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Background Developing chilling tolerant accessions of domesticated Asian rice is a potential source of significant crop improvement. The uniquely chilling sensitive nature of the tropically originating Oryza sativa make it the most important cereal crop that can gain significantly from improved tolerance to low temperatures. However, mechanisms underlying this complex trait are not fully understood. Oryza sativa has two subspecies with different levels of chilling tolerance, JAPONICA and INDICA, providing an ideal tool to investigate mechanistic differences in the chilling stress tolerance responses within this important crop species. Results The Rice Diversity Panel 1 (RDP1) was used to investigate a core set of Oryza sativa accessions. The tools available for this panel allowed for a comprehensive analysis of two chilling tolerance traits at multiple temperatures across a 354-cultivar subset of the RDP1. Chilling tolerance trait values were distributed as mostly subpopulation specific clusters of Tolerant, Intermediate, and Sensitive accessions. Genome-wide association study (GWAS) mapping approaches using all 354 accessions yielded a total of 245 quantitative trait loci (QTL), containing 178 unique QTL covering 25% of the rice genome, while 40 QTL were identified by multiple traits. QTL mappings using subsets of rice accession clusters yielded another 255 QTL, for a total of 500 QTL. The genes within these multiple trait QTL were analyzed for Gene Ontology (GO) term and potential pathway enrichments. Terms related to “carbohydrate biosynthesis”, “carbohydrate transmembrane transport”, “small molecule protein modification”, and “plasma membrane” were enriched from this list. Filtering was done to identify more likely candidate pathways involved in conferring chilling tolerance, resulting in enrichment of terms related to “Golgi apparatus”, “stress response”, “transmembrane transport”, and “signal transduction”. Conclusions Taken together, these GO term clusters revealed a likely involvement of Golgi-mediated subcellular and extracellular vesicle and intracellular carbohydrate transport as a general cold stress tolerance response mechanism to achieve cell and metabolic homeostasis under chilling stress.

International audience; In a context of reduced insecticide use, the development of cultivars resistant to insect pests is crucial for an integrated pest management. Pea (Pisum sativum) is a crop of major importance among cultivated legumes, for the supply of feed and food proteins and nitrogen in low-input cropping systems. However, yields of the pea crop have become more and more unstable due to rising insect damages with reduced use of pesticides on crops. The pea aphid (Acyrthosiphon pisum) is an insect pest species forming a complex of biotypes, each one adapted to feed on one or a few related legume species. This study aimed to identify resistant genotypes to A. pisum and the underlying genetic determinism by examining a pea collection of 240 genotypes. The collection was screened against a pea-adapted biotype and a non-adapted biotype of A. pisum to characterise their resistance phenotype, through a fecundity test of the aphid installed on the plant in a growth chamber. Partial resistance was observed in some pea genotypes exposed to the pea-adapted biotype. Many pea genotypes were completely resistant to non-adapted biotype, but some exhibited partial susceptibility. A genome association study, using pea exome-capture sequencing data, enabled the identification of a major-effect quantitative trait locus, ApRVII, on chromosome 7. ApRVII includes linkage disequilibrium blocks, which are significantly associated with resistance to one or both of the two pea-adapted and non-adapted aphid biotypes studied. Finally, we identified candidate genes underlying ApRVII that are potentially involved in plant-aphid interactions and marker haplotypes significantly associated with resistance. This study sets the ground for the functional characterization of molecular pathways involved in pea defence to the aphids but also is a step forward for breeding aphid-resistant cultivars.

Drought is one of the most detrimental abiotic stresses hampering seed germination, development, and productivity. Maize is more sensitive to drought than other cereals, especially at seedling stage. Our objective was to study genetic regulation of drought tolerance at germination and during seedling growth in maize. We evaluated 420 RIL with their parents from a multi-parent advanced generation inter-cross (MAGIC) population with PEG-induced drought at germination and seedling establishment. A genome-wide association study (GWAS) was carried out to identify genomic regions associated with drought tolerance. GWAS identified 28 and 16 SNPs significantly associated with germination and seedling traits under stress and well-watered conditions, respectively. Among the SNPs detected, two SNPs had significant associations with several traits with high positive correlations, suggesting a pleiotropic genetic control. Other SNPs were located in regions that harbored major QTLs in previous studies, and co-located with QTLs for cold tolerance previously published for this MAGIC population. The genomic regions comprised several candidate genes related to stresses and plant development. These included numerous drought-responsive genes and transcription factors implicated in germination, seedling traits, and drought tolerance. The current analyses provide information and tools for subsequent studies and breeding programs for improving drought tolerance., This research was funded by the École Nationale Supérieure Agronomique; PRIMA, a program supported by the European Union under H2020 framework programme; and Spanish Ministerio de Innovación y Universidades (MCIU), the Agencia Estatal de Investigación (AEI) and the European Fund for Regional Development (FEDER), UE (project code PID2019-108127RB-I00). Financial support has been also provided by PRIMA, a program supported by the European Union under the H2020 framework programme and by the project IN607A2021/07 from Xunta de Galicia.

Drought is a detrimental factor to gaining higher yields in rice (Oryza sativa L.), especially amid the rising occurrence of drought across the globe. To combat this situation, it is essential to develop novel drought-resilient varieties. Therefore, screening of drought-adaptive genotypes is required with high precision and high throughput. In contemporary emerging science, high throughput plant phenotyping (HTPP) is a crucial technology that attempts to break the bottleneck of traditional phenotyping. In traditional phenotyping, screening significant genotypes is a tedious task and prone to human error while measuring various plant traits. In contrast, owing to the potential advantage of HTPP over traditional phenotyping, image-based traits, also known as i-traits, were used in our study to discriminate 110 genotypes grown for genome-wide association study experiments under controlled (well-watered), and drought-stress (limited water) conditions, under a phenomics experiment in a controlled environment with RGB images. Our proposed framework non-destructively estimated drought-adaptive plant traits from the images, such as the number of leaves, convex hull, plant–aspect ratio (plant spread), and similarly associated geometrical and morphological traits for analyzing and discriminating genotypes. The results showed that a single trait, the number of leaves, can also be used for discriminating genotypes. This critical drought-adaptive trait was associated with plant size, architecture, and biomass. In this work, the number of leaves and other characteristics were estimated non-destructively from top view images of the rice plant for each genotype. The estimation of the number of leaves for each rice plant was conducted with the deep learning model, YOLO (You Only Look Once). The leaves were counted by detecting corresponding visible leaf tips in the rice plant. The detection accuracy was 86–92% for dense to moderate spread large plants, and 98% for sparse spread small plants. With this framework, the susceptible genotypes (MTU1010, PUSA-1121 and similar genotypes) and drought-resistant genotypes (Heera, Anjali, Dular and similar genotypes) were grouped in the core set with a respective group of drought-susceptible and drought-tolerant genotypes based on the number of leaves, and the leaves’ emergence during the peak drought-stress period. Moreover, it was found that the number of leaves was significantly associated with other pertinent morphological, physiological and geometrical traits. Other geometrical traits were measured from the RGB images with the help of computer vision.

As we look so different, our genomic sequences vary enormously. The differences in our genome, genetic variations, have played very significant roles in medical research and have contributed to improvement of medical managements in the last 2-3 decades. Genetic variations include germline variations, somatic mutations, and diversities in receptor genes of rearranged immune cells, T cells and B cells. Germline variants are in some cases causative of genetic diseases, are associated with the risk of various diseases, and also affect drug efficacies or adverse events. Some somatic mutations are causative of tumor development. Recent DNA sequencing technologies allow us to perform single-cell analysis or detailed repertoire analysis of B and T cells. It is critically important to investigate temporal changes in immune environment in various anatomical regions in the next one to two decades. In this review article, we would like to introduce the roles of genetic variations in medical fields in the past, at present and in the future.

ObjectiveThis study aims to identify novel candidate genes associated with osteonecrosis of the femoral head (ONFH).MethodsA transcriptome-wide association study (TWAS) was performed by integrating the genome-wide association study dataset of osteonecrosis (ON) in the UK Biobank with pre-computed mRNA expression reference weights of muscle skeleton (MS) and blood. The ON-associated genes identified by TWAS were further subjected to gene ontology (GO) analysis by the DAVID tool. Finally, a trans-omics comparative analysis of TWAS and genome-wide mRNA expression profiling was conducted to identify the common genes and the GO terms shared by both DNA-level TWAS and mRNA-level expression profile for ONFH.ResultsTWAS totally identified 564 genes that were with PTWAS value CBX1 (PTWAS = 0.0001 for MS), SRPK2 (PTWAS = 0.0002 for blood), and MYO5A (PTWAS = 0.0005 for blood). After comparing the genes detected by TWAS with the differentially expressed genes identified by mRNA expression profiling, we detected 59 overlapped genes, such as STEAP4 [PTWAS = 0.0270, FC (fold change)mRNA = 7.03], RABEP1 (PTWAS = 0.010, FCmRNA = 2.22), and MORC3 (PTWAS = 0.0053, FCmRNA = 2.92). The GO analysis of TWAS-identified genes discovered 53 GO terms for ON. Further comparing the GO results of TWAS and mRNA expression profiling identified four overlapped GO terms, including cysteine-type endopeptidase activity (PTWAS = 0.0006, PmRNA = 0.0227), extracellular space (PTWAS = 0.0342, PmRNA = 0.0012), protein binding (PTWAS = 0.0112, PmRNA = 0.0106), and ATP binding (PTWAS = 0.0464, PmRNA = 0.0033).ConclusionSeveral ONFH-associated genes and GO terms were identified by integrating TWAS and mRNA expression profiling. It provides novel clues to reveal the pathogenesis of ONFH.

Stripe rust, caused by the fungus Puccinia striiformis f. sp. tritici, is a worldwide disease of wheat that causes devastating crop losses. Resistant cultivars have been developed over the last 40 years that have significantly reduced the economic impact of the disease on growers, but in heavy infection years it is mostly controlled through the intensive application of fungicides. The Pacific Northwest of the United States has an ideal climate for stripe rust and has one of the most diverse race compositions in the country. This has resulted in many waves of epidemics that have overcome most of the resistance genes traditionally used in elite germplasm. The best way to prevent high yield losses, reduce production costs to growers, and reduce the heavy application of fungicides is to pyramid multiple stripe rust resistance genes into new cultivars. Using genotyping-by-sequencing, we identified 4662 high quality variant positions in a recombinant inbred line population of 196 individuals derived from a cross between Skiles, a highly resistant winter wheat cultivar, and Goetze, a moderately to highly susceptible winter wheat cultivar, both developed at Oregon State University. A subsequent genome wide association study identified two quantitative trait loci (QTL) on chromosomes 3B and 3D within the predicted locations of stripe rust resistance genes. Resistance QTL, when combined together, conferred high levels of stripe rust resistance above the level of Skiles in some locations, indicating that these QTL would be important additions to future breeding efforts of Pacific Northwest winter wheat cultivars.

Objective To identify rheumatoid arthritis (RA)-associated susceptibility genes and pathways through integrating genome-wide association study (GWAS) and gene expression profile data. Methods A transcriptome-wide association study (TWAS) was conducted by the FUSION software for RA considering EBV-transformed lymphocytes (EL), transformed fibroblasts (TF), peripheral blood (NBL), and whole blood (YBL). GWAS summary data was driven from a large-scale GWAS, involving 5539 autoantibody-positive RA patients and 20,169 controls. The TWAS-identified genes were further validated using the mRNA expression profiles and made a functional exploration. Results TWAS identified 692 genes with PTWAS values PEL = 0.01293, PTF = 0.00038, PNBL = 0.02839, PYBL = 0.0978), MUT (PEL = 0.00377, PTF = 0.00076, PNBL = 0.00778, PYBL = 0.00096), FOXRED1 (PEL = 0.03834, PTF = 0.01120, PNBL = 0.01280, PYBL = 0.00583), and EBPL (PEL = 0.00806, PTF = 0.03761, PNBL = 0.03540, PYBL = 0.04254) were collectively expressed in all the four tissues/cells. Eighteen genes, including ANXA5, AP4B1, ATIC (PTWAS = 0.0113, downregulated expression), C12orf65, CMAH, PDHB, RUNX3 (PTWAS = 0.0346, downregulated expression), SBF1, SH2B3, STK38, TMEM43, XPNPEP1, KIAA1530, NUFIP2, PPP2R3C, RAB24, STX6, and TLR5 (PTWAS = 0.04665, upregulated expression), were validated with integrative analysis of TWAS and mRNA expression profiles. TWAS-identified genes functionally involved in endoplasmic reticulum organization, regulation of cytokine production, TNF signaling pathway, immune response-regulating signaling pathway, regulation of autophagy, etc. Conclusion We identified multiple candidate genes and pathways, providing novel clues for the genetic mechanism of RA.

Background Distichiasis, an ocular disorder in which aberrant cilia (eyelashes) grow from the opening of the Meibomian glands of the eyelid, has been reported in Friesian horses. These misplaced cilia can cause discomfort, chronic keratitis, and corneal ulceration, potentially impacting vision due to corneal fibrosis, or, if secondary infection occurs, may lead to loss of the eye. Friesian horses represent the vast majority of reported cases of equine distichiasis, and as the breed is known to be affected with inherited monogenic disorders, this condition was hypothesized to be a simply inherited Mendelian trait. Results A genome wide association study (GWAS) was performed using the Axiom 670 k Equine Genotyping array (MNEc670k) utilizing 14 cases and 38 controls phenotyped for distichiasis. An additive single locus mixed linear model (EMMAX) approach identified a 1.83 Mb locus on ECA5 and a 1.34 Mb locus on ECA13 that reached genome-wide significance (pcorrected = 0.016 and 0.032, respectively). Only the locus on ECA13 withstood replication testing (p = 1.6 × 10− 5, cases: n = 5 and controls: n = 37). A 371 kb run of homozygosity (ROH) on ECA13 was found in 13 of the 14 cases, providing evidence for a recessive mode of inheritance. Haplotype analysis (hapQTL) narrowed the region of association on ECA13 to 163 kb. Whole-genome sequencing data from 3 cases and 2 controls identified a 16 kb deletion within the ECA13 associated haplotype (ECA13:g.178714_195130del). Functional annotation data supports a tissue-specific regulatory role of this locus. This deletion was associated with distichiasis, as 18 of the 19 cases were homozygous (p = 4.8 × 10− 13). Genotyping the deletion in 955 horses from 54 different breeds identified the deletion in only 11 non-Friesians, all of which were carriers, suggesting that this could be causal for this Friesian disorder. Conclusions This study identified a 16 kb deletion on ECA13 in an intergenic region that was associated with distichiasis in Friesian horses. Further functional analysis in relevant tissues from cases and controls will help to clarify the precise role of this deletion in normal and abnormal eyelash development and investigate the hypothesis of incomplete penetrance.

International audience; Schizophrenia is a multifactorial disease associated with widespread cognitive impairment. Although cognitive deficits are one of the factors most strongly associated with functional impairment in schizophrenia (SZ), current treatment strategies hardly tackle these impairments. To develop more efficient treatment strategies in patients, a better understanding of their pathogenesis is needed. Recent progress in genetics, driven by large genome-wide association studies (GWAS) and the use of polygenic risk scores (PRS), has provided new insights about the genetic architecture of complex human traits, including cognition and SZ. Here, we review the recent findings examining the genetic links between SZ and cognitive functions in population-based samples as well as in participants with SZ. The performed meta-analysis showed a negative correlation between the polygenetic risk score of schizophrenia and global cognition (p < 0.001) when the samples rely on general and healthy participants, while no significant correlation was detected when the three studies devoted to schizophrenia patients were meta-analysed (p > 0.05). Our review and meta-analysis therefore argues against universal pleiotropy for schizophrenia alleles and cognition, since cognition in SZ patients would be underpinned by the same genetic factors than in the general population, and substantially independent of common variant liability to the disorder.

Objective Genome wide association study was conducted to identify and validate candidate genes associated with fatty acid composition of pork. Methods A total of 480 purebreed Duroc pigs were genotyped using IlluminaPorcine60k bead chips while the association test was implemented following genome-wide rapid association using Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approach. Results A total of 25, 29, and 16 single nucleotide polymorphisms (SNPs) were significantly associated with stearic (18:0), oleic (18:1) and saturated fatty acids (SFA), respectively. Genome wide significant variants were located on the same region of swine chromosome 14 (SSC14) that spanned from 120 to 124 Mb. Top SNP ALGA008191 was located at 5 kb near the stearoyl-CoA desaturase (SCD) gene. This gene is directly involved in desaturation of stearic acid into oleic acid. General relationship of significant SNPs showed high linkage disequilibrium thus genome-wide signals was attributed to SCD gene. However, understanding the role of other genes like elongation of very long chain fatty acids-3 (ELOVL3) located on this chromosomal segment might help in further understanding of metabolism and biosynthesis of fatty acids. Conclusion Overall, this study provides evidence that validates SCD gene as strong candidate gene associated with fatty acid composition in Duroc pigs. Moreover, this study confirms significant SNPs near ELOVL3 gene.

Populations of European ash trees (Fraxinus excelsior) are being devastated by the invasive alien fungus Hymenoscyphus fraxineus, which causes ash dieback. We sequenced whole genomic DNA from 1,250 ash trees in 31 DNA pools, each pool containing trees with the same ash dieback damage status in a screening trial and from the same seed-source zone. A genome-wide association study identified 3,149 single nucleotide polymorphisms (SNPs) associated with low versus high ash dieback damage. Sixty-one of the 192 most significant SNPs were in, or close to, genes with putative homologues already known to be involved in pathogen responses in other plant species. We also used the pooled sequence data to train a genomic prediction model, cross-validated using individual whole genome sequence data generated for 75 healthy and 75 damaged trees from a single seed source. The model's genomic estimated breeding values (GEBVs) allocated these 150 trees to their observed health statuses with 67% accuracy using 10,000 SNPs. Using the top 20% of GEBVs from just 200 SNPs, we could predict observed tree health with over 90% accuracy. We infer that ash dieback resistance in F. excelsior is a polygenic trait that should respond well to both natural selection and breeding, which could be accelerated using genomic prediction.

Periodontal diseases and dental caries are the most common diseases of humans and the main cause of tooth loss. Both diseases can lead to nutritional compromise and negative impacts upon self‐esteem and quality of life. As complex chronic diseases, they share common risk factors, such as a requirement for a pathogenic plaque biofilm, yet they exhibit distinct pathophysiologies. Multiple exposures contribute to their causal pathways, and susceptibility involves risk factors that are inherited (e.g. genetic variants), and those that are acquired (e.g. socio‐economic factors, biofilm load or composition, smoking, carbohydrate intake). Identification of these factors is crucial in the prevention of both diseases as well as in their management. Aim. To systematically appraise the scientific literature to identify potential risk factors for caries and periodontal diseases. Methods. One systematic review (genetic risk factors), one narrative review (role of diet and nutrition) and reference documentation for modifiable acquired risk factors common to both disease groups, formed the basis of the report. Results & Conclusions. There is moderately strong evidence for a genetic contribution to periodontal diseases and caries susceptibility, with an attributable risk estimated to be up to 50%. The genetics literature for periodontal disease is more substantial than for caries and genes associated with chronic periodontitis are the vitamin D receptor (VDR), Fc gamma receptor IIA (Fc‐γRIIA) and Interleukin 10 (IL10) genes. For caries, genes involved in enamel formation (AMELX, AMBN, ENAM, TUFT, MMP20, and KLK4), salivary characteristics (AQP5), immune regulation and dietary preferences had the largest impact. No common genetic variants were found. Fermentable carbohydrates (sugars and starches) were the most relevant common dietary risk factor for both diseases, but associated mechanisms differed. In caries, the fermentation process leads to acid production and the generation of biofilm components such as Glucans. In periodontitis, glycaemia drives oxidative stress and advanced glycation end‐products may also trigger a hyper inflammatory state. Micronutrient deficiencies, such as for vitamin C, vitamin D or vitamin B12, may be related to the onset and progression of both diseases. Functional foods or probiotics could be helpful in caries prevention and periodontal disease management, although evidence is limited and biological mechanisms not fully elucidated. Hyposalivation, rheumatoid arthritis, smoking/tobacco use, undiagnosed or sub‐optimally controlled diabetes and obesity are common acquired risk factors for both caries and periodontal diseases.

The molecular mechanisms by which plants modulate their root growth rate (RGR) in response to nutrient deficiency are largely unknown. Using Arabidopsis thaliana accessions, we analyzed RGR variation under combinatorial mineral nutrient deficiencies involving phosphorus (P), iron (Fe), and zinc (Zn). While -P stimulated early RGR of most accessions, -Fe or -Zn reduced it. The combination of either -P-Fe or -P-Zn led to suppression of the growth inhibition exerted by -Fe or -Zn alone. Surprisingly, root growth responses of the reference accession Columbia (Col-0) were not representative of the species under -P nor -Zn. Using a systems approach that combines GWAS, network-based candidate identification, and reverse genetic screen, we identified new genes that regulate root growth in -P-Fe: VIM1, FH6, and VDAC3. Our findings provide a framework to systematically identifying favorable allelic variations to improve root growth, and to better understand how plants sense and respond to multiple environmental cues., Author summary Plants thrive in highly heterogenous soils. How they compute a multitude of contrasting stimuli and mount an adaptive response without a centralized information processing unit is an intriguing question. For instance, below ground, roots can sense and respond to the single or multiple nutrient stresses, and adjust its growth rate accordingly. Nevertheless, the genetic architecture of root growth responses under single and combined stress remains poorly understood. To fill this gap in our understanding about such crucial phenomenon for plant survival, we explored the natural variation of root growth rate (RGR) in Arabidopsis grown under single and combined nutritional stress, including deficiencies of iron (-Fe), zinc (-Zn), phosphate and iron (-P-Fe) and phosphate and zinc (-P-Zn). Our GWAS revealed distinct genetic architectures underlying root growth responses to single or combined nutrient stresses. By integrating GWAS and coexpression networks, we identified and validated genes controlling the variation of root growth to combined nutrient-deficiency, namely VARIANT IN METHYLATION 1, FORMIN-LIKE-PROTEIN-6 and VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 3. Our findings provide a framework to accelerate future research aiming at better understanding how plants sense and respond to multiple environmental inputs, and promise to help designing new agronomical and biotechnological strategies to improve root growth.

The molecular mechanisms by which plants modulate their root growth rate (RGR) in response to nutrient deficiency are largely unknown. Using Arabidopsis thaliana accessions, we analyzed RGR variation under combinatorial mineral nutrient deficiencies involving phosphorus (P), iron (Fe), and zinc (Zn). While -P stimulated early RGR of most accessions, -Fe or -Zn reduced it. The combination of either -P-Fe or -P-Zn led to suppression of the growth inhibition exerted by -Fe or -Zn alone. Surprisingly, root growth responses of the reference accession Columbia (Col-0) were not representative of the species under -P nor -Zn. Using a systems approach that combines GWAS, network-based candidate identification, and reverse genetic screen, we identified new genes that regulate root growth in -P-Fe: VIM1, FH6, and VDAC3. Our findings provide a framework to systematically identifying favorable allelic variations to improve root growth, and to better understand how plants sense and respond to multiple environmental cues.

Low back pain (LBP) is a highly prevalent musculoskeletal condition and the leading cause for workplace absenteeism. Lumbar disc degeneration (DD) is considered as a contributing factor to LBP. The role of genetic factors in the development of lumbar DD has been demonstrated to be significant, with heritability estimates ranging from 64% to 81%. Modic change (MC), a distinct phenotype of lumbar DD, is a subchondral and vertebral bone marrow change revealed only by magnetic resonance imaging (MRI). MC has been associated with LBP in both clinical samples and the general population. The genetic background of MC is largely unknown, and the heritability of MC has not previously been assessed. The aim of this study was to assess the heritability of MC using a twin study, identify predisposing genetic factors for MC in a family-based design using whole-exome sequencing and to identify genetic loci associated with MC using genome-wide association study (GWAS) meta-analysis. An additional aim was to study the prevalence, incidence and morphology of MC. The data consisted of two general population samples, the Northern Finland Birth Cohort 1966 (NFBC1966) and TwinsUK from the United Kingdom, as well as two Finnish families from the Oulu region. MC was found to be partly heritable with a heritability estimate of 30%. Two novel candidate genes, HSPG2 and MAML1, were found co-segregating with MC in two Finnish families. Both genes are important in the growth and differentiation of chondrocytes. Finally, a genetic locus on chromosome 9 was found to be significantly associated with MC using genome-wide meta-analysis of NFBC1966 and TwinsUK. These results showed that genetic factors play a role in the development of MC. In conclusion, this thesis increased the knowledge on the genetics of MC. However, the specific roles of these genes need to be studied further. Tiivistelmä Alaselkäkivun kansaterveydellinen merkitys on suuri, sillä jopa 84% aikuisista kärsii siitä elämänsä aikana. Selkäkivun vuoksi Suomessa kertyy yli 2 miljoona sairauslomapäivää vuodessa. Välilevyrappeumaa pidetään merkittävänä tekijänä alaselkäkivun synnyssä ja perinnölliset tekijät selittävät välilevyrappeuman synnystä jopa 74%. Modic-muutokset ovat selkärangan välilevyjen päätelevyjen ja subkondraalisen luun muutoksia, jotka voidaan havaita ainoastaan magneettikuvauksella. Niitä pidetään välilevyrappeuman alatyyppinä. Modic-muutosten on osoitettu olevan yhteydessä alaselkäkipuun, mutta etiologia tunnetaan huonosti. Perinnöllisyyden osuutta Modic-muutoksien synnyssä ei ole aiemmin tutkittu ja niiden taustalla vaikuttavat geneettiset tekijät ovat pääasiassa tuntemattomia. Tämän tutkimuksen tavoitteena oli arvioida perinnöllisyyden osuutta Modic-muutoksissa kaksoisaineistossa, tunnistaa Modic-muutoksille altistavia geneettisiä muutoksia perheaineistossa käyttäen eksomisekvensointia ja tunnistaa genomin alueita, jotka assosioituvat Modic-muutoksiin. Tutkimus perustui kahteen väestöperäiseen aineistoon: Pohjois-Suomen Syntymäkohorttiin 1966 ja TwinsUK-kaksosaineistoon Yhdistyneistä kuningaskunnista sekä kahteen pohjois-suomalaiseen perheeseen. Tutkimuksessa osoitettiin, että Modic-muutokset ovat perinnöllisiä ja, että perinnölliset tekijät selittävät noin 30% niiden ilmenemisestä. Lisäksi tutkimuksessa tunnistettiin kaksi uutta alttiusgeeniä; HSPG2- ja MAML1-geenit. Molemmilla geeneillä on tärkeä rooli rustosolujen kasvamisessa ja erilaistumisessa. Tutkimuksessa myös tunnistettiin kromosomista 9 genomin alue, joka assosioituu Modic-muutoksiin. Väitöskirjassani osoitettiin, että perinnöllisillä tekijöillä on merkitystä Modic-muutosten synnyssä. Kokonaisuudessaan tämä väitöskirja kasvattaa ymmärrystä Modic-muutoksista, mutta lisätutkimusta aiheesta tarvitaan.

In nature plants are often exposed to a multitude of biotic and abiotic stress factors (e.g. drought, herbivory and infections) that occur sequentially or simultaneously. To withstand these stresses plants have evolved defense mechanisms that allow them to cope with diverse stresses. However, still little is known about how these adaptive mechanisms cooperate to maximize plant survival under multistress conditions. Our research reveals that plants are well-capable of adjusting their defense strategy when encountering multiple stresses. To investigate how plants cope with multi-stress conditions, we analyzed the dynamics of whole-transcriptome profiles of Arabidopsis thaliana exposed to three individual and six sequential double stresses inflicted by combinations of: (i) infection by the necrotrophic fungus Botrytis cinerea, (ii) herbivory by caterpillars of Pieris rapae, and (iii) drought stress. Each of these stresses induced specific expression profiles over time, in which one-third of all differentially expressed genes was shared by at least two single stresses. Still, a first stress encounter leaves a transcriptional stress mark that can adversely affect plant defenses to a second stress event, indicating that plant multi-stress interactions are affected by simultaneous or sequential stresses. Aside from a flexible defense response, we also find natural variation in globally collected A. thaliana plants for their resistance to B. cinerea as individual stress or when preceded by drought stress or herbivory by P. rapae. In search for the genetics underlying the variation in plant susceptibility, we found genes that are potentially involved in plant adaptive responses to the applied sequential stresses. Genes with both known and putative roles in defense against each of the applied stresses were identified. In a subsequent study, we compared the tolerance of plants to diverse (a)biotic stresses and sequential stress combinations in order to find genes involved in plant multistress resistance. Plants that are resistant to multiple stresses are well-adapted to grow in diverse environmental settings and can therefore ensure efficient and sustainable food production in the future. With a genetic study we revealed genes involved in one or more (a)biotic stresses. Validation of one of the identified genes revealed its involvement in tolerance to multiple stresses, indicating that with our approach it is possible to find genes involved in plant multi-stress tolerance. To minimalize crop damage, prevention of stress encounters is another approach of reducing crop losses instead of looking for plant adaptive responses that allow plants to cope with multiple stresses. For instance, by preventing egg-deposition by butterflies, subsequent herbivory by their offspring is avoided. In search of plant traits that are unfavorable for P. rapae, we studied plant selection for egg-deposition on naturally occurring A. thaliana plants. We observed variation in egg-deposition that was partially influenced by daylight, the experimental cage setup, plant size, spontaneous chlorosis and necrosis and the presence of secondary metabolites. A genetic study revealed genes of which one gene was shown to significantly associate with plant defense against caterpillars, jasmonic acid induced defenses. Butterflies might be capable of detecting differences in jasmonic acid defenses and select host plants that will benefit their offspring the best. Future functional analysis of the JA biosynthesis gene and the other identified candidate genes will be required to reveal their role in host selection for oviposition by P. rapae. In sum, this research has shown that plants have an incredible ability to adapt to and integrate diverse stress signals into an effective defense response. Knowledge on these natural adaptive capabilities and the natural genetic variation hereof forms a valuable basis for the sustainable development of stress resilient future crops.

In nature plants are often exposed to a multitude of biotic and abiotic stress factors (e.g. drought, herbivory and infections) that occur sequentially or simultaneously. To withstand these stresses plants have evolved defense mechanisms that allow them to cope with diverse stresses. However, still little is known about how these adaptive mechanisms cooperate to maximize plant survival under multistress conditions. Our research reveals that plants are well-capable of adjusting their defense strategy when encountering multiple stresses. To investigate how plants cope with multi-stress conditions, we analyzed the dynamics of whole-transcriptome profiles of Arabidopsis thaliana exposed to three individual and six sequential double stresses inflicted by combinations of: (i) infection by the necrotrophic fungus Botrytis cinerea, (ii) herbivory by caterpillars of Pieris rapae, and (iii) drought stress. Each of these stresses induced specific expression profiles over time, in which one-third of all differentially expressed genes was shared by at least two single stresses. Still, a first stress encounter leaves a transcriptional stress mark that can adversely affect plant defenses to a second stress event, indicating that plant multi-stress interactions are affected by simultaneous or sequential stresses. Aside from a flexible defense response, we also find natural variation in globally collected A. thaliana plants for their resistance to B. cinerea as individual stress or when preceded by drought stress or herbivory by P. rapae. In search for the genetics underlying the variation in plant susceptibility, we found genes that are potentially involved in plant adaptive responses to the applied sequential stresses. Genes with both known and putative roles in defense against each of the applied stresses were identified. In a subsequent study, we compared the tolerance of plants to diverse (a)biotic stresses and sequential stress combinations in order to find genes involved in plant multistress resistance. Plants that are resistant to multiple stresses are well-adapted to grow in diverse environmental settings and can therefore ensure efficient and sustainable food production in the future. With a genetic study we revealed genes involved in one or more (a)biotic stresses. Validation of one of the identified genes revealed its involvement in tolerance to multiple stresses, indicating that with our approach it is possible to find genes involved in plant multi-stress tolerance. To minimalize crop damage, prevention of stress encounters is another approach of reducing crop losses instead of looking for plant adaptive responses that allow plants to cope with multiple stresses. For instance, by preventing egg-deposition by butterflies, subsequent herbivory by their offspring is avoided. In search of plant traits that are unfavorable for P. rapae, we studied plant selection for egg-deposition on naturally occurring A. thaliana plants. We observed variation in egg-deposition that was partially influenced by daylight, the experimental cage setup, plant size, spontaneous chlorosis and necrosis and the presence of secondary metabolites. A genetic study revealed genes of which one gene was shown to significantly associate with plant defense against caterpillars, jasmonic acid induced defenses. Butterflies might be capable of detecting differences in jasmonic acid defenses and select host plants that will benefit their offspring the best. Future functional analysis of the JA biosynthesis gene and the other identified candidate genes will be required to reveal their role in host selection for oviposition by P. rapae. In sum, this research has shown that plants have an incredible ability to adapt to and integrate diverse stress signals into an effective defense response. Knowledge on these natural adaptive capabilities and the natural genetic variation hereof forms a valuable basis for the sustainable development of stress resilient future crops.

In nature plants are often exposed to a multitude of biotic and abiotic stress factors (e.g. drought, herbivory and infections) that occur sequentially or simultaneously. To withstand these stresses plants have evolved defense mechanisms that allow them to cope with diverse stresses. However, still little is known about how these adaptive mechanisms cooperate to maximize plant survival under multistress conditions. Our research reveals that plants are well-capable of adjusting their defense strategy when encountering multiple stresses. To investigate how plants cope with multi-stress conditions, we analyzed the dynamics of whole-transcriptome profiles of Arabidopsis thaliana exposed to three individual and six sequential double stresses inflicted by combinations of: (i) infection by the necrotrophic fungus Botrytis cinerea, (ii) herbivory by caterpillars of Pieris rapae, and (iii) drought stress. Each of these stresses induced specific expression profiles over time, in which one-third of all differentially expressed genes was shared by at least two single stresses. Still, a first stress encounter leaves a transcriptional stress mark that can adversely affect plant defenses to a second stress event, indicating that plant multi-stress interactions are affected by simultaneous or sequential stresses. Aside from a flexible defense response, we also find natural variation in globally collected A. thaliana plants for their resistance to B. cinerea as individual stress or when preceded by drought stress or herbivory by P. rapae. In search for the genetics underlying the variation in plant susceptibility, we found genes that are potentially involved in plant adaptive responses to the applied sequential stresses. Genes with both known and putative roles in defense against each of the applied stresses were identified. In a subsequent study, we compared the tolerance of plants to diverse (a)biotic stresses and sequential stress combinations in order to find genes involved in plant multistress resistance. Plants that are resistant to multiple stresses are well-adapted to grow in diverse environmental settings and can therefore ensure efficient and sustainable food production in the future. With a genetic study we revealed genes involved in one or more (a)biotic stresses. Validation of one of the identified genes revealed its involvement in tolerance to multiple stresses, indicating that with our approach it is possible to find genes involved in plant multi-stress tolerance. To minimalize crop damage, prevention of stress encounters is another approach of reducing crop losses instead of looking for plant adaptive responses that allow plants to cope with multiple stresses. For instance, by preventing egg-deposition by butterflies, subsequent herbivory by their offspring is avoided. In search of plant traits that are unfavorable for P. rapae, we studied plant selection for egg-deposition on naturally occurring A. thaliana plants. We observed variation in egg-deposition that was partially influenced by daylight, the experimental cage setup, plant size, spontaneous chlorosis and necrosis and the presence of secondary metabolites. A genetic study revealed genes of which one gene was shown to significantly associate with plant defense against caterpillars, jasmonic acid induced defenses. Butterflies might be capable of detecting differences in jasmonic acid defenses and select host plants that will benefit their offspring the best. Future functional analysis of the JA biosynthesis gene and the other identified candidate genes will be required to reveal their role in host selection for oviposition by P. rapae. In sum, this research has shown that plants have an incredible ability to adapt to and integrate diverse stress signals into an effective defense response. Knowledge on these natural adaptive capabilities and the natural genetic variation hereof forms a valuable basis for the sustainable development of stress resilient future crops.

Background In 2016, a large meta-analysis brought the number of susceptibility loci for migraine to 38. While sub-type analysis for migraine without aura (MO) and migraine with aura (MA) found some loci showed specificity to MO, the study did not test the loci with respect to other subtypes of migraine. This study aimed to test the hypothesis that single nucleotide polymorphisms (SNPs) robustly associated with migraine are individually or collectively associated with menstrual migraine (MM). Methods Genotyping of migraine susceptibility SNPs was conducted using the Agena MassARRAY platform on DNA samples from 235 women diagnosed with menstrual migraine as per International Classification for Headache Disorders II (ICHD-II) criteria and 140 controls. Alternative genotyping methods including restriction fragment length polymorphism, pyrosequencing and Sanger sequencing were used for validation. Statistical analysis was performed using PLINK and SPSS. Results Genotypes of 34 SNPs were obtained and investigated for their potential association with menstrual migraine. Of these SNPs, rs2506142 located near the neuropilin 1 gene (NRP1), was found to be significantly associated with menstrual migraine (p = 0.003). Genomic risk scores were calculated for all 34 SNPs as well as a subset of 7 SNPs that were nearing individual significance. Overall, this analysis suggested these SNPs to be weakly predictive of MM, but of no prognostic or diagnostic value. Conclusions Our results suggest that NRP1 may be important in the etiology of MM. It also suggests some genetic commonality between common migraine subtypes (MA and MO) and MM. The identification of associated SNPs may be the starting point to a better understanding of how genetic factors may contribute to the menstrual migraine sub-type.

Background Coronary heart disease (CHD) is the most common cause of death worldwide. Previous studies have identified numerous common CHD susceptibility loci, with the vast majority identified in populations of European ancestry. How well these findings transfer to other racial/ethnic populations remains unclear. Methods and Results We examined the generalizability of the associations with 71 known CHD loci in African American, Latino and Japanese men and women in the Multiethnic Cohort (6,035 cases and 11,251 controls). In the combined multiethnic sample, 78% of the loci demonstrated odds ratios that were directionally consistent with those previously reported (p = 2 × 10−6), with this fraction ranging from 59% in Japanese to 70% in Latinos. The number of nominally significant associations across all susceptibility regions ranged from only 1 in Japanese to 11 in African Americans with the most statistically significant association observed through locus fine-mapping noted for rs3832016 (OR = 1.16, p = 2.5×10−5) in the SORT1 region on chromosome 1p13. Lastly, we examined the cumulative predictive effect of CHD SNPs across populations with improved power by creating genetic risk scores (GRSs) that summarize an individual’s aggregated exposure to risk variants. We found the GRSs to be significantly associated with risk in African Americans (OR = 1.03 per allele; p = 4.1×10−5) and Latinos (OR = 1.03; p = 2.2 × 10−8), but not in Japanese (OR = 1.01; p = 0.11). Conclusions While a sizable fraction of the known CHD loci appear to generalize in these populations, larger fine-mapping studies will be needed to localize the functional alleles and better define their contribution to CHD risk in these populations.

The quantities and proportions of protein fractions have notable effects on the nutritional and technological value of milk. Although much is known about the effects of genetic variants on milk proteins, the complex relationships among the set of genes and pathways regulating the different protein fractions synthesis and secretion into milk in dairy cows are still not completely understood. We conducted genome-wide association studies (GWAS) for milk nitrogen fractions in a cohort of 1,011 Brown Swiss cows, which uncovered 170 significant single nucleotide polymorphism (SNPs), mostly located on BTA6 and BTA11. Gene-set analysis and the network-based Associated Weight Matrix approach revealed that the milk proteins associated genes were involved in several biological functions, particularly ion and cation transmembrane transporter activity and neuronal and hormone signalling, according to the structure and function of casein micelles. Deeper analysis of the transcription factors and their predicted target genes within the network revealed that GFI1B, ZNF407 and NR5A1 might act as master regulators of milk protein synthesis and secretion. The information acquired provides novel insight into the regulatory mechanisms controlling milk protein synthesis and secretion in bovine mammary gland and may be useful in breeding programmes aimed at improving milk nutritional and/or technological properties.

Background Bakanae disease, caused by seed-borne Fusarium species, mainly F. fujikuroi, is a rice disease whose importance is considerably increasing in several rice growing countries, leading to incremental production losses. Results A germplasm collection of japonica rice was screened for F. fujikuroi resistance, allowing the identification of accessions with high-to-moderate levels of resistance to bakanae. A GWAS approach uncovered two genomic regions highly associated with the observed phenotypic variation for response to bakanae infection on the short arm of chromosome 1 (named as qBK1_628091) and on the long arm of chromosome 4 (named as qBK4_31750955). High levels of phenotypic resistance to bakanae were associated to the cumulated presence of the resistant alleles at the two resistance loci, suggesting that they can provide useful levels of disease protection in resistance breeding. A fine comparison with the genomic positions of qBK1_628091 and qBK4_31750955 with respect to the QTLs for bakanae resistance reported in the literature suggests that the resistant loci here described represent new genomic regions associated to F. fujikuroi resistance. A search for candidate genes with a putative role in bakanae resistance was conducted considering all the annotated genes and F. fujikuroi-related DEGs included in the two genomic regions highlighting several gene functions that could be involved in resistance, thus paving the way to the functional characterization of the resistance loci. Conclusions New effective sources for bakanae resistance were identified on rice chromosomes 1 and 4 and tools for resistance breeding are provided. Electronic supplementary material The online version of this article (doi:10.1186/s12284-017-0168-z) contains supplementary material, which is available to authorized users.

The emergence and re-emergence of plant pathogenic microorganisms are processes that imply perturbations in both host and pathogen ecological niches. Global change is largely assumed to drive the emergence of new etiological agents by altering the equilibrium of the ecological habitats which in turn places hosts more in contact with pathogen reservoirs. In this context, the number of epidemics is expected to increase dramatically in the next coming decades both in wild and crop plants. Under these considerations, the identification of the genetic variants underlying natural variation of resistance is a pre-requisite to estimate the adaptive potential of wild plant populations and to develop new breeding resistant cultivars. On the other hand, the prediction of pathogen's genetic determinants underlying disease emergence can help to identify plant resistance alleles. In the genomic era, whole genome sequencing combined with the development of statistical methods led to the emergence of Genome Wide Association (GWA) mapping, a powerful tool for detecting genomic regions associated with natural variation of disease resistance in both wild and cultivated plants. However, GWA mapping has been less employed for the detection of genetic variants associated with pathogenicity in microbes. Here, we reviewed GWA studies performed either in plants or in pathogenic microorganisms (bacteria, fungi and oomycetes). In addition, we highlighted the benefits and caveats of the emerging joint GWA mapping approach that allows for the simultaneous identification of genes interacting between genomes of both partners. Finally, based on co-evolutionary processes in wild populations, we highlighted a phenotyping-free joint GWA mapping approach as a promising tool for describing the molecular landscape underlying plant - microbe interactions.

International audience; Many QTL affecting meat quality and carcass traits have been reported. However, in most of the cases these QTL have been detected in non-commercial populations. Therefore, a family structured population of 457 F2 pigs issued from an inter-cross between 2 commercial sire lines was used to detect QTL affecting meat quality and carcass traits. All animals were genotyped using the Illumina PorcineSNP60 BeadChip platform. Genome-wide association studies were used in combination with linkage disequilibrium-linkage analysis to identify QTL. A total of 32 QTL were detected. Nine of these QTL exceeded the genome-wide 5% significance threshold. We detected 18 QTL affecting carcass composition traits and 16 QTL affecting meat quality traits. Using post-QTL bioinformatics analysis we highlighted 26 functional candidate genes related to fatness, muscle development, meat color and meat pH. Finally, our results shed light on the advantage of using different QTL detection methodologies to get a global overview of the QTL present in the studied population.

A panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, earliness and plant growth. Genome-wide association studies (GWAS) have become a method of choice in quantitative trait dissection. First limited to highly polymorphic and outcrossing species, it is now applied in horticultural crops, notably in tomato. Until now GWAS in tomato has been performed on panels of heirloom and wild accessions. Using modern breeding materials would be of direct interest for breeding purpose. To implement GWAS on a large panel of 300 tomato accessions including 168 breeding lines, this study assessed the genetic diversity and linkage disequilibrium decay and revealed the population structure and performed GWA experiment. Genetic diversity and population structure analyses were based on molecular markers (>11,000 SNP) covering the whole genome. Six genetic subgroups were revealed and associated to traits of agronomical interest, such as fruit weight and disease resistance. Estimates of linkage disequilibrium highlighted the heterogeneity of its decay among genetic subgroups. Haplotype definition allowed a fine characterization of the groups and their recombination landscape revealing the patterns of admixture along the genome. Selection footprints showed results in congruence with introgressions. Taken together, all these elements refined our knowledge of the genetic material included in this panel and allowed the identification of several associations for fruit weight, plant growth and earliness, deciphering the genetic architecture of these complex traits and identifying several new loci useful for tomato breeding.

International audience

Imaging genetics is an emerging field in which the association between genes and neuroimaging-based quantitative phenotypes are used to explore the functional role of genes in neuroanatomy and neurophysiology in the context of healthy function and neuropsychiatric disorders. The main obstacle for researchers in the field is the high dimensionality of the data in both the imaging phenotypes and the genetic variants commonly typed. In this article, we develop a novel method that utilizes Gene Ontology, an online database, to select and prioritize certain genes, employing a stratified false discovery rate (sFDR) approach to investigate their associations with imaging phenotypes. sFDR has the potential to increase power in genome wide association studies (GWAS), and is quickly gaining traction as a method for multiple testing correction. Our novel approach addresses both the pressing need in genetic research to move beyond candidate gene studies, while not being overburdened with a loss of power due to multiple testing. As an example of our methodology, we perform a GWAS of hippocampal volume using both the Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA2) and the Alzheimer's Disease Neuroimaging Initiative datasets. The analysis of ENIGMA2 data yielded a set of SNPs with sFDR values between 10 and 20%. Our approach demonstrates a potential method to prioritize genes based on biological systems impaired in a disease.

Genome-Wide Association Study (GWAS) aims to identify genetic variants that are significantly associated with genetic traits. To analyze GWAS data that often contains 0.5 to 1 million Single Nucleotide Polymorphisms (SNPs) genotyped from thou-sands of individuals, stringent statistical significant thresholds are pre-defined for multiple testing adjustment, e.g., with p-value < 10−8 for single SNP detection and at least < 10−12 for SNP-SNP interaction detection. Such stringent thresholds were used for efficiency computation but it hinders the discovery of many true genetic variants and more practical approaches are needed to conduct GWAS.In this paper, we propose a machine learning approach to identify groups of predictive SNPs in GWAS analysis. Our method differs from other methods by first translates the genomics knowledge into SNP grouping as priors, then select a list of most predictive SNP groups using linear regression regularized by group sparse constraints, solved by Group-lasso (Least Absolute Shrinkage and Selection Operator). The selected SNPs groups compose a sparse feature space which yields a higher predictive power for continuous trait prediction.We conduct experiment on SiMES (Singapore Malay Eye Study) data set, with 3280 Malay individuals genotyped on Illumina 610 quad arrays. We investigate one discrete trait (Glaucoma) and two glaucoma-related quantitative traits, optic Disc-Cup-Ratio (CDR) and Intraocular Pressure (IOP). The hypothesis is that, with more biological knowledge embedded, a learning mechanism yields higher predictive power. Our preliminary results support the above hypothesis. Further analysis reveals that our approach can identify groups of SNPs highly associated with a particular genetic trait, in spite of the small sample size and the incomplete biological knowledge.

Homocysteine is a risk factor for atherosclerosis, and the level of homocysteine in plasma is known to be strongly influenced by genetic factors-not only rare variants, but also common polymorphisms. This report describes a comprehensive postgenomic strategy for elucidating useful genetic information about homocysteine metabolism. The standard method for gathering such information is the candidate gene approach, which is an effective method based on known biological information. After collecting evidence from independent research projects, a critical epidemiological review permits a determination as to whether a putative association is true or not. A genome-wide association study (GWAS), which requires no biological information, can identify new candidates and confirm associations suggested by the candidate gene approach. The importance of methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism, which was shown in a randomized controlled trial conducted by the present author, and in other studies, was independently confirmed by a large-scale GWAS. GWASs have also identified new candidate genes, but these must be confirmed by independent studies. In homocysteine metabolism, the classical candidate gene approach was sufficiently robust to detect the true association. However, candidate markers newly discovered by GWAS need to be confirmed by well-designed epidemiological studies to determine their significance. International statements, such as CONSORT and STREGA, provide useful principles for conducting such research.

Background Genome-wide association (GWA) mapping has recently emerged as a valuable approach for refining the genetic basis of polygenic resistance to plant diseases, which are increasingly used in integrated strategies for durable crop protection. Aphanomyces euteiches is a soil-borne pathogen of pea and other legumes worldwide, which causes yield-damaging root rot. Linkage mapping studies reported quantitative trait loci (QTL) controlling resistance to A. euteiches in pea. However the confidence intervals (CIs) of these QTL remained large and were often linked to undesirable alleles, which limited their application in breeding. The aim of this study was to use a GWA approach to validate and refine CIs of the previously reported Aphanomyces resistance QTL, as well as identify new resistance loci. Methods A pea-Aphanomyces collection of 175 pea lines, enriched in germplasm derived from previously studied resistant sources, was evaluated for resistance to A. euteiches in field infested nurseries in nine environments and with two strains in climatic chambers. The collection was genotyped using 13,204 SNPs from the recently developed GenoPea Infinium® BeadChip. Results GWA analysis detected a total of 52 QTL of small size-intervals associated with resistance to A. euteiches, using the recently developed Multi-Locus Mixed Model. The analysis validated six of the seven previously reported main Aphanomyces resistance QTL and detected novel resistance loci. It also provided marker haplotypes at 14 consistent QTL regions associated with increased resistance and highlighted accumulation of favourable haplotypes in the most resistant lines. Previous linkages between resistance alleles and undesired late-flowering alleles for dry pea breeding were mostly confirmed, but the linkage between loci controlling resistance and coloured flowers was broken due to the high resolution of the analysis. A high proportion of the putative candidate genes underlying resistance loci encoded stress-related proteins and others suggested that the QTL are involved in diverse functions. Conclusion This study provides valuable markers, marker haplotypes and germplasm lines to increase levels of partial resistance to A. euteiches in pea breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2429-4) contains supplementary material, which is available to authorized users.

Highlight Tomato quality could be improved under deficit irrigation while maintaining yield. The underlying genetic architecture is polygenic and varies with water availability. Candidate genes related to primary metabolism were identified., Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions. A subset of 55 accessions exhibited increased metabolite contents and maintained yield under water deficit. Using 6100 single nucleotide polymorphisms (SNPs), association mapping revealed 31, 41, and 44 quantitative trait loci (QTLs) under drought, control, and both conditions, respectively. Twenty-five additional QTLs were interactive between conditions, emphasizing the interest in accounting for QTLs by watering regime interactions in fruit quality improvement. Combining our results with the loci previously identified in a biparental progeny resulted in 11 common QTLs and contributed to a first detailed characterization of the genetic determinants of response to water deficit in tomato. Major QTLs for fruit quality traits were dissected and candidate genes were proposed using expression and polymorphism data. The outcomes provide a basis for fruit quality improvement under deficit irrigation while limiting yield losses.

International audience

Background Coccidiosis is the most common and costly disease in the poultry industry and is caused by protozoans of the Eimeria genus. The current control of coccidiosis, based on the use of anticoccidial drugs and vaccination, faces serious obstacles such as drug resistance and the high costs for the development of efficient vaccines, respectively. Therefore, the current control programs must be expanded with complementary approaches such as the use of genetics to improve the host response to Eimeria infections. Recently, we have performed a large-scale challenge study on Cobb500 broilers using E. maxima for which we investigated variability among animals in response to the challenge. As a follow-up to this challenge study, we performed a genome-wide association study (GWAS) to identify genomic regions underlying variability of the measured traits in the response to Eimeria maxima in broilers. Furthermore, we conducted a post-GWAS functional analysis to increase our biological understanding of the underlying response to Eimeria maxima challenge. Results In total, we identified 22 single nucleotide polymorphisms (SNPs) with q value

Improving the nutritional content of staple crops through breeding (biofortification) is promoted as cheap and sustainable approach for alleviating vitamin A and other micronutrient deficiencies across the world. Maize is one of the target crops for provitamin A biofortification, since it is a major staple for millions of people in developing countries, and has a great genetic potential for accumulating provitamin A in its grain. This PhD study addressed three research objectives aimed at accelerating the biofortification of maize with provitamin A. To achieve the objectives, a diverse set of inbred lines developed from different crosses having mixed genetic background of temperate and tropical germplasm were employed. In the first research objective, the efficiency of PCR based functional markers proposed for high provitamin A maize breeding was investigated. Out of eight polymorphisms for three key carotenoid biosynthesis genes tested, the 3'TE and 5'TE polymorphisms of the gene crtRB1 showed the strongest association. About 18 percent of the inbred lines studied had the favourable alleles for these two polymorphisms. The second research objective assessed the association of genome-wide SNP markers with provitamin A and non-provitamin A carotenoids using GWAS and pathway level association analysis. This study detected known major and minor effect carotenoid genes (lcyE, crtRB1, ZEP1 and others), plus novel loci, such as ARF20, that may be involved in regulation of carotenoid biosynthesis in maize endsosperm. In the last research objective 24 yellow maize inbred lines were inter-crossed using factorial mating scheme for studying their combining abilities and heterotic effects for carotenoids and key agronomic traits. The result demonstrated the predominance of additive genetic effects in the inheritance of endosperm carotenoid content. Small percentage of non-additive genetic effect was also detected for provitamin A which is important for expression of heterosis in the trait. Hybrids combining good agronomic performance and high provitamin A content were identified. This study will serve as a basis for establishing heterotic pattern in IITA's yellow maize germplasm which is crucial for development of hybrid and synthetic varieties that can meet existing and emerging demands, while incorporating high level of provitamin A in the grain. 2016-05-13

International audience; All crop species are current or ancient polyploids. Following whole genome duplication, structural and functional modifications result in differential gene content or regulation in the duplicated regions, which can play a fundamental role in the diversification of genes underlying complex traits. We have investigated this issue in Brassica napus, a species with a highly duplicated genome, with the aim of studying the structural and functional organization of duplicated regions involved in quantitative resistance to stem canker, a disease caused by the fungal pathogen Leptosphaeria maculans. Genome-wide association analysis on two oilseed rape panels confirmed that duplicated regions of ancestral blocks E, J, R, U, and W were involved in resistance to stem canker. The structural analysis of the duplicated genomic regions showed a higher gene density on the A genome than on the C genome and a better collinearity between homoeologous regions than paralogous regions, as overall in the whole B. napus genome. The three ancestral sub-genomes were involved in the resistance to stem canker and the fractionation profile of the duplicated regions corresponded to what was expected from results on the B. napus progenitors. About 60% of the genes identified in these duplicated regions were single-copy genes while less than 5% were retained in all the duplicated copies of a given ancestral block. Genes retained in several copies were mainly involved in response to stress, signaling, or transcription regulation. Genes with resistance-associated markers were mainly retained in more than two copies. These results suggested that some genes underlying quantitative resistance to stem canker might be duplicated genes. Genes with a hydrolase activity that were retained in one copy or R-like genes might also account for resistance in some regions. Further analyses need to be conducted to indicate to what extent duplicated genes contribute to the expression of the resistance phenotype.

International audience; Rapid and uniform seed germination is a crucial prerequisite for crop establishment and high yield levels in crop production. A disclosure of genetic factors contributing to adequate seed vigor would help to further increase yield potential and stability. Here we carried out a genome-wide association study in order to define genomic regions influencing seed germination and early seedling growth in oilseed rape (Brassica napus L.). A population of 248 genetically diverse winter-type B. napus accessions was genotyped with the Brassica 60k SNP Illumina genotyping array. Automated high-throughput in vitro phenotyping provided extensive data for multiple traits related to germination and early vigor, such as germination speed, absolute germination rate and radicle elongation. The data obtained indicate that seed germination and radicle growth are strongly environmentally dependent, but could nevertheless be substantially improved by genomic-based breeding. Conditions during seed production and storage were shown to have a profound effect on seed vigor, and a variable manifestation of seed dormancy appears to contribute to differences in germination performance in B. napus. Several promising positional and functional candidate genes could be identified within the genomic regions associated with germination speed, absolute germination rate, radicle growth and thousand seed weight. These include B. napus orthologs of the Arabidopsis thaliana genes SNOWY COTYLEDON 1 (SCO1), ARABIDOPSIS TWO-COMPONENT RESPONSE REGULATOR (ARR4), and ARGINYL-t-RNA PROTEIN TRANSFERASE 1 (ATE1), which have been shown previously to play a role in seed germination and seedling growth in A. thaliana.

Highlight Plant-model-assisted phenotyping and metabolomics enable phenotypic and genetic dissection of early vigour traits in a rice diversity panel., Early vigour of rice, defined as seedling capacity to accumulate shoot dry weight (SDW) rapidly, is a complex trait. It depends on a genotype propensity to assimilate, store, and/or use non-structural carbohydrates (NSC) for producing large and/or numerous leaves, involving physiological trade-offs in the expression of component traits and, possibly, physiological and genetic linkages. This study explores a plant-model-assisted phenotyping approach to dissect the genetic architecture of rice early vigour, applying the Genome Wide Association Study (GWAS) to morphological and NSC measurements, as well as fitted parameters for the functional–structural plant model, Ecomeristem. Leaf size, number, SDW, and source-leaf NSC concentration were measured on a panel of 123 japonica accessions. The data were used to estimate Ecomeristem genotypic parameters driving organ appearance rate, size, and carbon dynamics. GWAS was performed based on 12 221 single-nucleotide polymorphisms (SNP). Twenty-three associations were detected at P

Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs., This work has been funded by the EU seventh Framework Programme (http://ec.europa.eu/research/fp7/index_en.cfm) through the project “FruitBreedomics: Integrated Approach for increasing breeding efficiency in fruit tree crops” (Grant #FP7- 265582; http://fruitbreedomics.com/); by the Ministero delle Politiche Agricole Alimentari e Forestali -Italy (MiPAAF, http://www.politicheagricole.it) through the project ‘‘DRUPOMICS: Sequenziamento del genoma del pesco ed utilizzo della sequenza in programmi di miglioramento della qualita` del frutto del pesco e della resistenza alle malattie’’ (Grant # DM14999/7303/08) and “ESPLORA: Esplorazione della biodiversità vegetale ed animale alla ricerca di alleli superiori da inserire nei programmi avanzati di miglioramento genetico a sostegno dell’agricoltura nazionale” (Grant #DM 14658/7303/10); by the Spanish Ministry of Science and Innovation (http://www.micinn.es/) through the project AGL2012-40228-C02-01 (uso de la secuencia genomica para la caracterizacion de la variabilidad intraclonal e interespecifica en Melocotonero y almendro) and by the INIA (http://www.inia.es/) through the Project RF2012-00024-C04-04 (“conservación y caracterización de germoplasma introducido”).

Dans la filière « poule pondeuse », les candidats à la sélection sont actuellement évalués à partir de leur valeur génétique estimée (Estimated Breeding Value, EBV) en appliquant un modèle statistique prenant en compte l’ensemble des phénotypes disponibles sur leurs apparentés (BLUP). Le développement récent d’une puce de génotypage à haute densité (600K Affymetrix® Axiom® HD), permet d’envisager la mise en place d’une sélection génomique dans cette filière. La valeur génomique estimée (Genomic Estimated Breeding Value, GEBV) serait potentiellement plus précise que l’EBV, disponible dès la naissance de l’individu et potentiellement pour un plus grand nombre de candidats, engendrant ainsi un gain de progrès génétique. Par ailleurs, un même type génétique de poule pondeuse étant largement diffusé à travers le monde, les animaux produisent dans des environnements différents (alimentation, température, normes d’hygiène…). Des interactions génotype – environnement pourraient donc affecter l’estimation des valeurs génétiques des candidats à la sélection. L’objectif premier de ce travail est de préciser l’impact de celles-ci sur un panel large de caractères de production et de qualité des oeufs. De plus, les conséquences de l’architecture génétique des caractères sur l’estimation des valeurs génétiques ont été étudiées. Ainsi, 438 coqs de lignée pure ont été génotypés et les phénotypes de 31 381 de leurs filles croisées ont été mesurés pour des caractères de production et de qualité des oeufs. Une moitié de leur descendantes a été nourrie avec un régime bas en énergie métabolisable (2455 kcal) et l’autre moitié avec un régime haut en énergie métabolisable (2881 kcal). Par des analyses GWAS réalisées sur la moyenne et l’écart-type des performances de ces poules, nous avons pu mettre en évidence l’existence de QTL en interaction avec le régime et avec l’âge. Alors que pour la moyenne, 45% des QTL présentaient une interaction significative avec le régime alimentaire et/ou l’âge, 98% des QTL détectés dans l’étude sur l’écart-type présentaient une interaction significative avec l’environnement. Il semble donc que la variance des caractères soit plus sensible aux interactions génotype – environnement que la moyenne. Par la suite, nous avons étudié l’impact de ces interactions sur l’évaluation génétique ou génomique des candidats à la sélection. Pour cela, des coqs ont été évalués par 3 méthodes différentes (génotypique, génétique et génomique) pour 3 caractères d’architectures génétiques différentes (nombre de QTL et interactions avec le régime). Nous avons mis en évidence que les interactions génotype – régime n’influençaient pas le classement des candidats, les corrélations génétiques ou génomiques entre les caractères mesurés dans chacun des régimes étant supérieures à 0,95 dans tous les cas. Nous avons également montré que l’évaluation génomique permettrait, dans certains cas, une évaluation plus précise des candidats. En conclusion, il semble que l’environnement influence l’architecture génétique des caractères, car des QTL ayant des effets différents en fonction de l’environnement ont été identifiés. Néanmoins, les interactions génotype – régime mises en évidence n’impactent pas le classement des candidats à la sélection. La mise en place d’une sélection spécifique au régime ne semble donc pas nécessaire. L’implémentation de la sélection génomique dans la filière « poule pondeuse » semble prometteuse, car elle permettrait une estimation plus précise des valeurs génétiques, et cela plus précocement dans la vie des individus, que l’évaluation sur pedigree.

The Brazilian cattle industry is presented as highlighted on the world stage and the significant participation of this productive sector in the economy means that there is concern with production losses, among which stands out those caused by infestation of Rhipicephalus (Boophilus) microplus, main ectoparasite vector cattle and various diseases. The genetic variability for resistance to the cattle tick shows that this trait can be genetically improved. For the execution of this work, it was used a study of genome wide association (GWAS) for resistance to Rhipicephalus (Boophilus) microplus, performed by Dr. Fernando Flores Cardoso, with 260 Hereford and 500 Braford animals. The monitoring of the infestation was accomplished by counting tick females larger than 4.5 mm from one of the animal's body side, and the degree of infestation was evaluated for each animal by averaging at least two consecutive counts, with intervals of approximately thirty days, in the months of highest incidence of the parasite. The animals were genotyped using a 50K SNP chip, and it was found a total of 37,346 SNPs that passed in quality test. Among these markers, 178 showed significant effects and allowed the mining of 175 genes in these regions, at an interval of 200 Kb (100 Kb for each side of each marker). Most of these polymorphisms associated with the trait is located in regions without defined functions (intronic and intergenic), and only one of them is located in the splicing region. The most significant regions of the GWAS were identified on chromosomes 7, 21 and 23, which were found 72 genes in linkage disequilibrium with the molecular markers. Therefore, a functional annotation of the genes on these 3 chromosomes was performed, allowing the choice of 11 candidate genes for the study of various metabolic pathways in which they are inserted. Among these pathways, the most important are those related to immune responses, secretion and intracellular transport, calcium influx and epidermal growth and differentiation. A bovinocultura brasileira apresenta-se como destaque no cenário mundial e a expressiva participação deste setor produtivo na economia faz com que haja preocupação com as perdas produtivas, dentre as quais destaca-se aquelas causadas pela infestação do carrapato Rhipicephalus (Boophilus) microplus, principal ectoparasita de bovinos e vetor de diversas doenças. A variabilidade genética observada para a resistência dos bovinos ao carrapato permite que essa característica seja melhorada geneticamente, como forma alternativa de controle desses ectoparasitos. Para a execução do presente trabalho, foi utilizado um estudo de associação genômica ampla (GWAS) para a resistência ao carrapato R. microplus, o qual foi realizado pela equipe do Dr. Fernando Flores Cardoso (Embrapa Pecuária Sul), com 260 animais da raça Hereford e 500 animais da raça Braford. O monitoramento das infestações foi realizado por meio da contagem de fêmeas do carrapato com tamanho superior a 4,5 mm em um dos lados do corpo do animal, e o grau de infestação de cada animal foi avaliado pela média de pelo menos duas contagens consecutivas, com intervalos de aproximadamente trinta dias, conduzidas no sobreano, nos meses de maior incidência do parasito. Os animais foram genotipados com utilização de um chip de SNPs de 50 K e, após a realização do GWAS, verificou-se que um total de 37.346 SNPs passou nos teste de qualidade. Dentre esses marcadores, 178 SNPs apresentaram efeitos significativos e permitiram a mineração de 175 genes nessas regiões, em um intervalo de 200 Kb (100 Kb para cada lado de cada marcador). A maioria dos polimorfismos associados com a característica está localizada em regiões sem funções determinadas (intergênicas e intrônicas), apenas um deles encontra-se em região de splicing. Sendo assim, estes marcadores podem constituir mutações não causais que se encontram em desequilíbrio de ligação com mutações funcionais. As regiões mais significativas do GWAS foram identificadas nos cromossomos 7, 21 e 23, onde foram identificados 72 genes em desequilíbrio de ligação com os marcadores moleculares. Portanto, foi realizada uma anotação funcional dos genes localizados nesses 3 cromossomos, o que permitiu a seleção de 11 genes candidatos para um estudo mais aprofundado das vias metabólicas nas quais eles estão inseridos. Verificou-se que esses genes participam de processos importantes em vias já relacionadas com a resistência a carrapatos, tais como apresentação de antígenos, transporte e secreção intracelular e diferenciação da epiderme.

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International audience

Phenotypic variation in natural populations results from a combination of genetic effects, environmental effects, and gene-by-environment interactions. Despite the vast amount of genomic data becoming available, many pressing questions remain about the nature of genetic mutations that underlie functional variation. We present the results of combining genome-wide association analysis of 41 different phenotypes in ~5,000 inbred maize lines to analyze patterns of high-resolution genetic association among of 28.9 million single-nucleotide polymorphisms (SNPs) and ~800,000 copy-number variants (CNVs). We show that genic and intergenic regions have opposite patterns of enrichment, minor allele frequencies, and effect sizes, implying tradeoffs among the probability that a given polymorphism will have an effect, the detectable size of that effect, and its frequency in the population. We also find that genes tagged by GWAS are enriched for regulatory functions and are ~50% more likely to have a paralog than expected by chance, indicating that gene regulation and neofunctionalization are strong drivers of phenotypic variation. These results will likely apply to many other organisms, especially ones with large and complex genomes like maize.

Taking advantage of the 600K Affymetrix® Axiom® HD genotyping array, the aim of this study is to detect QTL influencing egg quality traits in layers. A population of 438 sires from a pure line was genotyped. Their 31,381 F1 crossbred daughters were phenotyped for egg quality traits at 50 and 70 weeks of age. Moreover, to observe the putative existence of QTL by environment interactions, these layers were divided into 2 groups, fed with two different diets. The egg shell color and its components (redness, yellowness, lightness), the egg shell strength, stiffness and shape, the short length of egg and the egg weight were recorded. GWAS analyses have been showed 13,547 SNP with a significant (1% chromosome wide level) association with at least one egg quality trait. Thus, QTL have been detected and genotype by environment interactions have been observed.

Dissertação de Mestrado em Biologia Humana e Ambiente apresentada à Faculdade de Ciências de Universidade de Lisboa, 2012. Dissertação defendida e aprovada em 12 de Dezembro de 2012. Trabalho de investigação realizado no Departamento de Promoção da Saúde e Prevenção de Doenças não Transmissíveis, do Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Grupo de Neurogenética e Saúde Mental (Setembro 2011 – Setembro 2012). Astrid Moura Vicente: Departamento de Promoção da Saúde e Prevenção de Doenças não Transmissíveis do Instituto Nacional de Saúde Doutor Ricardo Jorge, IP. O Acidente Vascular Cerebral (AVC) é um evento neurológico agudo resultante de uma doença cardiovascular, no qual a afluência de sangue ao cérebro se vê comprometida, seja por um bloqueio ou por uma ruptura num vaso sanguíneo cerebral. Esta doença representa uma das principais causas de morte e morbilidade em todo o mundo, pelo que o estudo das componentes ambientais e genéticas nela envolvidas se torna fundamental para a implementação de planos de prevenção que visem minimizar as suas consequências. Com vista a contribuir para o desenvolvimento do estudo das variantes genéticas implicadas quer na susceptibilidade, quer na recuperação após um AVC, os objectivos deste estudo foram os de, por um lado, estudar a relevância do Single Nucleotide Polymorphism (SNP) rs1229984 do gene ADH1B sobre o risco de AVC e, por outro, identificar novos polimorfismos envolvidos no processo de recuperação. Recorrendo a um TaqMan® Drug Metabolism Genotyping Assay foi feita uma análise comparativa de dois grupos de indivíduos, um grupo saudável (controlos) e outro de doentes que sofreram AVC (casos) e verificou-se que o SNP rs1229984 do gene ADH1B, implicado no metabolismo do álcool, está, de facto, envolvido na susceptibilidade ao AVC. Porém, a mediação desta relação pelo consumo de álcool não se verificou, pelo que se sugere a replicação do estudo. Tendo por base um rastreio genómico previamente efectuado através de um Genome Wide Association Study (GWAS) em pooled samples, cujo objectivo era a identificação de genes envolvidos na recuperação após um AVC, realizou-se um novo estudo acerca da recuperação após um AVC, como mesmo objectivo. Seleccionaram-se diversos SNPs segundo critérios bem definidos (e distintos do primeiro estudo), para genotipagem individual, através de ferramentas como Sequenom iPLEX e TaqMan® Pre-Designed SNP Genotyping Assays e Restriction Fragment Lenght Polymorphism (RFLP), em grupos de indivíduos com recuperação desigual três meses após um AVC. Este estudo permitiu identificar um novo gene candidato envolvido na recuperação, o CDKAL1 e confirmar o potencial envolvimento do gene BBS9 no mesmo processo, o qual já tinha sido identificado anteriormente como gene associado à recuperação. Foi também possível aferir alguns aspectos relacionados com a interpretação dos resultados de um GWAS em pooled samples, nomeadamente acerca da importância das réplicas da formação dos pools e das réplicas de alelotipagem e acerca da necessidade de validação dos resultados por genotipagem individual. Tendo em conta a identificação de genes candidatos para a recuperação após um AVC, sugere-se que sejam desenvolvidos trabalhos futuros, nomeadamente estudos funcionais, no sentido de compreender as vias através das quais os referidos genes actuarão sobre o processo de recuperação após um AVC. Estudos de replicação em outras populações são também aconselhados, para validação das conclusões tiradas neste estudo. [eng] Pre-Designed SNP Genotyping Assays e Restriction Fragment Lenght Polymorphism (RFLP), em grupos de indivíduos com recuperação desigual três meses após um AVC. Este estudo permitiu identificar um novo gene candidato envolvido na recuperação, o CDKAL1 e confirmar o potencial envolvimento do gene BBS9 no mesmo processo, o qual já tinha sido identificado anteriormente como gene associado à recuperação. Foi também possível aferir alguns aspectos relacionados com a interpretação dos resultados de um GWAS em pooled samples, nomeadamente acerca da importância das réplicas da formação dos pools e das réplicas de alelotipagem e acerca da necessidade de validação dos resultados por genotipagem individual. Tendo em conta a identificação de genes candidatos para a recuperação após um AVC, sugere-se que sejam desenvolvidos trabalhos futuros, nomeadamente estudos funcionais, no sentido de compreender as vias através das quais os referidos genes actuarão sobre o processo de recuperação após um AVC. Estudos de replicação em outras populações são também aconselhados, para validação das conclusões tiradas neste estudo. Stroke is an acute neurological event resulting from a cardiovascular disease in which the blood supply to the brain gets compromised either by a blockage or a rupture in a cerebral blood vessel. This disease is a significant cause of death and disability worldwide, thus the study of genetic and environmental variants involved in stroke susceptibility and outcome becomes essential to allow the implementation of effective prevention plans aiming to minimize its consequences. To contribute to the study of genetic variants involved in stroke susceptibility or stroke recovery, the main objectives of this study were to determine the relevance of the ADH1B gene in stroke risk and to identify new genetic variants involved in stroke recovery. Using a TaqMan® Drug Metabolism Genotyping Assay we compared genotypes at the rs1229984 within ADH1B gene in a group of healthy individuals with a group of stroke patients and found that ADH1B gene, which is involved in alcohol metabolism, is associated with stroke susceptibility. We progressed with the analysis of a previous Genome Wide Association Study (GWAS) for stroke recovery in pooled samples. Several most relevant Single Nucleotide Polymorphisms (SNPs) were selected according to well defined criteria and were individually genotyped in groups of individuals with good and poor outcome at three months evaluation. Genotyping was performed using Sequenom iPLEX, TaqMan® Pre- Designed SNP Genotyping Assays and Restriction Fragment Lenght Polymorphism (RFLP). This study allowed the identification of a new candidate gene involved in stroke recovery, CDKAL1, and also allowed to confirm the involvement of a previously identified candidate gene BBS9 in the same process. It was also possible to assess some aspects related to the interpretation of the results of a GWAS in pooled samples that are important for the wider use of this technology in genomic studies. Given the identification of candidate genes, we suggest the development of future studies, including functional studies in order to understand which pathways of recovery the candidate genes affect. Replication in other populations is also suggested as a mean of validating the conclusions drawn in this study.

Due to decreasing costs of sequencing and genotyping, genome-wide association studies (GWAS) are becoming a standard approach for studying the genetics of natural variation. A major problem in such studies is the complicated dependencestructure of the data. Mixed models have emerged as a general and flexible approach for dealing with this problem. Here we extend this approach to handle correlated phenotypes by deriving a fully parameterized multi-trait mixed model (MTMM) that considers simultaneously both the within- and between-trait variance components for multiple traits. Phenotypic correlation can be due to either a common genetic architecture (pleiotropy) or to a common environmental effect. Dissecting these different causes is of interest not only because of the importance of understanding pleiotropy, but also because we may expect increased power compared to marginal analyses. To illustrate the utility of the MTMM for traits that are correlated, we reanalyzed data obtained for a set of geographically diverse ecotypes, which were grown in replicated common garden experiments in four European field sites. This data have been used successfully before to access the genetic basis for local adaptation and contain both: data for multiple phenotypes measured in the same environment, and measurements of the same phenotypes in different environments. Here we show how the genetic and environmental contribution to a specific trait can be assessed through the use of MTMM. Additionally we report newly associated markers improving our global understanding of both genetic and environmental variation on life-history traits.

The Venous Thromboembolism (VTE) risk factors are environmental and genetic. The well established risk factors are anti-thrombin, protein C, protein S deficiency, Factor V Leiden and factor II mutation and ABO gene, with A1 and B allele increasing the risk of VTE. While an important part of VTE heritability remains unexplained, contemporary studies fail to discover new susceptibility genes with weaker effects. In order to increase the discovery power, I searched for genetic geterminism of two intermediary phenotypes of VTE : Factor VIII plasmatic activity (FVIII) and von Willebrand factor antigenemia (vWF)First, I performed a linkage study of FVIII and vWF from a sample of 5 large pedigrees (N=255). Four loci have been identified. One included ABO gene. I searched for candidate genes located in the others loci by studying in silico results from o Genome Wide Association Study (GWAS) of the VTE including 419 cases and and 1228 controls. témoins. Two candidate genes were identified : STAB2 et BAI3. Then I performed association studies of five SNPs in BAI3 with FVIII and vWF. One of them was associated to vWF (in a sample of 108 nuclear families and 916 VTE patients), and associated to VTE in two case-controls samples (respectively 916 cases and 801 controls, and 250 cases et 607 controls).Second, I performed a meta-analysis of three GWAS of FVIII and vWF from the same 5 pedigrees and two samples of VTE (N=972 and 570) adjusted on ABO blood group. No polymorphisms were significant after Bonferoni correction (p