The origin and evolution of a recent agricultural weed: population genetic diversity of weedy populations of sunflower (Helianthus annuus L.) in Spain and France

The recurrent evolution of crop-related weeds during agricultural history raises serious economic problems and challenging scientific questions. Weedy forms of sunflower, a species native from America, have been reported in European sunflower fields for a few decades. In order to understand their origin, we analysed the genetic diversity of a sample of weedy populations from France and Spain, and of conventional and ornamental varieties. A crop-specific maternally inherited marker was present in all weeds. At 16 microsatellite loci, the weedy populations shared most of their diversity with the conventional varieties. But they showed a large number of additional alleles absent from the cultivated pool. European weedy populations thus most probably originated from the unintentional pollination of maternal lines in seed production fields by wild plants growing nearby, resulting in the introduction of crop-wild hybrids into the farmers’ fields. The wide diversity and the low population structure detected were indicative of a multiplicity of introductions events rather than of field-to-field propagation. Further studies are required to understand the local evolutionary dynamics of a weedy population, and especially the respective roles of crop-to-weed gene flow and selection in the fate of an initial source of crop-wild hybrids

Genetic structure and core collection of the World Olive Germplasm Bank of Marrakech: towards the optimised management and use of Mediterranean olive genetic resources

The conservation of cultivated plants in ex-situ collections is essential for the optimal management and use of their genetic resources. For the olive tree, two world germplasm banks (OWGB) are presently established, in Córdoba (Spain) and Marrakech (Morocco). This latter was recently founded and includes 561 accessions from 14 Mediterranean countries. Using 12 nuclear microsatellites (SSRs) and three chloroplast DNA markers, this collection was characterised to examine the structure of the genetic diversity and propose a set of olive accessions encompassing the whole Mediterranean allelic diversity range. We identified 505 SSR profiles based on a total of 210 alleles. Based on these markers, the genetic diversity was similar to that of cultivars and wild olives which were previously characterised in another study indicating that OWGB Marrakech is representative of Mediterranean olive germplasm. Using a model-based Bayesian clustering method and principal components analysis, this OWGB was structured into three main gene pools corresponding to eastern, central and western parts of the Mediterranean Basin. We proposed 10 cores of 67 accessions capturing all detected alleles and 10 cores of 58 accessions capturing the 186 alleles observed more than once. In each of the 10 cores, a set of 40 accessions was identical, whereas the remaining accessions were different, indicating the need to include complementary criteria such as phenotypic adaptive and agronomic traits. Our study generated a molecular database for the entire OWGB Marrakech that may be used to optimise a strategy for the management of olive genetic resources and their use for subsequent genetic and genomic olive breeding

Analysis and structuration of the genetic diversity of Pyrenean maize populations with a 50K SNP array by a bulk and an one individual plant approach

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: Genetic diversity of maize in Europe : molecular analysis of ancient DNA from herbariums and comparison with molecular analysis of a large collection of populations

European maize was introduced from Central America in the South of Europe at the end of the 15th century, and from Northern America in the North of Europe following the expeditions of the early 16th century. In order to better understand its later history in Europe, we compared the genetic diversity of European maize in the 19th century and the first half of the 20th century, represented by plants collected in an ancient herbarium, with the diversity of American and European maize populations collected around 50 years ago and maintained as living samples in collections. Samples were obtained from the herbarium of Paris (MNHN). Fractions of leaves or spikelets (from 2 to 37 mg) were collected from 17 plates. Samples are 138 years old in average (from the second half of the 18th century to 1949). They originated from all over France, with half in the Paris basin. DNA was successfully extracted from leave or spikelet fragments, using the Kit Qiagen® method. Precautions were taken to avoid contamination with foreign DNA. A total of 80 μl of DNA was obtained per sample. DNA samples were analysed with 14 nuclear mocrosatellite markers, ten of them displaying a tetra nucleotidic motive. From 4 to 14 markers could be analysed per sample.L'objectif de l'étude est d'analyser la diversité des maïs en Europe en confrontant la diversité analysée à partir d'herbiers anciens avec celle trouvée dans une étude réalisée sur 273 populations de maïs d'origine américaine et européenne, conservées en semences et renouvelées régulièrement depuis cinquante ans environ. L'étude a porté sur 17 planches de l'Herbier du Muséum d'Histoire Naturelle de Paris datant de 138 ans en moyenne, prélevées en France et majoritairement dans le Bassin parisien. A partir de fragments de feuilles ou d'épillets, l'ADN a été extrait par la méthode du Kit Qiagen et analysé avec succès pour 4 à 14 marqueurs microsatellites nucléaires. Analysée à l'aide d'une matrice de distance de Roger, la variabilité génétique se structure en trois groupes où sont majoritaires respectivement : les populations nord américaines anciennes (Northern Flint), les autres populations américaines, les populations européennes. Les plantes d'herbier se positionnent essentiellement dans le groupe des populations européennes. Ce résultat est confirmé par l'identification des populations les plus proches de chaque planche d'herbier. L'hybridation entre les Northern Flint et les populations Caraïbes et du sud de l'Espagne, qui est supposée avoir donné naissance à la diversité européenne, apparaît donc antérieure à la collecte des plantes d'herbier

Cultivated Olive Diversification at Local and Regional Scales: Evidence From the Genetic Characterization of French Genetic Resources

International audienceMolecular characterization of crop genetic resources is a powerful approach to elucidate the origin of varieties and facilitate local cultivar management. Here we aimed to decipher the origin and diversification of French local olive germplasm. The 113 olive accessions of the ex situ collection of Porquerolles were characterized with 20 nuclear microsatellites plus their plastid haplotype. We then compared this collection to Mediterranean olive varieties from the Worldwide Olive Germplasm Bank of Marrakech, Morocco. High genetic diversity was observed within local French varieties, indicating a high admixture level, with an almost equal contribution from the three main Mediterranean gene pools. Nearly identical and closely related genotypes were observed among French and Italian/Spanish varieties. A high number of parent-offspring relationships were also detected among French varieties and between French and two Italian varieties ('Frantoio' and 'Moraiolo') and the Spanish variety ('Gordal Sevillana'). Our investigations indicated that French olive germplasm resulted from the diffusion of material from multiple origins followed by diversification based on parentage relationships between varieties. We strongly suggest that farmers have been actively selecting olives based on local French varieties. French olive agroecosystems more affected by unexpected frosts than southernmost regions could also be seen as incubators and as a bridge between Italy and Spain that has enhanced varietal olive diversification

: Genetic diversity of maize in Europe : molecular analysis of ancient DNA from herbariums and comparison with molecular analysis of a large collection of populations

European maize was introduced from Central America in the South of Europe at the end of the 15th century, and from Northern America in the North of Europe following the expeditions of the early 16th century. In order to better understand its later history in Europe, we compared the genetic diversity of European maize in the 19th century and the first half of the 20th century, represented by plants collected in an ancient herbarium, with the diversity of American and European maize populations collected around 50 years ago and maintained as living samples in collections. Samples were obtained from the herbarium of Paris (MNHN). Fractions of leaves or spikelets (from 2 to 37 mg) were collected from 17 plates. Samples are 138 years old in average (from the second half of the 18th century to 1949). They originated from all over France, with half in the Paris basin. DNA was successfully extracted from leave or spikelet fragments, using the Kit Qiagen® method. Precautions were taken to avoid contamination with foreign DNA. A total of 80 μl of DNA was obtained per sample. DNA samples were analysed with 14 nuclear mocrosatellite markers, ten of them displaying a tetra nucleotidic motive. From 4 to 14 markers could be analysed per sample.L'objectif de l'étude est d'analyser la diversité des maïs en Europe en confrontant la diversité analysée à partir d'herbiers anciens avec celle trouvée dans une étude réalisée sur 273 populations de maïs d'origine américaine et européenne, conservées en semences et renouvelées régulièrement depuis cinquante ans environ. L'étude a porté sur 17 planches de l'Herbier du Muséum d'Histoire Naturelle de Paris datant de 138 ans en moyenne, prélevées en France et majoritairement dans le Bassin parisien. A partir de fragments de feuilles ou d'épillets, l'ADN a été extrait par la méthode du Kit Qiagen et analysé avec succès pour 4 à 14 marqueurs microsatellites nucléaires. Analysée à l'aide d'une matrice de distance de Roger, la variabilité génétique se structure en trois groupes où sont majoritaires respectivement : les populations nord américaines anciennes (Northern Flint), les autres populations américaines, les populations européennes. Les plantes d'herbier se positionnent essentiellement dans le groupe des populations européennes. Ce résultat est confirmé par l'identification des populations les plus proches de chaque planche d'herbier. L'hybridation entre les Northern Flint et les populations Caraïbes et du sud de l'Espagne, qui est supposée avoir donné naissance à la diversité européenne, apparaît donc antérieure à la collecte des plantes d'herbier

Diversity of maize landraces from south-west of France: origin and morphological differentiation analyzes

National audienc

Phenotypic_data

The excel file has both the data, and a worksheet explaining each of the columns/fields

Patterns of Molecular Evolution Associated With Two Selective Sweeps in the Tb1–Dwarf8 Region in Maize

We focused on a region encompassing a major maize domestication locus, Tb1, and a locus involved in the flowering time variation, Dwarf8 (D8), to investigate the consequences of two closely linked selective sweeps on nucleotide variation and gain some insights into maize geographical diffusion, through climate adaptation. First, we physically mapped D8 at ∼300 kb 3′ of Tb1. Second, we analyzed patterns of nucleotide variation at Tb1, D8, and seven short regions (400–700 bp) located in the Tb1–D8 region sequenced on a 40 maize inbred lines panel encompassing early-flowering temperate and late-flowering tropical lines. The pattern of polymorphism along the region is characterized by two valleys of depleted polymorphism while the region in between exhibits an appreciable amount of diversity. Our results reveal that a region ∼100 kb upstream of the D8 gene exhibits hallmarks of divergent selection between temperate and tropical lines and is likely closer than the D8 gene to the target of selection for climate adaptation. Selection in the tropical lines appears more recent than in the temperate lines, suggesting an initial domestication of early-flowering maize. Simulation results indicate that the polymorphism pattern is consistent with two interfering selective sweeps at Tb1 and D8