or only slightly affected by climatic changes, where the populations would not have experienced frequent extinction, and in areas that appear to have been recently recolonized. In the putatively recolonized areas, we found patches of several thousands of hectares homogeneous for chloroplast variation that can be interpreted as the effect of recolonization processes from several geographical origins. In addition, we observed that, for both chloroplast and nuclear genomes, the populations in newly recolonized areas exhibited a significantly smaller allelic richness than others. Controlling for geographic distance, we also detected a significant correlation between chloroplast and nuclear population differentiation. This result indicates a cytonuclear disequilibrium that can be interpreted as a historical signal of a genetic divergence between fragmented populations. In conclusion, the spatial genetic structure of contemporary V. americana populations shows evidence that this species has experienced large extinction‐recolonization events, which were possibly caused by past climatic change.

Reduced density due to logging and its consequences on mating system and pollen flow in the African mahogany Entandrophragma cylindricum

In tropical forests, selective logging removes large trees that are often the main contributors to pollination. We studied pollination patterns of the African mahogany, Entandrophragma cylindricum (Sapelli). We investigated two plots in Cameroon corresponding to three tree densities: unlogged forest (Ndama 2002), a mildly logged forest 1 year after logging (Ndama 2003) and a severely logged forest 30 years after logging (Dimako). We used four microsatellite markers to perform paternity analysis. Selfing remained below 2% in all treatments. Pollen flow was mainly long distance but with some proximity effects. Average observed within-plot pollination distances were 338, 266 and 385 m, and pollination by trees outside the plots was 70% (Ndama 2002), 74% (Ndama 2003) and 66% (Dimako). Despite sampling a limited number of seeds from a limited number of mother trees, we obtained seeds sired by 35.6–38.3% of the potential within-plot pollen donors. While trees 20 cm in diameter contributed to pollination, results in Dimako suggest that individual larger trees contribute more to pollination than small ones. This effect was not detected in the other treatments. The results suggest extensive pollen flow in Sapelli. Hence, in Sapelli, the main limiting factor for regeneration after logging may be a reduction in the number of trees capable of producing seeds rather genetic effects due to limits to pollen dispersal.

Evolutionary history of almond tree domestication in the Mediterranean basin.

Genetic diversity of contemporary domesticated species is shaped by both natural and human‐driven processes. However, until now, little is known about how domestication has imprinted the variation of fruit tree species. In this study, we reconstruct the recent evolutionary history of the domesticated almond tree, Prunus dulcis, around the Mediterranean basin, using a combination of nuclear and chloroplast microsatellites [i.e. simple sequence repeat (SSRs)] to investigate patterns of genetic diversity. Whereas conservative chloroplast SSRs show a widespread haplotype and rare locally distributed variants, nuclear SSRs show a pattern of isolation by distance with clines of diversity from the East to the West of the Mediterranean basin, while Bayesian genetic clustering reveals a substantial longitudinal genetic structure. Both kinds of markers thus support a single domestication event, in the eastern side of the Mediterranean basin. In addition, model‐based estimation of the timing of genetic divergence among those clusters is estimated sometime during the Holocene, a result that is compatible with human‐mediated dispersal of almond tree out of its centre of origin. Still, the detection of region‐specific alleles suggests that gene flow from relictual wild preglacial populations (in North Africa) or from wild counterparts (in the Near East) could account for a fraction of the diversity observed.

Breeding system and pollination biology of the semi- domesticated fruit tree, Tamarindus indica L. (Leguminosae: Caesalpinioideae): Implications for fruit production, selective breeding, and conservation of genetic resources

In this paper, we provide data on the breeding system of Tamarindus indica, examining fruit production as well as pollen tube growth under different controlled pollination experiments (open, cross and self pollination). We discuss implications of the results for management for fruit production in Tamarind, conservation of genetic resources and the potential for selective breeding. Observation of the germination and the pollen tubes growth under various pollination modes show that the tamarind is an incompatible species partially. This incompatibility appears at the pre level zygotic (IE on the level of the stigmatic, style and ovary) and post zygotic by the abortion of seeds.

Polymorphic microsatellite loci from #Dacryodes edulis# (Burseraceae), a Central African rainforest and fruit-tree species

PREMISE OF THE STUDY Microsatellite markers were isolated and characterized from Dacryodes edulis (Burseraceae), a tropical rainforests fruit tree of central Africa. METHODS AND RESULTS Using an enrichment protocol, six microsatellites loci were developed from Dacryodes edulis. We investigated polymorphism using 45 trees from three widely separated populations in Cameroon. All loci were polymorphic, with the number of alleles ranging from 2 to 15. Polymorphism was widely variable among loci and expected heterozygosities ranged from 0.06 to 0.84 with a mean value of 0.49. CONCLUSIONS These loci will be useful for the in-depth analysis of population structure and phylogeographic variation throughout the distribution range of Dacryodes edulis and other related taxa, Dacryodes buettneri and D. normandii, in which all loci were also amplified. Furthermore, they will offer the opportunity to study early domestication processes acting on the genetic diversity of Dacryodes edulis.