Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae)

<p>Abstract</p> <p>Background</p> <p>The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, <it>i.e</it>. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (<it>Cichorium intybus </it>L.) constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae.</p> <p>Findings</p> <p>Two bacterial artificial chromosome (BAC) libraries, CinS2S2 and CinS1S4, were constructed from <it>Hin</it>dIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and <it>S</it>₂<it>S</it>₂for the <it>S</it>-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and <it>S</it>₁<it>S</it>₄. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers.</p> <p>Conclusions</p> <p>This indicated that both BAC libraries are valuable tools for molecular studies in chicory, one goal being the positional cloning of the <it>S</it>-locus in this Asteraceae species.</p

Study of the self-incompatibility in chicory (Cichorium intybus L., Asteraceae) : genetic and physical mapping of the locus S

L'autoincompatibilité (AI), généralement sous le contrôle d’un seul locus, le locus S, est la stratégie la plus répandue pour empêcher l'autofécondation chez les plantes hermaphrodites. Les déterminants de la réaction d’AI ont été identifiés dans quelques familles d’Angiospermes. Dans celle des Asteraceae, ces déterminants sont encore inconnus. La chicorée (Cichorium intybus L., Asteraceae) présente un système d’AI sporophytique. Afin d’identifier les déterminants de l’AI de cette espèce, une stratégie de clonage positionnel du locus S a été mise en place.Le locus S de la chicorée avait été cartographié à l'extrémité du groupe de liaison 2. Une carte haute densité a été obtenue à partir d’une approche BSA assistée par marqueurs : 5 marqueurs AFLP ont été identifiés, dont un coségrégeant avec le locus S. A partir d’une importante population (n = 2824), 2 cartes consensus haute résolution de la région du locus S ont été établies, l’une pour les méioses femelles (intervalle de 0,6 cM) et l’autre pour les méioses mâles (intervalle de 1,24 cM), en raison d’un phénomène d’hétérochiasmie.Deux banques BAC de chicorée ont été construites en collaboration avec le CNRGV. Elles ont permis d’initier et d’orienter la marche chromosomique vers le locus S. De plus, 6 clones BAC, soit 546 kb, ont été séquencés et analysés. Un rapport de 0,45 (méiose femelle) à 2 cM/Mb (méiose mâle) a été obtenu. La composition des séquences en éléments répétés et la fraction codante ont été étudiées (banques d’EST de Cichorium sp. et de peptides d’A.thaliana et de V.vinifera). Une relative conservation de la microsynténie a été observée entre ces gènes et leurs homologues chez 5 espèces Dicotylédones.Generally under the control of one locus, the S-locus, self-incompatibility (SI) is one of the most important strategies to prevent selfing in hermaphrodite plants. Determinants involved in the SI reaction have been identified in some Angiosperm families. In the Asteraceae family, determinants of SI are still unknown. Chicory (Cichorium intybus L., Asteraceae) is a sporophytic SI species. To identify determinants of chicory SI, a positional cloning strategy has been implemented.The chicory S-locus has been assigned to one end of linkage group 2. A high density map have been obtained from a marker assisted BSA (Bulk Segregant Analysis) approach: 5 AFLP markers were obtained, including one co-segregating with the S-locus. From a large population (n = 2.824), 2 consensus high-resolution map of the S-locus region were produced. Due to a heterochiasmy phenomenon, the S-locus was positioned in an interval of 0,6 cM or 1,24 cM considering female or male meiosis, respectively.Two BAC libraries of chicory were produced in collaboration with the CNRGV. They allowed us to start chromosome walking and to turn it toward the S-locus. Moreover, 6 BAC clones, corresponding to 546 kb, were sequenced and analyzed. A ratio of 0,5 Mb/cM for male meiosis and 2,2~Mb/cM for female meiosis were obtained. Repeated element composition and coding part of the sequences were studied (libraries of Cichorium sp. EST and Arabidopsis thaliana and Vitis vinifera peptides). A certain degree of conservation of microsynteny was observed between these genes and their homologues in five Dicotyledon species

Étude de l'autoincompatibilité chez la chicorée (Cichorium intybus L., Asteraceae) (cartographie génétique et physique du locus S)

L'autoincompatibilité (AI), généralement sous le contrôle d un seul locus, le locus S, est la stratégie la plus répandue pour empêcher l'autofécondation chez les plantes hermaphrodites. Les déterminants de la réaction d AI ont été identifiés dans quelques familles d Angiospermes. Dans celle des Asteraceae, ces déterminants sont encore inconnus. La chicorée (Cichorium intybus L., Asteraceae) présente un système d AI sporophytique. Afin d identifier les déterminants de l AI de cette espèce, une stratégie de clonage positionnel du locus S a été mise en place.Le locus S de la chicorée avait été cartographié à l'extrémité du groupe de liaison 2. Une carte haute densité a été obtenue à partir d une approche BSA assistée par marqueurs : 5 marqueurs AFLP ont été identifiés, dont un coségrégeant avec le locus S. A partir d une importante population (n = 2824), 2 cartes consensus haute résolution de la région du locus S ont été établies, l une pour les méioses femelles (intervalle de 0,6 cM) et l autre pour les méioses mâles (intervalle de 1,24 cM), en raison d un phénomène d hétérochiasmie.Deux banques BAC de chicorée ont été construites en collaboration avec le CNRGV. Elles ont permis d initier et d orienter la marche chromosomique vers le locus S. De plus, 6 clones BAC, soit 546 kb, ont été séquencés et analysés. Un rapport de 0,45 (méiose femelle) à 2 cM/Mb (méiose mâle) a été obtenu. La composition des séquences en éléments répétés et la fraction codante ont été étudiées (banques d EST de Cichorium sp. et de peptides d A.thaliana et de V.vinifera). Une relative conservation de la microsynténie a été observée entre ces gènes et leurs homologues chez 5 espèces Dicotylédones.Generally under the control of one locus, the S-locus, self-incompatibility (SI) is one of the most important strategies to prevent selfing in hermaphrodite plants. Determinants involved in the SI reaction have been identified in some Angiosperm families. In the Asteraceae family, determinants of SI are still unknown. Chicory (Cichorium intybus L., Asteraceae) is a sporophytic SI species. To identify determinants of chicory SI, a positional cloning strategy has been implemented.The chicory S-locus has been assigned to one end of linkage group 2. A high density map have been obtained from a marker assisted BSA (Bulk Segregant Analysis) approach: 5 AFLP markers were obtained, including one co-segregating with the S-locus. From a large population (n = 2.824), 2 consensus high-resolution map of the S-locus region were produced. Due to a heterochiasmy phenomenon, the S-locus was positioned in an interval of 0,6 cM or 1,24 cM considering female or male meiosis, respectively.Two BAC libraries of chicory were produced in collaboration with the CNRGV. They allowed us to start chromosome walking and to turn it toward the S-locus. Moreover, 6 BAC clones, corresponding to 546 kb, were sequenced and analyzed. A ratio of 0,5 Mb/cM for male meiosis and 2,2~Mb/cM for female meiosis were obtained. Repeated element composition and coding part of the sequences were studied (libraries of Cichorium sp. EST and Arabidopsis thaliana and Vitis vinifera peptides). A certain degree of conservation of microsynteny was observed between these genes and their homologues in five Dicotyledon species.LILLE1-Bib. Electronique (590099901) / SudocSudocFranceF

The Sheltered Genetic Load Linked to the S Locus in Plants: New Insights From Theoretical and Empirical Approaches in Sporophytic Self-Incompatibility

Inbreeding depression and mating systems evolution are closely linked, because the purging of deleterious mutations and the fitness of individuals may depend on outcrossing vs. selfing rates. Further, the accumulation of deleterious mutations may vary among genomic regions, especially for genes closely linked to loci under balancing selection. Sporophytic self-incompatibility (SSI) is a common genetic mechanism in angiosperm that enables hermaphrodite plants to avoid selfing and promote outcrossing. The SSI phenotype is determined by the S locus and may depend on dominance relationships among alleles. Since most individuals are heterozygous at the S locus and recombination is suppressed in the S-locus region, it has been suggested that deleterious mutations could accumulate at genes linked to the S locus, generating a “sheltered load.” In this article, we first theoretically investigate the conditions generating sheltered load in SSI. We show that deleterious mutations can accumulate in linkage with specific S alleles, and particularly if those S alleles are dominant. Second, we looked for the presence of sheltered load in Arabidopsis halleri using CO2 gas treatment to overcome self-incompatibility. By examining the segregation of S alleles and measuring the relative fitness of progeny, we found significant sheltered load associated with the most dominant S allele (S15) of three S alleles tested. This sheltered load seems to be expressed at several stages of the life cycle and to have a larger effect than genomic inbreeding depression

Global Soil Biodiversity Atlas

SPE EA Pôle BIOME The Atlas is divided in 8 chapters covering all the aspects of soil biodiversity: - Chapter I: The soil habitat - Chapter II: Diversity of soil organisms - Chapter III: Geographical and temporal distribution - Chapter IV: Ecosystem functions and services - Chapter V: Threats - Chapter VI: Interventions - Chapter VII: Policy, education and outreach - Chapter VIII: Conclusions Soil biodiversity experts from all over the world are involved in the project aiming at the creation of a reference publication not only for soil biodiversity researchers but also policy makers and general public.International audienceThe Global Soil Biodiversity Initiative (GSBI) and the Joint Research Centre (JRC) of European Commission announce the writing of the Global Soil Biodiversity Atlas (GSBA) in the frame of the Global Soil Biodiversity Assessment. The Atlas is a series of amazing photos, maps, charts, statistics, and shared information that scientists, educators, policy makers, and non-specialists alike can use as a toolkit for knowing and understanding soil biodiversity globally