The witchweed Striga gesnerioides and the cultivated cowpea: A geographical and historical analysis of their West African distribution points to the prevalence of agro-ecological factors and the parasite's multilocal evolution potential.

The increasing severity of Striga gesnerioides attacks on cowpea across West Africa has been related to its prolificity, seed mobility and longevity, and adaptation to aridity, in a context of agricultural intensification. To understand this fast extension, we analyzed (1) the distributions of the crop and the witchweed with ecological niche modeling and multivariate climate analysis, and (2) the chronological information available from collections and the literature. The ecoclimatic envelope of S. gesnerioides attacks on cowpea is the same as on wild hosts. Consistently, the modeled distribution of cowpea infestations is closely similar to the simple superposition of the parasite model (involving all hosts) and the crop model. Striga gesnerioides infestations are restricted to the driest component of the cultivated cowpea ecoclimatic niche, corresponding to the Sahelian and Sudano-Sahelian belts and the Dahomey gap. Thus, the parasite distribution, determined by its own requirements, does not constrain cowpea cultivation under Guinean climates. The spatial and temporal distributions of S. gesnerioides field infestations are consistent with an earlier impact on cowpea production in eastern West Africa, related itself to a similar trend in cowpea cultivation intensification from Niger, Nigeria and Benin to Burkina Faso and Ghana. Mali and Senegal were affected later, and literature reports of Senegalese strains of S. gesnerioides from the wild developing virulence on cowpea offer a model for the diffusion of witchweed parasitism by multilocal evolution, through host-driven selection, instead of epidemic diffusion. A contrario, in Côte d'Ivoire, cowpea is much less widespread, so the parasite has remained confined to the wild compartment. Thus, both historical and ecogeographic analyses refute the vision of S. gesnerioides as an invader. Instead, they point to the increasing importance and intensification of the crop, and the consequent loss of biodiversity, as the main drivers of the extension and diversification of its crop-specific strains.

The bracteatus pineapple genome and domestication of clonally propagated crops.

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.

Evolution of almond genetic diversity and farmer practices in Lebanon: impacts of the diffusion of a graft-propagated cultivar in a traditional system based on seed-propagation.

BACKGROUND: Under cultivation, many outcrossing fruit tree species have switched from sexual reproduction to vegetative propagation. Traditional production systems have persisted, where cultivar propagation is based on a mixed reproductive system. For millenia, almond, Prunus dulcis, has been propagated by seeds. Almond grafting remained of little importance until recently. In Lebanon, both sexual and clonal reproductions are used for almond propagation. We used 15 microsatellite markers to investigate the effect of introducing graft-propagated cultivars and associated practices, on the structure of the genetic diversity among and within the two main Lebanese cultivars. RESULTS: As expected, the sexually propagated cultivar Khachabi exhibited more genotypic and genetic diversity than the vegetatively propagated cultivar Halwani. It also exhibited lower differentiation among populations. The distribution of clones showed that propagation modes were not exclusive: farmers have introduced clonal propagation in the seed-propagated cultivar while they have maintained a diversity of genotypes within populations that were mostly graft-propagated. These practices are also important to avoid mate limitations that hamper fruit production in a self-incompatible species. 'Khachabi' is structured into two gene pools separated by the Lebanese mountains. As to 'Halwani', two different gene pools were introduced. The most ancient one shares the same geographic range as 'Khachabi'; longtime coexistence and sexual reproduction have resulted in admixture with 'Khachabi'. In contrast, the more recent introduction of the second gene pool in the Bekaa region followed an evolution towards more extensive clonal propagation of 'Halwani' limiting hybridizations. Furthermore, some pairs of geographically distant 'Halwani' orchards, exhibited low genetic distances, suggesting that a network of exchanges between farmers was effective on a large scale and/or that farmers brought clonal plant material from a common source. CONCLUSIONS: Almond diversification in Lebanon is clearly related to the evolution of propagation practices adapted to self-incompatible cultivars. The comparison between both cultivars demonstrated the genetic effects of the introduction of a new cultivar and the associated grafting propagation practices. Our study provided information to develop a strategy for in situ conservation of cultivars and to limit gene flow from introduced material to ancient orchards.

Past and present dynamics of sorghum and pearl millet diversity in Mount Kenya region.

Crop populations in smallholder farming systems are shaped by the interaction of biological, ecological, and social processes, occurring on different spatiotemporal scales. Understanding these dynamics is fundamental for the conservation of crop genetic resources. In this study, we investigated the processes involved in sorghum and pearl millet diversity dynamics on Mount Kenya. Surveys were conducted in ten sites distributed along two elevation transects and occupied by six ethnolinguistic groups. Varieties of both species grown in each site were inventoried and characterized using SSR markers. Genetic diversity was analyzed using both individual- and population-based approaches. Surveys of seed lot sources allowed characterizing seed-mediated gene flow. Past sorghum diffusion dynamics were explored by comparing Mount Kenya sorghum diversity with that of the African continent. The absence of structure in pearl millet genetic diversity indicated common ancestry and/or important pollen- and seed-mediated gene flow. On the contrary, sorghum varietal and genetic diversity showed geographic patterns, pointing to different ancestry of varieties, limited pollen-mediated gene flow, and geographic patterns in seed-mediated gene flow. Social and ecological processes involved in shaping seed-mediated gene flow are further discussed.

Distribution and differentiation of wild, feral, and cultivated populations of perennial upland cotton (Gossypium hirsutum L.) in Mesoamerica and the Caribbean.

Perennial forms of Gossypium hirsutum are classified under seven races. Five Mesoamerican races would have been derived from the wild race 'yucatanense' from northern Yucatán. 'Marie-Galante', the main race in the Caribbean, would have developed from introgression with G. barbadense. The racial status of coastal populations from the Caribbean has not been clearly defined. We combined Ecological Niche Modeling with an analysis of SSR marker diversity, to elucidate the relationships among cultivated, feral and wild populations of perennial cottons. Out of 954 records of occurrence in Mesoamerica and the Caribbean, 630 were classified into four categories cultivated, feral (disturbed and secondary habitats), wild/feral (protected habitats), and truly wild cotton (TWC) populations. The widely distributed three first categories cannot be differentiated on ecological grounds, indicating they mostly belong to the domesticated pool. In contrast, TWC are restricted to the driest and hottest littoral habitats, in northern Yucatán and in the Caribbean (from Venezuela to Florida), as confirmed by their climatic envelope in the factorial analysis. Extrapolating this TWC climatic model to South America and the Pacific Ocean points towards places where other wild representatives of tetraploid Gossypium species have been encountered. The genetic analysis sample comprised 42 TWC accessions from 12 sites and 68 feral accessions from 18 sites; at nine sites, wild and feral accessions were collected in close vicinity. Principal coordinate analysis, neighbor joining, and STRUCTURE consistently showed a primary divergence between TWC and feral cottons, and a secondary divergence separating 'Marie-Galante' from all other feral accessions. This strong genetic structure contrasts strikingly with the absence of geographic differentiation. Our results show that TWC populations of Mesoamerica and the Caribbean constitute a homogenous gene pool. Furthermore, the relatively low genetic divergence between the Mesoamerican and Caribbean domesticated pools supports the hypothesis of domestication of G. hirsutum in northern Yucatán.

Multiple lines of evidence for the origin of domesticated chili pepper, Capsicum annuum, in Mexico.

The study of crop origins has traditionally involved identifying geographic areas of high morphological diversity, sampling populations of wild progenitor species, and the archaeological retrieval of macroremains. Recent investigations have added identification of plant microremains (phytoliths, pollen, and starch grains), biochemical and molecular genetic approaches, and dating through (14)C accelerator mass spectrometry. We investigate the origin of domesticated chili pepper, Capsicum annuum, by combining two approaches, species distribution modeling and paleobiolinguistics, with microsatellite genetic data and archaeobotanical data. The combination of these four lines of evidence yields consensus models indicating that domestication of C. annuum could have occurred in one or both of two areas of Mexico: northeastern Mexico and central-east Mexico. Genetic evidence shows more support for the more northern location, but jointly all four lines of evidence support central-east Mexico, where preceramic macroremains of chili pepper have been recovered in the Valley of Tehuacán. Located just to the east of this valley is the center of phylogenetic diversity of Proto-Otomanguean, a language spoken in mid-Holocene times and the oldest protolanguage for which a word for chili pepper reconstructs based on historical linguistics. For many crops, especially those that do not have a strong archaeobotanical record or phylogeographic pattern, it is difficult to precisely identify the time and place of their origin. Our results for chili pepper show that expressing all data in similar distance terms allows for combining contrasting lines of evidence and locating the region(s) where cultivation and domestication of a crop began.