A framework for gene mapping in wheat demonstrated using the Yr7 yellow rust resistance gene

We used three approaches to map the yellow rust resistance gene Yr7 and identify associated SNPs in wheat. First, we used a traditional QTL mapping approach using a double haploid (DH) population and mapped Yr7 to a low-recombination region of chromosome 2B. To fine map the QTL, we then used an association mapping panel. Both populations were SNP array genotyped allowing alignment of QTL and genome-wide association scans based on common segregating SNPs. Analysis of the association panel spanning the QTL interval, narrowed the interval down to a single haplotype block. Finally, we used mapping-by-sequencing of resistant and susceptible DH bulks to identify a candidate gene in the interval showing high homology to a previously suggested Yr7 candidate and to populate the Yr7 interval with a higher density of polymorphisms. We highlight the power of combining mapping-by-sequencing, delivering a complete list of gene-based segregating polymorphisms in the interval with the high recombination, low LD precision of the association mapping panel. Our mapping-by-sequencing methodology is applicable to any trait and our results validate the approach in wheat, where with a near complete reference genome sequence, we are able to define a small interval containing the causative gene

Unraveling the genetic complexity underlying sorghum response to water availability

Understanding the adaptation mechanisms of sorghum to drought and the underlying genetic architecture may help to improve its production in a wide range of environments. By crossing a high yielding parent (HYP) and a drought tolerant parent (DTP), we obtained 140 recombinant inbred lines (RILs), which were genotyped with 120 DArT and SSR markers covering 14 linkage groups (LGs). A subset of 100 RILs was evaluated three times in control and drought treatments to genetically dissect their response to water availability. Plants with early heading date (HD) in the drought treatment maintained yield (YLD) level by reducing seed number SN and increasing hundred seed weight (HSW). In contrast, early HD in the control treatment increased SN, HSW and YLD. In total, 133 significant QTL associated with the measured traits were detected in ten hotspot regions. Antagonistic, pleiotropic effects of a QTL cluster mapped on LG-6 may explain the observed trade-offs between SN and HSW: Alleles from DTP reduced SN and the alleles from HYP increased HSW under drought stress, but not in the control treatment. Our results illustrate the importance of considering genetic and environmental factors in QTL mapping to better understand plant responses to drought and to improve breeding programs

High-density SNP-based association mapping of seed traits in fenugreek reveals homology with clover

Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs using double digest restriction site-associated DNA sequencing. We used 38,142 polymorphic SNPs to prove the suitability of the population for association mapping. One significant SNP was associated with both seed length and seed width, and another SNP was associated with seed color. Due to the lack of a comprehensive genetic map, it is neither possible to align the newly developed markers to chromosomes nor to predict the underlying genes. Therefore, systematic targeting of those markers to homologous genomes of other legumes can overcome those problems. A BLAST search using the genomic fenugreek sequence flanking the identified SNPs showed high homology with several members of the Trifolieae tribe indicating the potential of translational approaches to improving our understanding of the fenugreek genome. Using such a comprehensively-genotyped fenugreek population is the first step towards identifying genes underlying complex traits and to underpin fenugreek marker-assisted breeding programs

Mapping QTL underlying fruit quality traits in an F1 strawberry population

Understanding how strawberry nutritional and quality traits are genetically regulated and correlated is an essential step towards improving marker-assisted breeding programmes in this crop. A first step to achieve this goal was to construct a Single Nucleotide Polymorphism (SNP)- based genetic map of 140 F1 individuals of a cross between the two octoploid parents ‘Redgauntlet’ and ‘Hapil’. The map consisted of 3933 SNPs distributed over 28 linkage groups, representing the seven homoeologous groups expected in Fragaria (2n = 8x = 56), and covered a total length of 2624.7 cM with an average resolution of 0.7 cM/SNP. Two overlapping subsets of F1 individuals were evaluated in the field and glasshouse at East Malling Research and the University of Reading, respectively. Negative correlation was observed between Pelargonidin and the three traits L*, a* and b*, whereas positive correlations were observed within L*, a* and b*, and between Ellagic acid, Pelargonidin, and Cyanidin at both trial locations. QTL mapping revealed 29 significant QTL associated with the measured traits and mapped over 16 linkage groups. Two QTL for fruit Fresh Weight (FW) were co-located between day 1 and day 4 of shelf life, accounting for over 62 % of the variation. These data will enhance our understanding of the genetic basis and correlation of strawberry quality traits and provide the basis for refining QTL that underpin the genetic regulation of these quality traits

Genetic controls of short- and long-term stomatal CO2 responses in Arabidopsis thaliana

Background and Aims The stomatal conductance (g(s)) of most plant species decreases in response to elevated atmospheric CO2 concentration. This response could have a significant impact on plant water use in a future climate. However, the regulation of the CO2 induced stomatal closure response is not fully understood. Moreover, the potential genetic links between short-term (within minutes to hours) and long-term (within weeks to months) responses of g(s) to increased atmospheric CO2 have not been explored. Methods We used Arabidopsis thaliana recombinant inbred lines originating from accessions Col-0 (strong CO2 response) and C24 (weak CO2 response) to study short- and long-term controls of g(s) Quantitative trait locus (QTL) mapping was used to identify loci controlling short- and long-term g(s) responses to elevated CO2 as well as other stomata-related traits. Key Results Short- and long-term stomatal responses to elevated CO2 were significantly correlated. Both short-and long-term responses were associated with a QTL, at the end of chromosome 2. The location of this QTL was confirmed using near-isogonic lines and it was fine-mapped to a 410-kb region. The QTL did not correspond to any known gene involved in stomatal closure and had no effect on the responsiveness to abscisic acid. Additionally, we identified numerous other loci associated with stomatal regulation. Conclusions We identified and confirmed the effect of a strong QTL corresponding to a yet unknown regulator of stomatal closure in response to elevated CO2 concentration. The correlation between short- and long-term stomatal CO2 responses and the genetic link between these traits highlight the importance of understanding guard cell CO2 signalling to predict and manipulate plant water use in a world with increasing atmospheric CO2 concentration. This study demonstrates the power of using natural variation to unravel the genetic regulation of complex traits.Peer reviewe

Qualite de vie apres un accident vasculaire cerebral au Senegal: a propos de 50 cas

Introduction: L’accident vasculaire cérébral (AVC) constitue une cause majeure de mortalité et de handicap chez les survivants. La qualité de vie dépend de la nature du handicap et de sa perception par le patient, son entourage et la communauté.Objectif: Notre objectif était d’évaluer le handicap après un AVC et d’apprécier son retentissement sur la qualité de vie des patients victimes.Patients et Méthodes: Nous avons mené une étude prospective, longitudinale de février 2008 à mai 2009, à la clinique neurologique de FANN. Les patients étaient vus à la phase initiale de l’AVC et 6 mois après et soumis à un questionnaire comportant plusieurs items relatifs à la nature de l’accident vasculaire cérébral, le vécu psychoaffectif et socioprofessionnel, l’index de Barthel a été utilisé chez tous les malades.Résultats: Nous avons colligé 50 patients âgés de 15 à 82 ans, avec une sex-ratio de 1,27. L’accident était ischémique dans 70%, hémorragique dans 30% des cas. 66% des patients avaient un index de Barthel entre (60-100), 6% étaient entre (0-20). Le score était meilleur chez les jeunes (15ans-34ans) qui avait tous un index entre (60-100). Par ailleurs 50% des patients de la tranche supérieure à 75ans étaient dans l’intervalle (60-100). Les AVCH avaient des Meilleurs résultats avec 73,3% à un index entre (60-100). seul 12% ont été réinsérés, sur le plan professionnel. 54,05%, n’ont pas noté de changement dans leur vie conjugale. Sur le plan familial, 56% ne notaient aucun changement. Une grande partie de notre série 44% acceptaient bien leurs  déficits,. 70% ne faisaient plus d’activités de temps libre.Conclusion: La qualité de vie est un concept multidimensionnel qui incorpore outre la santé physique les aspects mentaux et sociaux de la maladie.Mots clés: AVC, qualité de vie, SénégalEnglish Title: Quality of life after stroke in Senegal: about 50 casesEnglish AbstractIntroduction: Stroke is a major cause of mortality and disability in survivors. The quality of life depends on the nature of disability and its perception by the patient, his or her environment and community. The aim of this study was to assess disability after stroke and its impact on quality of life of patients (victims).Patients And Methods: We conducted a prospective, longitudinal study from February 2008 to May 2009, at the Neurological Clinic of Fann. Patients were seen at the initial phase of stroke and 6 months later and answered a questionnary containing 13 items like nature of stroke disability psychological emotional and socioprofessional filds. The index of barthel was used at all the patient’s.Results: We collected, were like this 50 patients aged 15-82 years with a sex ratio of 1.27. The accident was ischemic in 70% of cases, hemorrhagic in 30% of cases. 66% had a Barthel index between (60-100), 6% were between (0-20). The score was significantly better in young series (15-34), which all have a Barthel index between (60-100), more over 50% of patients in the portion above 75 years were in the range (60 - 100). Hemorragic stroke had the best results with 73.3% a Barthel index between (60-100). On a professional level, only 12% patients were rehabilitated. 54.05% didn’t notice any change in their marital life. On the home front, 56% noted any change. A large part of our series 44% accepted although their deficits. 70% didn’t have any more free time activities.Keywords: quality of life, stroke, Senega

The Changing Landscape for Stroke\ua0Prevention in AF: Findings From the GLORIA-AF Registry Phase 2

Background GLORIA-AF (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients with Atrial Fibrillation) is a prospective, global registry program describing antithrombotic treatment patterns in patients with newly diagnosed nonvalvular atrial fibrillation at risk of stroke. Phase 2 began when dabigatran, the first non\u2013vitamin K antagonist oral anticoagulant (NOAC), became available. Objectives This study sought to describe phase 2 baseline data and compare these with the pre-NOAC era collected during phase 1. Methods During phase 2, 15,641 consenting patients were enrolled (November 2011 to December 2014); 15,092 were eligible. This pre-specified cross-sectional analysis describes eligible patients\u2019 baseline characteristics. Atrial fibrillation disease characteristics, medical outcomes, and concomitant diseases and medications were collected. Data were analyzed using descriptive statistics. Results Of the total patients, 45.5% were female; median age was 71 (interquartile range: 64, 78) years. Patients were from Europe (47.1%), North America (22.5%), Asia (20.3%), Latin America (6.0%), and the Middle East/Africa (4.0%). Most had high stroke risk (CHA2DS2-VASc [Congestive heart failure, Hypertension, Age  6575 years, Diabetes mellitus, previous Stroke, Vascular disease, Age 65 to 74 years, Sex category] score  652; 86.1%); 13.9% had moderate risk (CHA2DS2-VASc = 1). Overall, 79.9% received oral anticoagulants, of whom 47.6% received NOAC and 32.3% vitamin K antagonists (VKA); 12.1% received antiplatelet agents; 7.8% received no antithrombotic treatment. For comparison, the proportion of phase 1 patients (of N = 1,063 all eligible) prescribed VKA was 32.8%, acetylsalicylic acid 41.7%, and no therapy 20.2%. In Europe in phase 2, treatment with NOAC was more common than VKA (52.3% and 37.8%, respectively); 6.0% of patients received antiplatelet treatment; and 3.8% received no antithrombotic treatment. In North America, 52.1%, 26.2%, and 14.0% of patients received NOAC, VKA, and antiplatelet drugs, respectively; 7.5% received no antithrombotic treatment. NOAC use was less common in Asia (27.7%), where 27.5% of patients received VKA, 25.0% antiplatelet drugs, and 19.8% no antithrombotic treatment. Conclusions The baseline data from GLORIA-AF phase 2 demonstrate that in newly diagnosed nonvalvular atrial fibrillation patients, NOAC have been highly adopted into practice, becoming more frequently prescribed than VKA in Europe and North America. Worldwide, however, a large proportion of patients remain undertreated, particularly in Asia and North America. (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients With Atrial Fibrillation [GLORIA-AF]; NCT01468701

Genome-Wide Association Mapping of Grain Metal Accumulation in Wheat

Increasing wheat grain yield while ignoring grain quality and metal accumulation can result in metal deficiencies, particularly in countries where bread wheat accounts for the majority of daily dietary regimes. When the accumulation level exceeds a certain threshold, it becomes toxic and causes various diseases. Biofortification is an effective method of ensuring nutritional security. We screened 200 spring wheat advanced lines from the wheat association mapping initiative for Mn, Fe, Cu, Zn, Ni, and Cd concentrations. Interestingly, high-yielding genotypes had high essential metals, such as Mn, Fe, Cu, and Zn, but low levels of toxic metals, such as Ni and Cd. Positive correlations were found between all metals except Ni and Cd, where no correlation was found. We identified 142 significant SNPs, 26 of which had possible pleiotropic effects on two or more metals. Several QTLs co-located with previously mapped QTL for the same or other metals, whereas others were new. Our findings contribute to wheat genetic biofortification through marker-assisted selection, ensuring nutritional security in the long run

Assessment of oxLDL, anti-oxLDL antibodies and lipoprotein-associated phospholipase A2 as cardiovascular risk markers in obese adolescents with and without T1DM

Background: Oxidized low density lipoprotein (oxLDL), anti-oxLDL antibodies (oxLDL Ab) and lipoprotein-associated phospholipase A2 (Lp-PLA2) are the sequel of lipoprotein oxidation and were not studied contemporarily in obese adolescents with and without type 1 diabetes (T1DM). Subjects and methods: The current study enrolled seventy-five adolescents with T1DM who were selected as having hyperglycemia and seventy-five matched control subjects. Both the diabetic and the control groups were further divided into obese, normal weight and underweight subgroups according to body mass index (BMI). The following tests were performed: fasting plasma glucose (FG) glycated hemoglobin (HbA1c), insulin, apolipoprotein AI (apo AI), apolipoprotein B (apo B), oxLDL, oxLDL Ab and Lp-PLA2 mass. The diabetic subgroups were selected as having hyperglycemia. Results: Obese diabetic subgroup had higher insulin level and HOMA value than underweight and normal weight diabetic subgroups. oxLDL, oxLDL Ab and Lp-PLA2 showed higher concentrations in patients with T1DM than in control subjects (118.48 ± 23.7, 1231.8 ± 940 and 401.26 ± 97.2 vs. 58.1 ± 17.9, 424.9 ± 290.0 and 315.7 ± 70; p < 0.001).. In patients with T1DM, direct correlations were found between oxLDL, oxLDL Ab and Lp-PLA2 and cardiometabolic markers represented by apo B/apo AI ratio, FG and BMI. Conclusion: The current data provide evidence that oxLDL, its retroactive enzyme and antibody are present in circulation early in childhood when primed by obesity and hyperglycemia in T1DM and suggests that they could be useful markers for cardiovascular diseases (CVD). Keywords: OxLDL, OxLDL Ab, Lp-PLA2, Cardiometabolic markers, Obese, Diabete

Correction: Unraveling the genetic complexity underlying sorghum response to water availability.

[This corrects the article DOI: 10.1371/journal.pone.0215515.]