Objectives Persian walnut (Juglans regia L.), the walnut species cultivated for nut production, is grown worldwide in temperate areas. In this work, chronological phenotypic data have been collected regarding a part of the walnut genetic... more
Objectives Persian walnut (Juglans regia L.), the walnut species cultivated for nut production, is grown worldwide in temperate areas. In this work, chronological phenotypic data have been collected regarding a part of the walnut genetic resources of the French National Institute for Agricultural Research (INRA) of Bordeaux. Using a well described ontology, these data have been collected in order to assess the phenotypic variations among the accessions, and to better manage the germplasm collection. These data can also be helpful for any breeding program as they provide a clear phenotypic characterization of the main cultivars. Data description This paper introduces a dataset collected for 150 J. regia accessions for a period from 1965 to 2016, and for 3 observation sites, released as comma separated value spreadsheet. It includes observations about phenological traits (e.g. flowering dates), traits related to in-shell walnut (e.g. weight and size), and traits related to kernel (e.g...
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Il y a 450 millions d’années, des algues vertes conquirent les terres émergées : elles allaient devenir les plantes que nous connaissons. Cette conquête des continents, n’a probablement été rendue possible que par le développement d’une... more
Il y a 450 millions d’années, des algues vertes conquirent les terres émergées : elles allaient devenir les plantes que nous connaissons. Cette conquête des continents, n’a probablement été rendue possible que par le développement d’une association bénéfique entre les racines des plantes et des champignons. Cette association ancestrale, appelée la mycorhize à arbuscules, est la plus ancienne symbiose mutualiste entre plantes et microorganismes.Cette monographie synthétise les connaissances sur la mycorhize à arbuscules et les services rendus dans les agroécosystèmes, leurs impacts sur les interactions plus larges entre organismes (interactions plante-plante et interactions multi-trophiques plantes-champignons mycorhiziens-bactéries), les liens entre itinéraires de culture et mycorhization. Enfin, elle comporte un focus sur le projet « Mycoagra » qui aborde ces aspects sur le noyer
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International audienc
Additional file 2. Video of 3D reconstruction and individualization steps of a walnut.
Recently-introduced inter-specific Musa hybrids, bred for improved yield and resistance to diseases, have been found to be widely infected with banana streak virus (BSV), the causal agent of banana streak disease (BSD). One hypothesis... more
Recently-introduced inter-specific Musa hybrids, bred for improved yield and resistance to diseases, have been found to be widely infected with banana streak virus (BSV), the causal agent of banana streak disease (BSD). One hypothesis suggests: (1) that BSD occurrence in these inter-specific hybrids results from activation of BSV-Ol endogenous pararetrovirus sequences (EPRV) integrated into the Musa genome rather than from external sources of infection, and (2) that the process of genetic hybridisation may be one factor involved in triggering episomal expression of the BSV integrants. In order to test this hypothesis we carried out a genetic analysis of BSD incidence in a F1 triploid ( Musa AAB) population produced by inter-specific hybridisation between virus and disease-free diploid Musa balbisiana (BB) and tetraploid Musa acuminata (AAAA) parents. Half of the F1 progeny of this cross expressed BSV particles. Using PCR amplification to determine the presence or absence of BSV-Ol E...
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Additional file 1. List of the 161 accessions studied.
Additional file 3. Complete dataset.
Additional file 15: Figure S8. Level plot showing the Identical-By-State (IBS) values for the 170 accessions of the GWAS panel.
Additional file 14: Figure S7. Scatter plot showing the estimated kinship coefficients by the proportion of zero Identical-By-State (IBS0) in the F1 progeny.
Additional file 13: Figure S6. Principal Component Analysis performed on the GWAS panel. The two first principal components show accessions colored according to fastSTRUCTURE results with EEAs for Eastern Europe and Asia, and WEAm for... more
Additional file 13: Figure S6. Principal Component Analysis performed on the GWAS panel. The two first principal components show accessions colored according to fastSTRUCTURE results with EEAs for Eastern Europe and Asia, and WEAm for Western Europe and America.
Additional file 12: Figure S5. Detection of the number of clusters using a) Prob(K), and b) deltaK method (Evanno et al., 2005) in the GWAS panel.
Additional file 11: Figure S4. Density plots showing the two-year data related to phenological traits in Julian days for the 78 accessions of the F1 progeny.
Additional file 10: Figure S3. Scatter plots showing the two-year data related to phenological traits in Julian days for the 78 accessions of the F1 progeny.
Additional file 8: Figure S1. Scatter plots showing the two-year data related to phenological traits in Julian days for the 170 accessions of the GWAS panel.
Additional file 9: Figure S2. Density plots showing the two-year data related to phenological traits in Julian days for the 170 accessions of the GWAS panel.
Additional file 7: Table S7. Phenotypic raw dataset of the F1 progeny.
Additional file 6: Table S6. Phenotypic raw dataset of the GWAS panel.
Additional file 5: Table S5. Walnut trait ontology.
Additional file 3: Table S3. 'Franquette' and 'UK 6–2' parental maps for QTL detection.
Additional file 1: Table S1. List of association panel accessions with their origin, breeding level, pedigree when known, and their membership to clusters based on fastSTRUCTURE results for K = 3.
Additional file 4: Table S4. Genotyping results of SNP AX-171179714 by KASP.
Additional file 2: Table S2. Number of principal components required for bearing habit trait using Bayesian Information Criterion.
Additional file 16: Figure S9. Genetic maps and QTLs detected using two-year data. F(X) and U(X) are the linkage groups of 'Franquette' and 'UK 6–2' parental maps respectively. Legend of the QTLs: black for budbreak date,... more
Additional file 16: Figure S9. Genetic maps and QTLs detected using two-year data. F(X) and U(X) are the linkage groups of 'Franquette' and 'UK 6–2' parental maps respectively. Legend of the QTLs: black for budbreak date, red for beginning female flowering date, deep green for full female flowering date, blue for end female flowering date, yellow for beginning male flowering date, pink for full female flowering date, and light green for end female flowering date. Solid bars indicate the 95% confidence interval of the QTL, and terminal bars indicate the 99.9% confidence interval of the QTL. The marker names were changed with the corresponding chromosome number and its physical position for a better visualization.
Recently introduced inter-specific #Musa# hybrids, bred for improved yield and resistance to diseases, have been found to be widely infected with several Banana streak badnavirus (BSV-Obino I'Ewai (BSV-OI), BSV-Imove (BSV-Im) and... more
Recently introduced inter-specific #Musa# hybrids, bred for improved yield and resistance to diseases, have been found to be widely infected with several Banana streak badnavirus (BSV-Obino I'Ewai (BSV-OI), BSV-Imove (BSV-Im) and BSV-GoId Finger (BSV-Gf) strains), the causal agent of banana streak disease (BSD). One hypothesis suggests that BSD occurrence in these inter-specific hybrids results from activation of corresponding BSV endogenous pararetrovirus sequences (EPRVs) integrated into the Musa genome rather than from external sources of infection. The process of genetic hybridisation and abiotic stress such as micropropagation by #in vitro# culture may be responsible in triggering episomal expression of these BSV integrants. In order to test the first hypothesis we carried out a genetic analysis of banana streak disease incidence in a F1 triploid (AAB) population produced by hybridisation between virus- and disease-free #M. balbisiana# Pisang Klutug Wulung PKW (BB diploid) ...
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Inter-specific #Musa# hybrids have been found to be infected with several Banana streak pararetrovirus strains (BSV-Obino l'Ewai (BSV-Ol), BSV-Imove (BSV-Im) and BSV-Gold Finger (BSV-GF) strains) resulting from activation of BSV... more
Inter-specific #Musa# hybrids have been found to be infected with several Banana streak pararetrovirus strains (BSV-Obino l'Ewai (BSV-Ol), BSV-Imove (BSV-Im) and BSV-Gold Finger (BSV-GF) strains) resulting from activation of BSV endogenous pararetrovirus sequences (EPRVs) integrated into the #Musa# genome rather than from external sources of infection. The process of genetic hybridisation may be responsible in triggering episomal expression of the BSV integrants. In order to test this hypothesis we carried out a genetic analysis of BSD incidence in a F1 triploid (AAB) population produced by hybridisation between virus- and disease-free #M. balbisiana# (BB) and #M. acuminata# (AAAA) parents. Molecular AFLP markers were identified in the #M. balbisiana# genome only. Analysis of the segregation of these markers allowed the construction of a genetic map containing the locus associated with BSV infection called BSV Express locus (BEL). The BSV-Ol and BSV-Im strains appeared in almost...
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The preservation of maximum diversity within the smallest number of accessions is one of the challenges of germplasm management, and the assessment of the population structure, the relationships between the accessions, and the... more
The preservation of maximum diversity within the smallest number of accessions is one of the challenges of germplasm management, and the assessment of the population structure, the relationships between the accessions, and the construction of core collections are the key steps. The choice of suitable molecular markers is often the starting point. In this study, we analyzed a part of the INRAE walnut germplasm collection, which is highly diverse and unique in Europe, consisting of 150 accessions from American, European, and Asian continents. Based on genotypic data already available, using 13 SSRs or 364,275 SNPs, we showed that the first level of structure is detected equally. We also highlighted empirically that approximately 100 SNPs are needed to obtain similar clustering to 13 SSRs in Principal Coordinate Analysis (PCoA). We constructed eight core collections following two strategies (percentage of total allelic diversity or number of accessions) and two construction methods bas...
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Banana streak virus (BSV) sequences are integrated in the nuclear genome of Musa species. Some of these BSV endogenous pararetrovirus (BSV EPRVs), restricted to Musa balbisiana chromosome (noted B), can give rise to infectious episomal... more
Banana streak virus (BSV) sequences are integrated in the nuclear genome of Musa species. Some of these BSV endogenous pararetrovirus (BSV EPRVs), restricted to Musa balbisiana chromosome (noted B), can give rise to infectious episomal BSV particles upon stress conditions such as inter-specific genetic crosses. A genetic analysis of BSV incidence in a F1 triploid (Musa AAB) population produced by inter-specific hybridisation between virus-free diploid M. balbisiana (BB) and tetraploid M. acuminata (AAAA) parents showed that half of the F1 progeny expressed BSV particles. A PCR-based analysis determined that BSV EPRVs were restricted to the M. balbisiana genome only. A bulk AFLP segregant analysis revealed seven AFLP markers co-segregating with the presence of BSV infection and three with the absence of BSV infection. All of them were restricted to the M. balbisiana genome. Analysis of the segregation of these markers using a test-cross configuration allowed the construction of a gen...
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The preservation of maximum diversity within the smallest number of accessions is one of the challenges of germplasm management, and the assessment of the population structure, the relationships between the accessions, and the... more
The preservation of maximum diversity within the smallest number of accessions is one of the challenges of germplasm management, and the assessment of the population structure, the relationships between the accessions, and the construction of core collections are the key steps. The choice of suitable molecular markers is often the starting point. In this study, we analyzed a part of the INRAE walnut germplasm collection, which is highly diverse and unique in Europe, consisting of 150 accessions from American, European, and Asian continents. Based on genotypic data already available, using 13 SSRs or 364,275 SNPs, we showed that the first level of structure is detected equally. We also highlighted empirically that approximately 100 SNPs are needed to obtain similar clustering to 13 SSRs in Principal Coordinate Analysis (PCoA). We constructed eight core collections following two strategies (percentage of total allelic diversity or number of accessions) and two construction methods bas...
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Ces dernieres annees des hybrides interspecifiques bananiers ont developpe la maladie de la mosaique en tirets, sans possibilite de contamination externe par le Banana streak badnavirus-BSV responsable. L'explication proposee fait... more
Ces dernieres annees des hybrides interspecifiques bananiers ont developpe la maladie de la mosaique en tirets, sans possibilite de contamination externe par le Banana streak badnavirus-BSV responsable. L'explication proposee fait l'hypothese que les virions observes proviennent de sequences virales endogenes - EPRVs BSV, presentes dans le genome bananier. L'objectif de notre etude a ete de tenter de trouver une explication a l'expression de la maladie au cours de l'hybridation conventionnelle pour deux croisements #Musa# interspecifiques - PKW (BB) x IDN 110 4x (AAAA) et P. batu (BB) x P. pipit 4x (AAAA). Nous avons tout d'abord montre l'existence d'une segregation a caractere mendelien de la maladie sur les descendances F1 et revele la presence du BSV dans 50% des plants. L'etude de l'EPRV BSV souche Obino l'Ewai (BSV-O1) a montre sa presence a l'etat homozygote dans le genome #M. balbisiana# uniquement. Une carte genetique du locus ...
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Des fragments de genome de pararetrovirus ont ete observes, integres au genome de leur plante hote. Rien n'est actuellement connu sur l'origine de ces fragments; les pararetrovirus n'ont besoin a aucune etape de leur... more
Des fragments de genome de pararetrovirus ont ete observes, integres au genome de leur plante hote. Rien n'est actuellement connu sur l'origine de ces fragments; les pararetrovirus n'ont besoin a aucune etape de leur multiplication d'integrer le genome hote. La totalite du genome du virus de la mosaique du bananier -Banana streak badnavirus- est presente par fragments dans les chromosomes d'une des deux especes de bananier utilisees pour la creation d'hybrides interspecifiques: #Musa balbisiana#. Ces fragments endogenes sont suspectes sous l'action de stress comme la culture #in vitro# ou les croisements genetiques d'etre a l'origine de particules virales pathogenes. Nos travaux conduits sur l'expression du BSV au cours de la CIV ont montre l'effet determinant de l'etape "proliferation" sur l'apparition des particules virales a partir d'un hybride interspecifique sain possedant les sequences virales endogenes. Ceux co...
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Recently, it was demonstrated that Banana streak virus (BSV) sequences are integrated into the nuclear genome of #Musa balbisiana#. There is strong experimental evidence that some of these BSV integrated sequences, called BSV endogenous... more
Recently, it was demonstrated that Banana streak virus (BSV) sequences are integrated into the nuclear genome of #Musa balbisiana#. There is strong experimental evidence that some of these BSV integrated sequences, called BSV endogenous pararetroviruses (BSV EPRVs), can give rise to infectious episomal BSV genomes upon stress conditions. Such stress include interspecific genetic crosses, therefore this phenomenon represents a serious limitation to the creation of novel #Musa# hydrids between A and B genomes and to the diffusion of such hybrids. As part of an international effort within the #Musa# Genomics Consortium aimed at defining the integration patterns of BSV EPRV sequences into the nuclear genome of #Musa# species and the mechanisms leading to the activation of such BSV EPRV sequences, we have constructed and characterised three BAC libraries from #M. acuminata# 'Cavendish' (AAA), #M. acuminata# 'Calcutta 4' (AA) and #M. balbisiana# PKW (BB) nuclear genomes, r...
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As several other plants, the genome of banana and plantain contains integrations of Banana streak virus (BSV) sequences even though integration is not an essential step in the replication cycle of this virus. In banana two types of BSV... more
As several other plants, the genome of banana and plantain contains integrations of Banana streak virus (BSV) sequences even though integration is not an essential step in the replication cycle of this virus. In banana two types of BSV integrants exist. Ones are non functional sequences present in both common Musa species, Musa acuminata (denoted A) and Musa balbisiana (denoted B) and it is now assumed that the integrants of the other type, containing the complete viral genome and restricted to M. balbisiana genome, become infectious by reconstituting a complete replication-competent viral genome. Thereby, an increasing record of BSV outbreaks was observed fifteen years ago among banana breeding lines and micro propagated inter-specific Musa hybrids, worldwide. Today, three widespread BSV species, Banana streak Obino l'Ewai virus (BSOIV), Banana streak Imove virus (BSImV) and Banana streak Golfinger virus (BSGfV) are known to occur as infectious integrants in the M. balbisiana g...
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Banana streak virus (BSV) sequences are integrated in the nuclear genome of Musa species. There is strong experimental evidence that some of these BSV integrated sequences, preferentially restricted to Musa balbisiana chromosome (noted B)... more
Banana streak virus (BSV) sequences are integrated in the nuclear genome of Musa species. There is strong experimental evidence that some of these BSV integrated sequences, preferentially restricted to Musa balbisiana chromosome (noted B) and called BSV endogenous pararetrovirus (BSV EPRVs), can give rise to infectious episomal BSV particles upon stress conditions such as either inter-specific genetic crosses or in vitro micro propagation. As part of an international effort within the Musa Genomics Consortium aimed at defining the integration patterns of BSV EPRVs into Musa nuclear genome and the mechanisms leading to their activation, three BAC libraries were constructed and characterized from M. acuminata Cavendish (AAA), M. acuminata Calcutta 4 (AA) and M. balbisiana PKW (BB) nuclear genomes, respectively. Complete genomes of four BSV strains (BSV-Ol "Obino L'Ewai", BSV-Gf "Gold Finger", BSV-lm "Imove", BSV-Mys "Mysore") were used as pr...