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

National audienc

: 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

: 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

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

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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

Genetic diversity of maize landraces from the South-West of France

From the 17th century until the arrival of hybrids in 1960s, maize landraces were cultivated in the South-West of France, a traditional region for maize cultivation. A set of landraces were collected in this region between the 1950s and 1980s and were then conserved ex situ in a germplam collection. Previous studies using molecular markers on approx. twenty landraces fo this region showed that they belonged to a Pyrenees-Galicia Flint genetic group and originated from hybridization between Caribbean and Northern Flint germplasms introduced in Europe. In this study, we assessed the structure and genetic diversity of 194 SWF maize landraces to elucidate their origin, using a 50K SNP array and a bulk DNA approach. We identified two weakly differentiated genetic groups, one in the Western part and the other in the Eastern part. We highlighted the existence of a longitudinal gradient along the SWF area that was probably maintained through the interplay between genetic drifts and restricted gene flows, rather than through differential climatic adaptation. The contact zone between the two groups observed near the Garonne valley may be the result of these evolutionnary forces. We found only few significant cases of hybridization between Caribbean and Northern Flint germplasms in the region. We also found gene flows from various maize genetic groups to SWF landraces. Thus, we assumed that SWF landraces had a multiple origin with a slightly higher influence of Tropical germplasm in the West and preponderance of Northern Flint germplasm in the East

Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin

International audienceBackground: In Sub-Saharan Africa, Borassus aethiopum Mart. (African fan palm) is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic diversity and population structure of B. aethiopum across nine collection sites spanning the three climatic regions of Benin, West Africa, through the use of microsatellite markers. Results: During a first phase we relied on the reported transferability of primers developed in other palm species. We find that, in disagreement with previously published results, only 22.5% of the markers tested enable amplification of B. aethiopum DNA and polymorphism detection is very low. In a second phase, we generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it for the de novo detection of microsatellite loci. Among the primer pairs targeting these, 11 detected polymorphisms and were further used for analyzing genetic diversity. Across the nine sites, expected heterozygosity (He) ranges from 0.263 to 0.451 with an overall average of 0.354, showing a low genetic diversity. Analysis of molecular variance (AMOVA) shows that within-site variation accounts for 53% of the genetic variation. Accordingly, the low number of migrants and positive values of the fixation index (F) in sites from both the Central (Sudano-Guinean) an

Characterization of Worldwide Olive Germplasm Banks of Marrakech (Morocco) and Córdoba (Spain): Towards management and use of olive germplasm in breeding programs

International audienceOlive (Olea europaea L.) is a major fruit crop in the Mediterranean Basin. Ex-situ olive management is essential to ensure optimal use of genetic resources in breeding programs. The Worldwide Olive Germplasm Bank of Córdoba (WOGBC), Spain, and Marrakech (WOGBM), Morocco, are currently the largest existing olive germplasm collections. Characterization, identification, comparison and authentication of all accessions in both collections could thus provide useful information for managing olive germplasm for its preservation, exchange within the scientific community and use in breeding programs. Here we applied 20 microsatellite markers (SSR) and 11 endocarp morphological traits to discriminate and authenticate 1091 olive accessions belonging to WOGBM and WOGBC (554 and 537, respectively). Of all the analyzed accessions, 672 distinct SSR profiles considered as unique genotypes were identified, but only 130 were present in both collections. Combining SSR markers and endocarp traits led to the identification of 535 cultivars (126 in common) and 120 authenticated cultivars. No significant differences were observed between collections regarding the allelic richness and diversity index. We concluded that the genetic diversity level was stable despite marked contrasts in varietal composition between collections, which could be explained by their different collection establishment conditions. This highlights the extent of cultivar variability within WOGBs. Moreover, we detected 192 mislabeling errors, 72 of which were found in WOGBM. A total of 228 genotypes as molecular variants of 74 cultivars, 79 synonyms and 39 homonyms as new cases were identified. Both collections were combined to define the nested core collections of 55, 121 and 150 sample sizes proposed for further studies. This study was a preliminary step towards managing and mining the genetic diversity in both collections while developing collaborations between olive research teams to conduct association mapping studies by exchanging and phenotyping accessions in contrasted environmental sites