L'intégration de l'ethnobotanique et de la génétique des populations met en évidence l'agrobiodiversité des palmiers dattiers de l'oasis de Siwa (Égypte) et leur importance pour l'histoire évolutive de l'espèce.

Crop diversity is shaped by biological and social processes interacting at different spatiotemporal scales. Here we combined population genetics and ethnobotany to investigate date palm (Phoenix dactylifera L.) diversity in Siwa Oasis, Egypt. Based on interviews with farmers and observation of practices in the field, we collected 149 date palms from Siwa Oasis and 27 uncultivated date palms from abandoned oases in the surrounding desert. Using genotyping data from 18 nuclear and plastid microsatellite loci, we confirmed that some named types each constitute a clonal line, i.e. a true-to-type cultivar. We also found that others are collections of clonal lines, i.e. ethnovarieties, or even unrelated samples, i.e. local categories. This alters current assessments of agrobiodiversity, which are visibly underestimated, and uncovers the impact of low-intensity, but highly effective, farming practices on biodiversity. These hardly observable practices, hypothesized by ethnographic survey and confirmed by genetic analysis, are enabled by the way Isiwans conceive and classify living beings in their oasis, which do not quite match the way biologists do: a classic disparity of etic vs. emic categorizations. In addition, we established that Siwa date palms represent a unique and highly diverse genetic cluster, rather than a subset of North African and Middle Eastern palm diversity. As previously shown, North African date palms display evidence of introgression by the wild relative Phoenix theophrasti, and we found that the uncultivated date palms from the abandoned oases share even more alleles with this species than cultivated palms in this region. The study of Siwa date palms could hence be a key to the understanding of date palm diversification in North Africa. Integration of ethnography and population genetics promoted the understanding of the interplay between diversity management in the oasis (short-time scale), and the origins and dynamic of diversity through domestication and diversification (long-time scale)

A small XY chromosomal region explains sex determination in wild dioecious V. vinifera and the reversal to hermaphroditism in domesticated grapevines

Publis014-agap-029Background In Vitis vinifera L., domestication induced a dramatic change in flower morphology: the wild sylvestris subspecies is dioecious while hermaphroditism is largely predominant in the domesticated subsp. V. v. vinifera. The characterisation of polymorphisms in genes underlying the sex-determining chromosomal region may help clarify the history of domestication in grapevine and the evolution of sex chromosomes in plants. In the genus Vitis, sex determination is putatively controlled by one major locus with three alleles, male M, hermaphrodite H and female F, with an allelic dominance M > H > F. Previous genetic studies located the sex locus on chromosome 2. We used DNA polymorphisms of geographically diverse V. vinifera genotypes to confirm the position of this locus, to characterise the genetic diversity and traces of selection in candidate genes, and to explore the origin of hermaphroditism. Results In V. v. sylvestris, a sex-determining region of 154.8 kb, also present in other Vitis species, spans less than 1% of chromosome 2. It displays haplotype diversity, linkage disequilibrium and differentiation that typically correspond to a small XY sex-determining region with XY males and XX females. In male alleles, traces of purifying selection were found for a trehalose phosphatase, an exostosin and a WRKY transcription factor, with strikingly low polymorphism levels between distant geographic regions. Both diversity and network analysis revealed that H alleles are more closely related to M than to F alleles. Conclusions Hermaphrodite alleles appear to derive from male alleles of wild grapevines, with successive recombination events allowing import of diversity from the X into the Y chromosomal region and slowing down the expansion of the region into a full heteromorphic chromosome. Our data are consistent with multiple domestication events and show traces of introgression from other Asian Vitis species into the cultivated grapevine gene pool. La vigne domestiquée, Vitis vinifera ssp. vinifera, cultivée pour la production de fruit et de vin à travers le monde, dérive de la vigne sauvage, Vitis vinifera ssp. sylvestris, sous-espèce endémique de l'Eurasie. Au cours de la domestication, le système de reproduction a évolué de la diécie à l'hermaphrodisme. Nous montrons que la région du sexe est sous le contrôle d'une région chromosomique qui couvre au maximum 154kpbp, moins de 1% du chromosome 2. La caractérisation de ce locus en terme de diversité haplotypique, de signature de sélection et de déséquilibre de liaison a permis de révéler un système de détermination sexuelle de type XY. La petite taille de cette région chromosomique semble indiquer un stade très précoce dans l'évolution de chromosomes sexuels, malgré que la diécie soit le trait ancestral chez toutes les espèces de Vitis, ayant divergé du sous-genre Muscadinia il y a plusieurs millions d'années. L'analyse des distances génétiques entre haplotypes dans le locus du sexe a révélé que l'hermaphrodisme observé chez la vigne domestiquée résulte de la mutation de l'allèle mâle présent chez la vigne sauvage. Le réseau d'haplotypes a montré qu'en plus de la contribution de V. sylvestris, une autre espèce de Vitis asiatique a pu contribuer à la constitution du génome actuel de la vigne cultivée moderne. Ces travaux résultent d'une collaboration entre l'équipe DAAV d'AGAP et l'UMR CBAE (Montpellier)

The discovery of wild date palms in oman reveals a complex domestication history involving centers in the middle east and africa

For many crops, wild relatives constitute an extraordinary resource for cultivar improvement [1, 2] and also help to better understand the history of their domestication [3]. However, the wild ancestor species of several perennial crops have not yet been identified. Perennial crops generally present a weak domestication syndrome allowing cultivated individuals to establish feral populations difficult to distinguish from truly wild populations, and there is frequently ongoing gene flow between wild relatives and the crop that might erode most genetic differences [4]. Here we report the discovery of populations of the wild ancestor species of the date palm (Phoenix dactylifera L.), one of the oldest and most important cultivated fruit plants in hot and arid regions of the Old World. We discovered these wild individuals in remote and isolated mountainous locations of Oman. They are genetically more diverse than and distinct from a representative sample of Middle Eastern cultivated date palms and exhibit rounded seed shapes resembling those of a close sister species and archeological samples, but not modern cultivars. Whole-genome sequencing of several wild and cultivated individuals revealed a complex domestication history involving the contribution of at least two wild sources to African cultivated date palms. The discovery of wild date palms offers a unique chance to further elucidate the history of this iconic crop that has constituted the cornerstone of traditional oasis polyculture systems for several thousand years [5]

Rheumatoid arthritis - treatment: 180. Utility of Body Weight Classified Low-Dose Leflunomide in Japanese Rheumatoid Arthritis

Background: In Japan, more than 20 rheumatoid arthritis (RA) patients died of interstitial pneumonia (IP) caused by leflunomide (LEF) were reported, but many of them were considered as the victims of opportunistic infection currently. In this paper, efficacy and safety of low-dose LEF classified by body weight (BW) were studied. Methods: Fifty-nine RA patients were started to administrate LEF from July 2007 to July 2009. Among them, 25 patients were excluded because of the combination with tacrolimus, and medication modification within 3 months before LEF. Remaining 34 RA patients administered 20 to 50 mg/week of LEF were followed up for 1 year and enrolled in this study. Dose of LEF was classified by BW (50 mg/week for over 50 kg, 40 mg/week for 40 to 50 kg and 20 to 30 mg/week for under 40 kg). The average age and RA duration of enrolled patients were 55.5 years old and 10.2 years. Prednisolone (PSL), methotrexate (MTX) and etanercept were used in 23, 28 and 2 patients, respectively. In case of insufficient response or adverse effect, dosage change or discontinuance of LEF were considered. Failure was defined as dosages up of PSL and MTX, or dosages down or discontinuance of LEF. Last observation carried forward method was used for the evaluation of failed patients at 1 year. Results: At 1 year after LEF start, good/ moderate/ no response assessed by the European League Against Rheumatism (EULAR) response criteria using Disease Activity Score, including a 28-joint count (DAS28)-C reactive protein (CRP) were showed in 14/ 10/ 10 patients, respectively. The dosage changes of LEF at 1 year were dosage up: 10, same dosage: 5, dosage down: 8 and discontinuance: 11 patients. The survival rate of patients in this study was 23.5% (24 patients failed) but actual LEF continuous rate was 67.6% (11 patients discontinued) at 1 year. The major reason of failure was liver dysfunction, and pneumocystis pneumonia was occurred in 1 patient resulted in full recovery. One patient died of sepsis caused by decubitus ulcer infection. DAS28-CRP score was decreased from 3.9 to 2.7 significantly. Although CRP was decreased from 1.50 to 0.93 mg/dl, it wasn't significant. Matrix metalloproteinase (MMP)-3 was decreased from 220.0 to 174.2 ng/ml significantly. Glutamate pyruvate transaminase (GPT) was increased from 19 to 35 U/l and number of leukocyte was decreased from 7832 to 6271 significantly. DAS28-CRP, CRP, and MMP-3 were improved significantly with MTX, although they weren't without MTX. Increase of GPT and leukopenia were seen significantly with MTX, although they weren't without MTX. Conclusions: It was reported that the risks of IP caused by LEF in Japanese RA patients were past IP history, loading dose administration and low BW. Addition of low-dose LEF is a potent safe alternative for the patients showing unsatisfactory response to current medicines, but need to pay attention for liver function and infection caused by leukopenia, especially with MTX. Disclosure statement: The authors have declared no conflicts of interes

Origins and insights into the historic Judean date palm based on genetic analysis of germinated ancient seeds and morphometric studies

Germination of 2000-year-old seeds of Phoenix dactylifera from Judean desert archaeological sites provides a unique opportunity to study the Judean date palm, described in antiquity for the quality, size, and medicinal properties of its fruit, but lost for centuries. Microsatellite genotyping of germinated seeds indicates that exchanges of genetic material occurred between the Middle East (eastern) and North Africa (western) date palm gene pools, with older seeds exhibiting a more eastern nuclear genome on a gradient from east to west of genetic contributions. Ancient seeds were significantly longer and wider than modern varieties, supporting historical records of the large size of the Judean date. These findings, in accord with the region’s location between east and west date palm gene pools, suggest that sophisticated agricultural practices may have contributed to the Judean date’s historical reputation. Given its exceptional storage potentialities, the date palm is a remarkable model for seed longevity research

Experimental waterlogging of grape seeds, impact on seed shape and geometrical reversing for morphometric inference

International audienceWhile the impact of charring on grape seed morphology is well documented, waterlogged pips have up to now been considered in morphometric studies to undergo very limited changes and to be directly comparable to reference collections of fresh seeds. In this study we investigate the impact of waterlogging using different chemicals (H2O2, HNO3, NaOH, KOH) on pips of various cultivars and wild grapevines. Pips are soaked individually in a given chemical solution for increasing periods of time, photographed at each stage, and their dorsal and lateral outlines analysed using Elliptic Fourier Transforms to quantify shape changes. We observe that the different products have comparable effects. The seeds start to swell and then return to their original shapes. Deformation is limited and primarily affects the beak which is slightly blunt and somewhat more pointed than on the original pips. These changes are reminiscent of the deformations observed in waterlogged archaeological seeds. Our results show that they are not strong enough to affect significantly the identification of wild and domesticated morphotypes by seed outline analyses. The effect is greater on the identifications at cultivars level but the accuracy can still be considered acceptable. We experiment the application of an average reverse vector of shape changes to compensate for some of the deformation of artificially waterlogged pips. This correction appears to have a positive effect on the accuracy of identifications for some cultivars. Our conclusion is that outline analysis can be confidently performed on archaeological waterlogged grape pips to identify wild or domesticated status and that it is more appropriate to aim at identifying groups of varieties than individual cultivars. Considering that deformations due to charring and waterlogging have differentiated effects on the identifications it is recommended to take into account both waterlogged and charred seed assemblages

Comparison of image acquisition techniques and morphometric methods to distinguish between Vitis vinifera subspecies and cultivars

International audienceFor decades, it has been known that the morphology of wild Vitis vinifera (grape) pips differ from domesticated ones. Based on these differences, computerised image analysis and morphometrics allow us to obtain excellent results to identify the domestication status of archaeological grape pips. However, various image analysis methodologies and morphometric methods have been applied in previous studies for this purpose. Our study has examined, for the first time, the different techniques of digital image acquisition (digital camera vs. scanner) of grape pips, with the aim of testing the identification performance using both traditional and geometric morphometric features to distinguish wild from domestic grape pips. The performance of different morphometric methods established that all image acquisition techniques and morphometric methods correctly distinguished between wild and domestic grapes. The use of the combined geometric morphometric features of both dorsal and lateral views of the pips provided the best accuracy in distinguishing individual cultivars

L’approvisionnement et la gestion de l’énergie combustible pour la production de poteries au cours du Haut Empire dans la moyenne vallée de l’Hérault. Actualité de la recherche anthracologique sur les ateliers de Saint-Pargoire/Contours et Aspiran/Saint-Bézard

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Archéo-biologie de la domestication de l'olivier en Méditerranée occidentale: de la remise en cause d'une histoire dogmatique à la révélation de son irrigation médiévale

The olive-tree is the symbol of the Mediterranean. His history has been enriched and renewed by the cross-over approches especially by genetic and bioarchaeological studies. This article sums up the principal recent results on the subject since the origin of this tree showing different centers of domestication until the medieval irrigation of olive fields

Actualités des recherches archéobotaniques sur les habitats almohades d’Igiliz (Anti-Atlas, Maroc)

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