High quality phased assembly of grape genome offer new opportunities in chimera detection

In perennial plants and especially those propagated through cuttings, several genotypes can coexist in a single individual, thus leading to chimeras. When the variant induces a noticeable phenotype modification, it can lead to a new cultivar. Viticulture already took economic advantage of this natural phenomenon: for instance, the berry skin of ‘Pinot gris’ derived from ‘Pinot noir’ by the selection of a chimera. Chimeras could also impact other crucial traits without being visually identified. Periclinal chimera where the variant has entirely colonized a cell layer is the most stable and can be propagated through cuttings. In grapevine, two functional cell layers are present in leaves, L1 and L2. However, lateral roots are formed from the L2 cell layer only. Thus, comparing DNA sequences of roots and leaves could allow chimera detection. In this study we used new generation Hifi long reads sequencing and recent bioinformatics tools applied to ‘Merlot’ to detect periclinal chimeras. Sequencing of ‘Magdeleine Noire des Charentes’ and ‘Cabernet franc’, the parents of ‘Merlot’, allowed haplotype resolved assembly. Pseudomolecules were built with few contigs, in some occasions only one per chromosome. This high resolution allowed haplotype comparison. Annotation from PN40024 was transferred to all pseudomolecules. Through variant detection, periclinal chimeras were found on both haplotypes. These results open new perspectives on chimera detection, which is an important resource to improve cultivars through clonal selection or breed new ones. Detailed results will be presented and discussed

Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp. sativa

Background: The first high quality draft of the grape genome sequence has just been published. This is a critical step in accessing all the genes of this species and increases the chances of exploiting the natural genetic diversity through association genetics. However, our basic knowledge of the extent of allelic variation within the species is still not sufficient. Towards this goal, we constructed nested genetic core collections (G-cores) to capture the simple sequence repeat (SSR) diversity of the grape cultivated compartment (Vitis vinifera L. subsp. sativa) from the world's largest germplasm collection (Domaine de Vassal, INRA Hérault, France), containing 2262 unique genotypes. Results: Sub-samples of 12, 24, 48 and 92 varieties of V. vinifera L. were selected based on their genotypes for 20 SSR markers using the M-strategy. They represent respectively 58%, 73%, 83% and 100% of total SSR diversity. The capture of allelic diversity was analyzed by sequencing three genes scattered throughout the genome on 233 individuals: 41 single nucleotide polymorphisms (SNPs) were identified using the G-92 core (one SNP for every 49 nucleotides) while only 25 were observed using a larger sample of 141 individuals selected on the basis of 50 morphological traits, thus demonstrating the reliability of the approach. Conclusion: The G-12 and G-24 core-collections displayed respectively 78% and 88% of the SNPs respectively, and are therefore of great interest for SNP discovery studies. Furthermore, the nested genetic core collections satisfactorily reflected the geographic and the genetic diversity of grape, which are also of great interest for the study of gene evolution in this species

Dissecting genetic architecture of grape proanthocyanidin composition through quantitative trait locus mapping

<p>Abstract</p> <p>Background</p> <p>Proanthocyanidins (PAs), or condensed tannins, are flavonoid polymers, widespread throughout the plant kingdom, which provide protection against herbivores while conferring organoleptic and nutritive values to plant-derived foods, such as wine. However, the genetic basis of qualitative and quantitative PA composition variation is still poorly understood. To elucidate the genetic architecture of the complex grape PA composition, we first carried out quantitative trait locus (QTL) analysis on a 191-individual pseudo-F1 progeny. Three categories of PA variables were assessed: total content, percentages of constitutive subunits and composite ratio variables. For nine functional candidate genes, among which eight co-located with QTLs, we performed association analyses using a diversity panel of 141 grapevine cultivars in order to identify causal SNPs.</p> <p>Results</p> <p>Multiple QTL analysis revealed a total of 103 and 43 QTLs, respectively for seed and skin PA variables. Loci were mainly of additive effect while some loci were primarily of dominant effect. Results also showed a large involvement of pairwise epistatic interactions in shaping PA composition. QTLs for PA variables in skin and seeds differed in number, position, involvement of epistatic interaction and allelic effect, thus revealing different genetic determinisms for grape PA composition in seeds and skin. Association results were consistent with QTL analyses in most cases: four out of nine tested candidate genes (<it>VvLAR1</it>, <it>VvMYBPA2</it>, <it>VvCHI1</it>, <it>VvMYBPA1</it>) showed at least one significant association with PA variables, especially <it>VvLAR1 </it>revealed as of great interest for further functional investigation. Some SNP-phenotype associations were observed only in the diversity panel.</p> <p>Conclusions</p> <p>This study presents the first QTL analysis on grape berry PA composition with a comparison between skin and seeds, together with an association study. Our results suggest a complex genetic control for PA traits and different genetic architectures for grape PA composition between berry skin and seeds. This work also uncovers novel genomic regions for further investigation in order to increase our knowledge of the genetic basis of PA composition.</p

Critical Exponents of the N-vector model

Recently the series for two RG functions (corresponding to the anomalous dimensions of the fields phi and phi^2) of the 3D phi^4 field theory have been extended to next order (seven loops) by Murray and Nickel. We examine here the influence of these additional terms on the estimates of critical exponents of the N-vector model, using some new ideas in the context of the Borel summation techniques. The estimates have slightly changed, but remain within errors of the previous evaluation. Exponents like eta (related to the field anomalous dimension), which were poorly determined in the previous evaluation of Le Guillou--Zinn-Justin, have seen their apparent errors significantly decrease. More importantly, perhaps, summation errors are better determined. The change in exponents affects the recently determined ratios of amplitudes and we report the corresponding new values. Finally, because an error has been discovered in the last order of the published epsilon=4-d expansions (order epsilon^5), we have also reanalyzed the determination of exponents from the epsilon-expansion. The conclusion is that the general agreement between epsilon-expansion and 3D series has improved with respect to Le Guillou--Zinn-Justin.Comment: TeX Files, 27 pages +2 figures; Some values are changed; references update

Two-loop self-dual Euler-Heisenberg Lagrangians (II): Imaginary part and Borel analysis

We analyze the structure of the imaginary part of the two-loop Euler-Heisenberg QED effective Lagrangian for a constant self-dual background. The novel feature of the two-loop result, compared to one-loop, is that the prefactor of each exponential (instanton) term in the imaginary part has itself an asymptotic expansion. We also perform a high-precision test of Borel summation techniques applied to the weak-field expansion, and find that the Borel dispersion relations reproduce the full prefactor of the leading imaginary contribution.Comment: 28 pp, 6 eps figure

Patterns of sequence polymorphism in the fleshless berry locus in cultivated and wild Vitis vinifera accessions

<p>Abstract</p> <p>Background</p> <p>Unlike in tomato, little is known about the genetic and molecular control of fleshy fruit development of perennial fruit trees like grapevine (<it>Vitis vinifera </it>L.). Here we present the study of the sequence polymorphism in a 1 Mb grapevine genome region at the top of chromosome 18 carrying the <it>fleshless berry </it>mutation (<it>flb</it>) in order, first to identify SNP markers closely linked to the gene and second to search for possible signatures of domestication.</p> <p>Results</p> <p>In total, 62 regions (17 SSR, 3 SNP, 1 CAPS and 41 re-sequenced gene fragments) were scanned for polymorphism along a 3.4 Mb interval (85,127-3,506,060 bp) at the top of the chromosome 18, in both <it>V. vinifera cv</it>. Chardonnay and a genotype carrying the <it>flb </it>mutation, <it>V. vinifera cv</it>. Ugni Blanc mutant. A nearly complete homozygosity in Ugni Blanc (wild and mutant forms) and an expected high level of heterozygosity in Chardonnay were revealed. Experiments using qPCR and BAC FISH confirmed the observed homozygosity. Under the assumption that <it>flb </it>could be one of the genes involved into the domestication syndrome of grapevine, we sequenced 69 gene fragments, spread over the <it>flb </it>region, representing 48,874 bp in a highly diverse set of cultivated and wild <it>V. vinifera </it>genotypes, to identify possible signatures of domestication in the cultivated <it>V. vinifera </it>compartment. We identified eight gene fragments presenting a significant deviation from neutrality of the Tajima's D parameter in the cultivated pool. One of these also showed higher nucleotide diversity in the wild compartments than in the cultivated compartments. In addition, SNPs significantly associated to berry weight variation were identified in the <it>flb </it>region.</p> <p>Conclusions</p> <p>We observed the occurrence of a large homozygous region in a non-repetitive region of the grapevine otherwise highly-heterozygous genome and propose a hypothesis for its formation. We demonstrated the feasibility to apply BAC FISH on the very small grapevine chromosomes and provided a specific probe for the identification of chromosome 18 on a cytogenetic map. We evidenced genes showing putative signatures of selection and SNPs significantly associated with berry weight variation in the <it>flb </it>region. In addition, we provided to the community 554 SNPs at the top of chromosome 18 for the development of a genotyping chip for future fine mapping of the <it>flb </it>gene in a F2 population when available.</p

Origins and rationele of centres for parents and young children together

The range of centres where parents and children come together has mushroomed in different parts of the world, as new social work practices address the emerging non-material needs of parents in changing demographic contexts. In this paper, we explore the origins and modi operandi of these centres in Belgium, France, Italy and Japan. Analysis of previous studies and policy documents reveal diverse political rationales, including addressing declining birth rates, preventing psychosocial problems and social isolation of mothers and promoting social cohesion and equality of educational opportunities. Remarkably, despite the diverse cultural and socio-political contexts and rationales, these centres also share very similar ways of functioning and provide an informal type of social support to parents with young children. As these recently emerged centres are seldom studied, further research is welcomed to explore parents' and professionals' perspectives

Genetic variability of berry size in grapevine (Vitis vinifera L.)

Background and Aims: Berry weight in the grapevine, as in the tomato, is variable, ranging from less than 1 g to10 g. In the tomato, berry weight depends on cell number and volume but also on carpel number. The aim of this work was to decipher the range of variation and to propose a role for subtraits possibly underlying berry size variation in a highly diverse collection of cultivated grapevines.Methods and Results: Cell division before and after anthesis and cell expansion after anthesis appeared to be the major determinants of flesh weight variation between cultivars. Carpel number varied between cultivars, with two and three carpels per ovary. This trait, however, and also the seed weight did not clearly contribute to berry size variation, although a positive correlation was found between seed weight and number and berry weight at the intragenotypic level, in agreement with previous results.Conclusions: This work deciphered the main anatomical factors underlying variation in berry size in Vitis vinifera;they involved both common fleshy fruits factors but also specific vine factors.Significance of the Study: Further studies of the variation in berry size of the the grape will be assisted by the anatomical factors identified in this study