Dissecting quantitative trait variation in the resequencing era: complementarity of bi-parental, multi-parental and association panels

Quantitative trait loci (QTL) have been identified using traditional linkage mapping and positional cloning identified several QTLs. However linkage mapping is limited to the analysis of traits differing between two lines and the impact of the genetic background on QTL effect has been underlined. Genome-wide association studies (GWAs) were proposed to circumvent these limitations. In tomato, we have shown that GWAs is possible, using the admixed nature of cherry tomato genomes that reduces the impact of population structure. Nevertheless, GWAs success might be limited due to the low decay of linkage disequilibrium, which varies along the genome in this species. Multi-parent advanced generation intercross (MAGIC) populations offer an alternative to traditional linkage and GWAs by increasing the precision of QTL mapping. We have developed a MAGIC population by crossing eight tomato lines whose genomes were resequenced. We showed the potential of the MAGIC population when coupled with whole genome sequencing to detect candidate single nucleotide polymorphisms (SNPs) underlying the QTLs. QTLs for fruit quality traits were mapped and related to the variations detected at the genome sequence and expression levels. The advantages and limitations of the three types of population, in the context of the available genome sequence and resequencing facilities, are discussed.This work was supported by CEA-IG/CNG, by performing the DNA QC and providing access to INRA-EPGV to their Illumina Sequencing Platform. We acknowledge groups of Anne Boland (DNA and Cell Bank service) and Marie-Thérèse Bihoreau (Illumina HT Sequencing). The ANR MAGIC-Tom SNP project 09-GENM-109G and the European Solanaceae Integrated Project EUSOL (Food-CT-2006-016214) supported this work. LP was supported by a postdoctoral INRA fellowship, EA by an INRA PhD fellowship and JD by a grant from the Embassy of France in Thailand in Junior Research Fellowship Program 2014.Peer reviewe

Reworking of intra-oceanic rocks in a deep sea basin: example from the Bou-Maiza complex (Edough massif, eastern Algeria)

International audienceMetagabbros and amphibolites exposed in the Bou-Maïza area of the Edough massif (northeast Algeria) are described in detail. Field and petro-structural observations point to the syn-sedimentary emplacement of gabbros as clasts, blocks and lenses of polymictic gabbroic breccias. Associated amphibolites display fine-scale parallel sedimentary bedding and represent mafic epiclastites, litharenites and mafic greywackes. The mafic beds and lenses are intercalated with aluminous pelitic schists of continental origin, quartzite and marble. It is concluded that all mafic rocks from this locality derive from the erosion of an oceanic plutono-volcanic complex of MORB affinity that was reworked in a block matrix mélange and emplaced as turbidites and debris flows during the Mesozoic. We propose a convergent plate margin setting for these formations connected with the subducted Calabrian branch of the Tethyan slab

Geochemical study (major, trace elements and Pb-Sr-Nd isotopes) of mantle material obducted onto the North African margin (Edough Massif, North Eastern Algeria): Tethys fragments or lost remnants of the Liguro-Provencal basin?

International audienceThe Maghrebides, Betics and some parts of the Calabrian, NE Sicilian and Tuscan allochtons constitute dismembered fragments of the Alpine belt that resulted from the Cenozoic collision between Africa and Eurasia and the opening of the Western Mediterranean basin. Mineral and whole-rock geochemical analyses have been performed on three distinct outcrops of mantle material from the Edough Massif of NE Algeria, namely the Bou Maiza (BM) gabbros, the La Voile Noire (LVN) amphibolites and the Sidi Mohamed (SM) peridotites. In all samples, Sr isotopes are largely affected by seawater alteration (87Sr/86Sract. > 0.70384 and up to 0.70888) and cannot be used to evaluate the nature of the source reservoirs. SM peridotites display variable depleted mantle Nd isotopic signatures (εNdact. from + 7.0 to + 12.2) and geochemical features suggesting no significant chemical depletion as a result of partial melting and melt extraction (Mg# + 7.9) and are likely cogenetic, but without filiation with the SM peridotites. Pb isotopes indicate a contribution of sediments in the source reservoir, which is attributed to contamination solely by hydrous fluids released from a sedimentary component. This observation, together with a LILE-enrichment, suggests a back-arc basin environment. These results indicate that BM and LVN units were obducted onto the North African margin and subsequently fragmented, probably during doming and exhumation of the lower continental crust of the Edough massif. Doming resulted in opposite movements of the overlying oceanic units, southward for the BM units and northward for LVN amphibolites

Deciphering the genetic control of quantitative traits with magic

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Discovery of metamorphic diamonds in garnets from the Edough massif (Northeastern Algeria): LA-ICP-MS U-Pb constraints

International audienceInclusions in a garnet megacryst (≥ 5 cm) from the Edough Massif (NE Algeria) have been studied and we report for the first time the discovery of diamond inclusions (5-30 micrometer in size), identified by Raman spectroscopy and the characteristic sharp band at 1332 cm-1 for crystalline diamond. The garnet is adjacent to actinolite and ultramafic boudins and slices of marbles that are inserted within a major mylonite-ultramyloniteband. This tectonic contact sharply delineates the Kef Lakhal oceanic unit from the granite-gneiss core below. This 1 km thick slab of amphibolites and pyrigarnites, derived from layered gabbros of MORB affinity, rest above the granite-gneiss units from the core complex. Garnet-forming reactions and dehydration melting are the oldest metamorphic stages recognized in the Kef Lakhal mafic complex (≥ 800 ◦C, ≥ 17 Kbar). The diamond-bearing garnets display a dense rutile acicular network interpreted as exsolutions. Zircons inclusions have been also observed in this garnet megacryst. Diamond crystals, up to 50 micrometer across, were identified first by optical microscopy and later by Raman spectroscopy. Major and trace elements show a gradual but significant zonation from core to rim, and a sharp increase in grossular component in the rim. Trace element analyses of prismatic rutile inclusions up to 300 micrometer in size indicate that the host metamorphic rock was a mafic protolith of MORB affinity. The Zr-in-rutile thermometry indicates a temperature range of 724-778 ◦C that we relate to rutile growth, either during prograde metamorphism or under peak UHP metamorphic conditions of ≥ 3.6 GPa that were reached during subduction of the UHP-rock precursors. In situ U-Pb dating obtained on rutile inclusions yield a 32.4+/ 3.3 Ma interpreted as the age of the UHP metamorphic event. LA-ICP-MS U-Pb ages on zircon provide a 20.9 +/- 2.2 Ma age attributed to the thrusting onto the North-African margin. We suggest that the mafic protolith of the analyzed garnet megacryst originates from the subducted retreating Tethyan slab, which broke or tore, and which fragments were dragged upward and thrust onto the North African margin along with the Kef Lakhal unit, shortly followed by building up of the Edough dome and opening of the Algerian basin

Metamorphic diamonds in a garnet megacryst from the Edough Massif (northeastern Algeria). Recognition and geodynamic consequences

International audienceWe report for the first time the discovery of diamond inclusions (5–30 μm in size), identified by Raman spectroscopy and the characteristic sharp band at 1332 cm− 1 for crystalline diamond, in a garnet megacryst (≥ 5 cm) from the Edough Massif (NE Algeria). The garnet is adjacent to actinolite and ultramafic boudins and slices of marbles that are inserted within a major mylonite–ultramylonite band. This tectonic contact sharply delineates the Kef Lakhal oceanic unit from the granite-gneiss core below. The host garnet is almandine-dominant and is rich in exsolution of acicular rutile needles. Major and trace elements show a gradual but significant zonation from core to rim, and a sharp increase in grossular component in the rim. Trace element analyses of prismatic rutile inclusions up to 300 μm in size indicate that the host metamorphic rock was a mafic protolith of MORB affinity. The Zr-in-rutile thermometry indicates a temperature range of 724–778 °C that we relate to rutile growth, either during prograde metamorphism or under peak UHP metamorphic conditions of ≥ 3.6 GPa that were reached during subduction of the UHP-rock precursors. We suggest that the mafic protolith originates from the subducted retreating Calabrian branch of the Tethyan slab, that broke or tore, and which fragments were dragged upward and thrust onto the North African margin along with the Kef Lakhal unit, shortly followed by formation of the Edough dome and opening of the Algerian basin

Permo-Carboniferous and early Miocene geological evolution of the internal zones of the Maghrebides - New insights on the western Mediterranean evolution

International audienceGeochemical and geochronological analyses were performed on metamorphic rocks from the footwall of an oceanic unit thrusted onto the North African margin. The footwall is mainly constituted by metamorphosed sediments and interlayered mafic rocks with scarce ultramafic lenses. Major and trace elements geochemistry of the sediments is consistent with a passive margin setting (16.9 < K2O/Na2O < 20.9; 18.2 < Zr/Th < 24.6). U–Pb analyses of detrital zircons indicate that deposition of the sedimentary sequence is younger than 307 ± 7 Ma (2σ) and concur with a provenance of the detritus from the Eastern Meseta and High Atlas of Morocco. The age of a crosscutting orthogneiss (281 ± 4 Ma) further constrains deposition to the upper Carboniferous/lower Permian times (307–281 Ma), in good agreement with the 295 ± 2 Ma age of an interbedded amphibolite. Geochemistry of the mafic and ultramafic rocks displays subduction related features (LILE and LREE enrichments, HFSE depletion). Pb, Sr, Nd and Hf isotopes further indicate a depleted mantle reservoir modified by a continental crust-derived component brought into the mantle during an ancient subduction event. The range of isotopic compositions and geochemical signatures displayed by the Carboniferous mafic rocks suggest they inherited their geochemical characteristics during melting of a heterogeneous lithospheric mantle containing variable metasomatic additions. Geochronological results indicate that the HT metamorphic evolution of this upper Paleozoic sequence resulted from two distinct events, each followed by fast cooling. The first one, dated at 20.85 ± 0.34 Ma (2σ), followed HP metamorphism and thrusting of the Kef Lakhal oceanic complex onto the Northern margin of Africa. The second event occurred at 17.65 ± 0.46 Ma (2σ) and is coeval with exhumation and anatexis of the lower crustal units of the neighbouring Edough dome. Fast cooling of the footwall rocks, through the closure temperatures of muscovite and biotite, occurred synchronously at 16.94 ± 0.10 Ma (2σ) and 17.02 ± 0.19 Ma (2σ) respectively. This study documents a further example of the complex history recorded by rocks of the Peri-Mediterranean area that contains an imbrication of geological units, witnesses of a protracted history related to Permo-Carboniferous and Miocene events

Age of UHP metamorphism in the Western Mediterranean: Insight from rutile and minute zircon inclusions in a diamond-bearing garnet megacryst (Edough Massif, NE Algeria)

International audienceDiamond-bearing UHP metamorphic rocks witness for subduction of lithospheric slabs into the mantle and their return to shallow levels. In this study we present U–Pb and trace elements analyses of zircon and rutile inclusions from a diamond-bearing garnet megacryst collected in a mélange unit exposed on the northern margin of Africa (Edough Massif, NE Algeria). Large rutile crystals (up to 300 μm in size) analyzed in situ provide a U–Pb age of interpreted as dating the prograde to peak subduction stage of the mafic protolith. Trace element analyses of minute zircons (≤30 μm) indicate that they formed in equilibrium with the garnet megacryst at a temperature of 740–810 °C, most likely during HP retrograde metamorphism. U–Pb analyses provide a significantly younger age of attributed to exhumation of the UHP units. This study allows bracketing the age of UHP metamorphism in the Western Mediterranean Orogen to the Oligocene/early Miocene, thus unambiguously relating UHP metamorphism to the Alpine history. Exhumation of these UHP units is coeval with the counterclockwise rotation of the Corsica–Sardinia block and most likely resulted from subduction rollback that was driven by slab pull

Vestiges of a fore-arc oceanic crust in the Western Mediterranean: Geochemical constraints from North-East Algeria

International audienceThe present day architecture of the Western Mediterranean mainly results from the interplay of different litho-spheric plates and the Cenozoic consumption of various branches of the Alpine Tethys and Neo-Tethys Oceans.Identifying relicsofthese oceanic domains inthe peri-Mediterranean belts enables pinpointing the earlieststagesof this evolutionary framework. In NE Algeria, the Kef Lakhal Complex (Edough Massif) is composed of amphib-olites and meta-gabbros metamorphosed under amphibolite facies conditions and thrust onto the northernAfrican margin during earliest Miocene. Geochemical analyses reveal that amphibolites and metagabbros havemajor and trace element signatures characteristic of tholeiitic basalts and gabbros and display N-MORB (La/SmN=0.7–0.9) toE-MORB (La/SmN=1.1–1.2) affinities. Enrichments in U and alkalis (Cs, Rb) and high87Sr/86Sriratios on bulk rocks and minerals (up to 0.70856) are typical of seawater alteration and indicate thatthe Kef Lakhal Complex represents a piece of altered oceanic crust. Parental magmas were derived from a De-pleted Mantle source (WRεNdi= 8.2–9.9 andεHfi= 10.4–14.4) that preserved some canonical MORB ratios(Ti/Eu = 5700–7600 and Y/Ho = 27.4–29.0), but which was contaminated by a component akin to recycled oce-anic crust and associated sediments (Ce/Pb = 10.5–22.2;206Pb/204Pbi=18.41–18.74;207Pb/204Pbi=15.49–15.59;208Pb/204Pbi=37.73–38.37). The sedimentary component is consistent with a volcaniclastic originand substantiatesanintra-oceanic setting.The geochemicalcharacteristics oftheKef Lakhalrocksare comparableto present day (Mariana, W Pacific Ocean) or fossil (Xigaze, SE Tibet) fore-arc oceanic crust. An overview of theWestern Mediterranean geodynamic indicates that the most likely period for initiating formation of a fore-arccorresponds either to the Early/Late Cretaceous or to the Middle Eocene.40Ar/39Ar dating on amphibole furtherindicate that after thrusting onto the African margin, the Kef Lakhal Complex cooled down toc.550 °C at18.14 ± 0.27 Ma (2σ)

Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era

Open Access.Identification of the polymorphisms controlling quantitative traits remains a challenge for plant geneticists. Multiparent advanced generation intercross (MAGIC) populations offer an alternative to traditional linkage or association mapping populations by increasing the precision of quantitative trait loci (QTL) mapping. Here, we present the first tomato MAGIC population and highlight its potential for the valorization of intraspecific variation, QTL mapping and causal polymorphism identification. The population was developed by crossing eight founder lines, selected to include a wide range of genetic diversity, whose genomes have been previously resequenced. We selected 1536 SNPs among the 4 million available to enhance haplotype prediction and recombination detection in the population. The linkage map obtained showed an 87% increase in recombination frequencies compared to biparental populations. The prediction of the haplotype origin was possible for 89% of the MAGIC line genomes, allowing QTL detection at the haplotype level. We grew the population in two greenhouse trials and detected QTLs for fruit weight. We mapped three stable QTLs and six specific of a location. Finally, we showed the potential of the MAGIC population when coupled with whole genome sequencing of founder lines to detect candidate SNPs underlying the QTLs. For a previously cloned QTL on chromosome 3, we used the predicted allelic effect of each founder and their genome sequences to select putative causal polymorphisms in the supporting interval. The number of candidate polymorphisms was reduced from 12 284 (in 800 genes) to 96 (in 54 genes), including the actual causal polymorphism. This population represents a new permanent resource for the tomato genetics community.This work was supported by the ANR MAGIC-Tom SNP project 09-GENM-109G. LP was supported by a postdoctoral INRA fellowship.Peer reviewe