Chimeras in Merlot grapevine revealed by phased assembly.

Chimerism is the phenomenon when several genotypes coexist in a single individual. Used to understand plant ontogenesis they also have been valorised through new cultivar breeding. Viticulture has been taking economic advantage out of chimeras when the variant induced an important modification of wine type such as berry skin colour. Crucial agronomic characters may also be impacted by chimeras that aren't identified yet. Periclinal chimera where the variant has entirely colonised a cell layer is the most stable and can be propagated through cuttings. In grapevine, leaves are derived from both meristem layers, L1 and L2. However, lateral roots are formed from the L2 cell layer only. Thus, comparing DNA sequences of roots and leaves allows chimera detection. In this study we used new generation Hifi long reads sequencing, recent bioinformatics tools and trio-binning with parental sequences to detect periclinal chimeras on 'Merlot' grapevine cultivar. Sequencing of cv. 'Magdeleine Noire des Charentes' and 'Cabernet Franc', the parents of cv. 'Merlot', allowed haplotype resolved assembly. Pseudomolecules were built with a total of 33 to 47 contigs and in few occasions a unique contig for one chromosome. This high resolution allowed haplotype comparison. Annotation was transferred from PN40024 VCost.v3 to all pseudomolecules. After strong selection of variants, 51 and 53 'Merlot' specific periclinal chimeras were found on the Merlot-haplotype-CF and Merlot-haplotype-MG respectively, 9 and 7 been located in a coding region. A subset of positions was analysed using Molecular Inversion Probes (MIPseq) and 69% were unambiguously validated, 25% are doubtful because of technological noise or weak depth and 6% invalidated. These results open new perspectives on chimera detection as an important resource to improve cultivars through clonal selection or breeding.

[Contraception's choice: women's opinion, satisfaction and profile. Results of a French national survey of a representative sample of 5963 women]. / Contraception des femmes françaises de 15 à 45ans: enquête nationale sur un échantillon représentatif de 5963 femmes.

OBJECTIVES: To describe French women's use of contraceptive methods and study their satisfaction and expectations about contraception. PATIENTS AND METHODS: A survey carried out by mail questionnaire filled in by a representative sample group of French women aged 15 to 45 years (Panel Postal Metascope TNS Sofres) in June 2007. RESULTS: Of 10,000 questionnaires sent out, 6044 questionnaires were returned, of which 5963 were usable. Seventy-three percent of women surveyed used some method of contraception, of which 46% was an oral contraceptive, 15% an IUD and 7% used condoms. A minority used new contraceptive methods (implant, patch, vaginal ring). The average age at first sexual relationship was 17.8 years. It was 18.5 among 40-45-year-olds and gradually reduced to 16.7 in the under 25-year-olds. Twenty-three percent of pregnancies remain unwanted and unplanned. For 96% of patients, the choice of contraception was considered to be important. Thirty-six percent thought that contraception could be harmful to health. Only 63% of women believed themselves to be well informed the first time they used contraception. Satisfaction for contraception method was evaluated from 7.3/10 (condom) to 9.7/10 (sterilization). DISCUSSION AND CONCLUSION: Twenty-seven percent of women do not use any contraception and 23% of pregnancies are unwanted despite a large offering of contraceptives. Our study enables the drawing of 'patient-profiles' for the main methods of contraception in order to better determine women's expectations and to pass the findings on to health professionals.

[Reducing the frequency of menses: extended contraception, a review]. / Diminuer la fréquence des règles: le point sur la contraception étendue.

The extended use of combined hormonal contraception contributes to a reduction of the frequency of menses by shortening the hormone free interval or the number of withdrawal weeks by year. Numerous regimen have been studied, with cycles from 49 to 365days. Most extended/continuous cycle regimens result in fewer scheduled bleeding episodes but in more unscheduled bleedings or spottings, that decrease with time. An extended contraception may be effective in reducing some menstrual symptoms such as menorrhagia or dysmenorrhea, or some menstrual related symptoms such as migraine headaches. This article reviews existing data about extended combined hormonal contraception, women's and providers' attitude, bleeding pattern, efficacy and tolerance.

Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness.

Among the several linkage disequilibrium measures known to capture different features of the non-independence between alleles at different loci, the most commonly used for diallelic loci is the r(2) measure. In the present study, we tackled the problem of the bias of r(2) estimate, which results from the sample structure and/or the relatedness between genotyped individuals. We derived two novel linkage disequilibrium measures for diallelic loci that are both extensions of the usual r(2) measure. The first one, r(S)(2), uses the population structure matrix, which consists of information about the origins of each individual and the admixture proportions of each individual genome. The second one, r(V)(2), includes the kinship matrix into the calculation. These two corrections can be applied together in order to correct for both biases and are defined either on phased or unphased genotypes.We proved that these novel measures are linked to the power of association tests under the mixed linear model including structure and kinship corrections. We validated them on simulated data and applied them to real data sets collected on Vitis vinifera plants. Our results clearly showed the usefulness of the two corrected r(2) measures, which actually captured 'true' linkage disequilibrium unlike the usual r(2) measure.

High throughput analysis of grape genetic diversity as a tool for germplasm collection management.

Using 20 SSR markers well scattered across the 19 grape chromosomes, we analyzed 4,370 accessions of the INRA grape repository at Vassal, mostly cultivars of Vitis vinifera subsp. sativa (3,727), but also accessions of V. vinifera subsp. sylvestris (80), interspecific hybrids (364), and rootstocks (199). The analysis revealed 2,836 SSR single profiles: 2,323 sativa cultivars, 72 wild individuals (sylvestris), 306 interspecific hybrids, and 135 rootstocks, corresponding to 2,739 different cultivars in all. A total of 524 alleles were detected, with a mean of 26.20 alleles per locus. For the 2,323 cultivars of V. vinifera, 338 alleles were detected with a mean of 16.9 alleles per locus. The mean genetic diversity (GDI) was 0.797 and the level of heterozygosity was 0.76, with broad variation from 0.20 to 1. Interspecific hybrids and rootstocks were more heterozygous and more diverse (GDI = 0.839 and 0.865, respectively) than V. vinifera cultivars (GDI = 0.769), Vitis vinifera subsp. sylvestris being the least divergent with GDI = 0.708. Principal coordinates analysis distinguished the four groups. Slight clonal polymorphism was detected. The limit between clonal variation and cultivar polymorphism was set at four allelic differences out of 40. SSR markers were useful as a complementary tool to traditional ampelography for cultivar identification. Finally, a set of nine SSR markers was defined that was sufficient to distinguish 99.8% of the analyzed accessions. This set is suitable for routine characterization and will be valuable for germplasm management.

Prevalence and associated factors of sexual problems after early-stage breast cancer treatment: results of a French exploratory survey.

OBJECTIVE: The objective of this study was to assess the prevalence and associated factors of sexual activity, sexual problems or sexual satisfaction in French early-stage breast cancer survivors (BCS). METHODS: Eight hundred and fifty eligible, post-treatment (6 months-5 years) female patients, aged 18-70 years, randomly selected from a consultation list, were invited to fill in questionnaires exploring quality of life (EORTC QLQ-C30 and QLQ-BR23), body image scale, and sexuality (Sexual Activity Questionnaire-SAQ; Relationship and Sexuality Scale; French Sexual Behaviour Survey-CSF). RESULTS: Fifty-three percent of BCS agreed to participate. Participating women (n=378) were younger, more often premenopausal at diagnosis and with a more recent diagnosis than non-respondents. The prevalence of sexual problems was significantly higher in BCS compared with adjusted data from a French female representative sample (p<0.0001). In logistic regression, no sexual activity (R(2) =0.37) or sexual dissatisfaction (R(2) =0.28) were associated with the feeling of emotional separation in the couple or of partner's fear of sexual intercourse, lower emotional functioning, poorer body image, or co-morbidities. In sexually active women (71% of respondents), lower frequency of sexual activity (R(2) =0.26), lower sexual pleasure (R(2) =0.22), or higher sexual discomfort (R(2) =0.22) were associated with the feeling of emotional separation in the couple or of partner's fear of sexual intercourse, lower emotional functioning, age (>50 years), nausea, or insomnia (all Hosmer-Lemeshow tests: p=NS). CONCLUSIONS: Psychological factors including the perception of the couple relationship appeared prominent in BCS women's experience of sexual problems.

[Shared medical decision making in gynaecology]. / La décision médicale partagée en gynécologie.

When two options or more can be chosen in medical care, the final decision implies two steps: facts analysis, and patient evaluation of preferences. Shared Medical Decision-Making is a rational conceptual frame that can be used in such cases. In this paper, we describe the concept, its practical modalities, and the questions raised by its use. In gynaecology, many medical situations involve "sensitive preferences choice": for example, contraceptive choice, menorrhagia treatment, and approach of menopause. Some tools from the "Shared Medical Decision Making" concept are useful to structure medical consultations, to convey information, and to reveal patients preferences. Decision aid are used in clinical research settings, but some of them may also be easily used in usual practice, and help physicians to improve both quality and traceability of the decisional process.

Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.).

Polymorphisms in the grape transcription factor family VvMybA are responsible for variation in anthocyanin content in the berries of cultivated grapevine (Vitis vinifera L. subsp. sativa). Previous study has shown that white grapes arose through the mutation of two adjacent genes: a retroelement insertion in VvMybA1 and a single-nucleotide polymorphism mutation in VvMybA2. The purpose of this study was to understand how these mutations emerged and affected genetic diversity at neighbouring sites and how they structured the genetic diversity of cultivated grapevines. We sequenced a total of 3225 bp of these genes in a core collection of genetic resources, and carried out empirical selection tests, phylogenetic- and coalescence-based demographic analyses. The insertion in the VvMybA1 promoter was shown to have occurred recently, after the mutation of VvMybA2, both mutations followed by a selective sweep. The mutational pattern for these colour genes is consistent with progressively relaxed selection from constrained ancestral coloured haplotypes to light coloured and finally white haplotypes. Dynamics of population size in the VvMybA genes showed an initial exponential growth, followed by population size stabilization. Most ancestral haplotypes are found in cultivars from western region, whereas recent haplotypes are essentially present in table cultivars from eastern regions where intense breeding practices may have replaced the original diversity. Finally, the emergence of the white allele was followed by a recent strong exponential growth, showing a very fast diffusion of the initial white allele.

Linkage disequilibrium in wild French grapevine, Vitis vinifera L. subsp. silvestris.

Association mapping based on linkage disequilibrium (LD) can provide high resolution for whole-genome mapping of genes underlying phenotypic variation. This field has received considerable attention over the last decade. We present here the first characterization of LD in wild French grapevine, Vitis vinifera L. subsp. silvestris. To assess the pattern and extent of LD, we used a sample of 85 plants from southern France and 36 microsatellite markers distributed over 5 linkage groups. LD was evaluated with independence tests and multiallelic r(2), using both unphased genotypic data and reconstructed haplotypic data. LD decayed rapidly, with r(2) values decreasing to 0.1 within 2.7 cM for genotypic data and within 1.4 cM for haplotypic data. Compared to the results of a previous study on cultivated grapevine subsp. sativa, where significant LD was found up to 16.8 cM, LD in subsp. silvestris was no longer significant past 1.4 cM. LD was therefore 12 times further extended in cultivated than wild grapevine, even though LD in wild grapevine seemed to extend slightly further than in wild relatives of other crops. Domestication bottlenecks and vegetative propagation are the primary factors responsible for this difference between cultivated and wild grapevine. The rapid decay of LD observed in this study seems promising for future association mapping studies of functional variation in wild V. vinifera grapevine.

Multiple origins of cultivated grapevine (Vitis vinifera L. ssp. sativa) based on chloroplast DNA polymorphisms.

The domestication of the Eurasian grape (Vitis vinifera ssp. sativa) from its wild ancestor (Vitis vinifera ssp. sylvestris) has long been claimed to have occurred in Transcaucasia where its greatest genetic diversity is found and where very early archaeological evidence, including grape pips and artefacts of a 'wine culture', have been excavated. Whether from Transcaucasia or the nearby Taurus or Zagros Mountains, it is hypothesized that this wine culture spread southwards and eventually westwards around the Mediterranean basin, together with the transplantation of cultivated grape cuttings. However, the existence of morphological differentiation between cultivars from eastern and western ends of the modern distribution of the Eurasian grape suggests the existence of different genetic contribution from local sylvestris populations or multilocal selection and domestication of sylvestris genotypes. To tackle this issue, we analysed chlorotype variation and distribution in 1201 samples of sylvestris and sativa genotypes from the whole area of the species' distribution and studied their genetic relationships. The results suggest the existence of at least two important origins for the cultivated germplasm, one in the Near East and another in the western Mediterranean region, the latter of which gave rise to many of the current Western European cultivars. Indeed, over 70% of the Iberian Peninsula cultivars display chlorotypes that are only compatible with their having derived from western sylvestris populations.

An integrated SSR map of grapevine based on five mapping populations.

A grapevine (mainly Vitis vinifera L., 2n = 38) composite genetic map was constructed with CarthaGene using segregation data from five full-sib populations of 46, 95, 114, 139 and 153 individuals, to determine the relative position of a large set of molecular markers. This consensus map comprised 515 loci (502 SSRs and 13 other type PCR-based markers), amplified using 439 primer pairs (426 SSRs and 13 others) with 50.1% common markers shared by at least two crosses. Out of all loci, 257, 85, 74, 69 and 30 were mapped in 1, 2, 3, 4 and 5 individual mapping populations, respectively. Marker order was generally well conserved between maps of individual populations, with only a few significant differences in the recombination rate of marker pairs between two or more populations. The total length of the integrated map was 1,647 cM Kosambi covering 19 linkage groups, with a mean distance between neighbour loci of 3.3 cM. A framework-integrated map was also built, with marker order supported by a LOD of 2.0. It included 257 loci spanning 1,485 cM Kosambi with a mean inter-locus distance of 6.2 cM over 19 linkage groups. These integrated maps are the most comprehensive SSR-based maps available so far in grapevine and will serve either for choosing markers evenly scattered over the whole genome or for selecting markers that cover particular regions of interest. The framework map is also a useful starting point for the integration of the V. vinifera physical and genetic maps.

Development of a standard set of microsatellite reference alleles for identification of grape cultivars.

In order to investigate the comparability of microsatellite profiles obtained in different laboratories, ten partners in seven countries analyzed 46 grape cultivars at six loci (VVMD5, VVMD7, VVMD27, VVS2, VrZAG62, and VrZAG79). No effort was made to standardize equipment or protocols. Although some partners obtained very similar results, in other cases different absolute allele sizes and, sometimes, different relative allele sizes were obtained. A strategy for data comparison by means of reference to the alleles detected in well-known cultivars was proposed. For each marker, each allele was designated by a code based on the name of the reference cultivar carrying that allele. Thirty-three cultivars, representing from 13 to 23 alleles per marker, were chosen as references. After the raw data obtained by the different partners were coded, more than 97% of the data were in agreement. Minor discrepancies were attributed to errors, suboptimal amplification and visualization, and misscoring of heterozygous versus homozygous allele pairs. We have shown that coded microsatellite data produced in different laboratories with different protocols and conditions can be compared, and that it is suitable for the identification and SSR allele characterization of cultivars. It is proposed that the six markers employed here, already widely used, be adopted as a minimal standard marker set for future grapevine cultivar analyses, and that additional cultivars be characterized by means of the coded reference alleles presented here. The complete database is available at http://www.genres.de/eccdb/vitis/ Cuttings of the 33 reference cultivars are available on request from the Institut National de la Recherche Agronomique Vassal collection (didier.vares@ensam.inra.fr).

Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics.

The aim of the present work was to develop a microsatellite marker-based map of the Vitis vinifera genome (n=19), useful for genetic studies in this perennial heterozygous species, as SSR markers are highly transferable co-dominant markers. A total of 346 primer pairs were tested on the two parents (Syrah and Grenache) of a full sib population of 96 individuals (S x G population), successfully amplifying 310 markers. Of these, 88.4% markers were heterozygous for at least one of the two parents. A total of 292 primer pairs were then tested on Riesling, the parent of the RS1 population derived from selfing (96 individuals), successfully amplifying 299 markers among which 207 (62.9%) were heterozygous. Only 6.7% of the markers were homozygous in all three genotypes, stressing the interest of such markers in grape genetics. Four maps were constructed based on the segregation of 245 SSR markers in the two populations. The Syrah map was constructed from the segregations of 177 markers that could be ordered into 19 linkage groups (total length 1,172.2 cM). The Grenache map was constructed with the segregations of 178 markers that could be ordered into 18 linkage groups (total length 1,360.6 cM). The consensus S x G map was constructed with the segregations of 220 markers that were ordered into 19 linkage groups (total length 1,406.1 cM). One hundred and eleven markers were scored on the RS1 population, among them 27 that were not mapped using the S x G map. Out of these 111 markers, 110 allowed to us to construct a map of a total length of 1,191.7 cM. Using these four maps, the genome length of V. vinifera was estimated to be around 2,200 cM. The present work allowed us to map 123 new SSR markers on the V. vinifera genome that had not been ordered in a previous SSR-based map (Riaz et al. 2004), representing an average of 6.5 new markers per linkage group. Any new SSR marker mapped is of great potential usefulness for many applications such as the transfer of well-scattered markers to other maps for QTL detection, the use of markers in specific regions for the fine mapping of genes/QTL, or for the choice of markers for MAS.

[Raloxifene and breast: from the SERMs concept to its place in clinical practice]. / Raloxifène et tissu mammaire : du concept des SERMs à la place de ce composé en pratique clinique.

Raloxifene is a second generation Selective Estrogen Receptor Modulator. It is indicated in prevention and treatment of post-menopausal osteoporosis. This drug has an estrogen agonistic effect on bone tissue, an estrogen-antagonistic effect in breast and endometrial tissue. It inhibits estrogen induced breast cells proliferation and, in animal studies, it prevents the growth of chemically induced mammary tumors. Raloxifene has a limited effectiveness in women with advanced breast cancers. The effects of raloxifene after treated breast cancer and sequential use of tamoxifene after raloxifene (or the contrary) are not known and should be tested in specific pre-clinical and clinical studies. In osteoporotic women included in the MORE trial, the risk reduction of hormone-dependent breast cancer due to raloxifene raises the issue of some effectiveness of raloxifene in breast cancer prevention. The STAR trial is currently comparing tamoxifene vs raloxifene in breast cancer prevention in women at increased risk of breast cancer. Like tamoxifene, raloxifene increases the risk of venous thrombo-embolic events. On the other hand, in a subgroup of women at increased vascular risk in the MORE trial, the reduction of cardiovascular events raises the issue of an effect of raloxifene in the prevention of coronary events. The ongoing RUTH trial is testing this assumption and it is comparing raloxifene to a placebo in women at increased vascular risk. Today, in clinical practice, before the results of ongoing trail, raloxifene should be used in the setting of osteoporosis prevention and treatment.

Efficacy and tolerability of pulsed estrogen therapy: a 12-week double-blind placebo-controlled study in highly symptomatic postmenopausal women.

OBJECTIVE: To confirm the efficacy and safety of pulsed estrogen therapy, a transient daily hormone exposure, for climacteric symptoms in highly symptomatic postmenopausal women. PATIENTS AND METHODS: In this multicenter, double-blind, parallel-group study, early postmenopausal women with at least seven moderate to severe vasomotor symptoms per day were randomized to receive intranasal estradiol, 150 or 300 microg/day, or placebo, for 12 weeks. The primary outcome measure was the mean daily number of moderate to severe vasomotor symptoms, as recorded in patient diaries. RESULTS: A total of 165 patients were randomized. The mean daily number of moderate to severe vasomotor symptoms decreased significantly more (p < 0.001) in the 150-microg/day (-7.86) and 300-microg/day (-9.39) groups than in the placebo group (-5.22). The decrease reached significance more rapidly with the 300-microg/day dose (from week 2) than with the 150-microg/day dose (from week 8). The rate of emergent adverse events with both doses was similar to that with placebo. CONCLUSIONS: Pulsed estrogen therapy, achieved by intranasal estradiol 150 microg/day and 300 microg/day, significantlyreduced the incidence of moderate to severe vasomotor symptoms, compared with placebo. The 300-microg/day dose demonstrated a greater and more rapid therapeutic effect, with no clinically significant difference in tolerability, compared with the 150-microg/day dose, and therefore offers the best efficacy/safety ratio when initiating treatment with intranasal estradiol.

[Explosive growth of uterine leiomyomas and carcinologic ovarian risk in a non-menopausal patient with BRCA1-BRCA2 mutation treated by tamoxifen]. / Croissance explosive de myome utérin et risque carcinologique ovarien sous tamoxifène chez une patiente non ménopausée porteuse d'une mutation BRCA1-BRCA2.

OBJECTIVE: To report the case of significant growth of a myoma in a premenopausal woman with a suspicion of BRCA1 and BRCA2 mutation, treated by tamoxifen for a hormonodependent breast cancer and to point out the carcinologic ovarian risks with a mutation BRCA1-BRCA2 in this context. Case. Four months after surgical treatment, chemotherapy and the beginning of tamoxifen, an explosive growth of the abdomen justified pelvic echography and laparoscopy confirming the diagnosis of uterine myoma. A polymyomectomy by laparotomy was performed. CONCLUSION: Use of tamoxifen in premenopausal woman with subjacent gynecological pathologies, whether BRCA1-BRCA2 mutation is present or not can prove to be delicate. A regular clinical and echographic monitoring is necessary.

[Approach of menopause in women at risk for breast cancer]. / Approche de la ménopause chez la femme à risque de cancer du sein.

The small but significant increase in risk of discovering breast cancer in women with hormone replacement therapy and the recent discussion of coronary benefit of this treatment have led many authors to insist on the necessity to evaluate the benefit/risks ratio before administration. This evaluation is particularly important for women that are already at high risk of breast cancer because of some genetic predisposition, family history or some benign breast diseases. In these cases, it is important to evaluate the absolute risk of breast cancer, to define the patient's needs more precisely, to specify menopausal symptoms; it is also important to evaluate the risk of osteoporosis, to review the various therapeutic possibilities, which are not only estrogen/progestin treatments (there are alternative treatments), and to give the patients honest information. Before obtaining the results of current trials, we are proposing here a pragmatic attitude and a decision algorithm to adopt a therapeutic attitude more easily which will be decided together by both patients and their physicians.

Genetic mapping of grapevine ( Vitis vinifera L.) applied to the detection of QTLs for seedlessness and berry weight.

Parental and consensus genetic maps of Vitis vinifera L. (2n = 38) were constructed using a F(1) progeny of 139 individuals from a cross between two partially seedless genotypes. The consensus map contained 301 markers [250 amplification fragment length polymorphisms (AFLPs), 44 simple sequence repeats (SSRs), three isozymes, two random amplified polymorphic DNAs (RAPDs), one sequence-characterized amplified region (SCAR), and one phenotypic marker, berry color] mapped onto 20 linkage groups, and covered 1,002 cM. The maternal map consisted of 157 markers covering 767 cM (22 groups). The paternal map consisted of 144 markers covering 816 cM (23 groups). Differences in recombination rates between these maps and another unpublished map are discussed. The major gene for berry color was mapped on both the paternal and consensus maps. Quantitative trait loci (QTLs) for several quantitative subtraits of seedlessness in 3 successive years were searched for, based on parental maps: berry weight, seed number, seed total fresh and dry weights, seed percent dry matter, and seed mean fresh and dry weights. QTLs with large effects (R(2) up to 51%) were detected for all traits and years at the same location on one linkage group, with some evidence for the existence of a second linked major QTL for some of them. For these major QTLs, differences in relative parental effects were observed between traits. Three QTLs with small effects (R(2) from 6% to 11%) were also found on three other linkage groups, for berry weight and seed number in a single year, and for seed dry matter in 2 different years.