Candidate Genes In Pathways Research Articles

Comparative transcriptome analysis of roots, stems and leaves of Isodon amethystoides reveals candidate genes involved in Wangzaozins biosynthesis

BackgroundIsodon amethystoides (Ben-th) Cy Wu et Hsuan is an important traditional medicinal plant endowed with pharmacological properties effective in the treatment of various diseases, including pulmonary tuberculosis. The tetracyclic diterpenoids, Wangzaozins (Wangzaozin A, glaucocalyxin A, glaucocalyxin B), are the major bioactive compounds of I. amethystoides. However, the molecular information about the biosynthesis of these compounds still remains unclear.ResultsAn examination of the accumulated levels of Wangzaozins in I. amethystoides revealed considerable variations in the root, stem, and leaf tissues of this plant, indicating possible differences in metabolite biosynthesis and accumulation among various tissues. To better elucidate the tetracyclic diterpenoid biosynthesis pathway, we generated transcriptome sequences from the root, stem, and leaf tissues, and performed de novo sequence assembly, yielding 230,974 transcripts and 114,488 unigenes, with average N50 lengths of 1914 and 1241 bp, respectively. Putative functions could be assigned to 73,693 transcripts (31.9%) based on BLAST searches against annotation databases, including GO, KEGG, Swiss-Prot, NR, and Pfam. Moreover, the candidate genes involving in the diterpenoid biosynthesis, such as CPS, KSL, were also analyzed. The expression profiles of eight transcripts, involving the tetracyclic diterpenoid biosynthesis, were validated in different I. amethystoides tissues by qRT-PCR, unraveling the gene expression profile of the pathway. The differential expressions of ISPD, ISPF and ISPH (MEP pathway), and IaCPS and IaKSL (diterpenoid pathway) candidate genes in leaves and roots, may contribute to the high accumulation of Wangzaozins in I. amethystoides leaves.ConclusionThe genomic dataset and analyses reported here lay the foundations for further research on this important medicinal plant.

Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne).

Revealing DNA sequence variation within the Lolium perenne genepool is important for genetic analysis and development of breeding applications. We reviewed current literature on plant development to select candidate genes in pathways that control agronomic traits, and identified 503 orthologues in L. perenne. Using targeted resequencing, we constructed a comprehensive catalogue of genomic variation for a L. perenne germplasm collection of 736 genotypes derived from current cultivars, breeding material and wild accessions. To overcome challenges of variant calling in heterogeneous outbreeding species, we used two complementary strategies to explore sequence diversity. First, four variant calling pipelines were integrated with the VariantMetaCaller to reach maximal sensitivity. Additional multiplex amplicon sequencing was used to empirically estimate an appropriate precision threshold. Second, a de novo assembly strategy was used to reconstruct divergent alleles for each gene. The advantage of this approach was illustrated by discovery of 28 novel alleles of LpSDUF247, a polymorphic gene co-segregating with the S-locus of the grass self-incompatibility system. Our approach is applicable to other genetically diverse outbreeding species. The resulting collection of functionally annotated variants can be mined for variants causing phenotypic variation, either through genetic association studies, or by selecting carriers of rare defective alleles for physiological analyses.

ATRA reduces inflammation and improves alveolar epithelium regeneration in emphysematous rat lung

Pulmonary emphysema characterized by alveolar wall destruction is resultant of persistent chronic inflammation. All-trans retinoic acid (ATRA) has been reported to reverse elastase-induced emphysema in rats. However, the underlying molecular mechanisms are so far unknown. To investigate the therapeutic potential effect of ATRA via the amelioration of the ERK/JAK-STAT pathways in the lungs of emphysematous rats. In silico analysis was done to find the binding efficiency of ATRA with receptor and ligands of ERK & JAK-STAT pathway. Emphysema was induced by porcine pancreatic elastase in Sprague-Dawley rats and ATRA was supplemented as therapy. Lungs were harvested for histopathological, genomics and proteomics analysis. In silico docking, analysis confirms that ATRA interferes with the normal binding of ligands (TNF-α, IL6ST) and receptors (TNFR1, IL6) of ERK/JAK-STAT pathways respectively. ATRA restored the histology, proteases/antiproteases balance, levels of inflammatory markers, antioxidants, expression of candidate genes of ERK and JAK-STAT pathways in the therapy group. ATRA ameliorates ERK/JAK-STAT pathway in emphysema condition, resulting in alveolar epithelium regeneration. Hence, ATRA may prove to be a potential drug in the treatment of emphysema.

Gene expression profiles of glomerular endothelial cells support their role in the glomerulopathy of diabetic mice

Endothelial dysfunction promotes the pathogenesis of diabetic nephropathy (DN), which is considered to be an early event in disease progression. However, the molecular changes associated with glomerular endothelial cell (GEC) injury in early DN are not well defined. Most gene expression studies have relied on the indirect assessment of GEC injury from isolated glomeruli or renal cortices. Here, we present transcriptomic analysis of isolated GECs, using streptozotocin-induced diabetic wildtype (STZ-WT) and diabetic eNOS-null (STZ-eNOS-/-) mice as models of mild and advanced DN, respectively. GECs of both models in comparison to their respective nondiabetic controls showed significant alterations in the regulation of apoptosis, oxidative stress, and proliferation. The extent of these changes was greater in STZ-eNOS-/- than in STZ-WT GECs. Additionally, genes in STZ-eNOS-/- GECs indicated further dysregulation in angiogenesis and epigenetic regulation. Moreover, a biphasic change in the number of GECs, characterized by an initial increase and subsequent decrease over time, was observed only in STZ-eNOS-/- mice. This is consistent with an early compensatory angiogenic process followed by increased apoptosis, leading to an overall decrease in GEC survival in DN progression. From the genes altered in angiogenesis in STZ-eNOS-/- GECs, we identified potential candidate genes, Lrg1 and Gpr56, whose function may augment diabetes-induced angiogenesis. Thus, our results support a role for GEC in DN by providing direct evidence for alterations of GEC gene expression and molecular pathways. Candidate genes of specific pathways, such as Lrg1 and Gpr56, can be further explored for potential therapeutic targeting to mitigate the initiation and progression of DN.

Case-only analyses for identifying genotypes that modify the effect of finasteride in the Prostate Cancer Prevention Trial (PCPT): SWOG S9217.

1551Background: The Prostate Cancer Prevention Trial (PCPT) reported decreased risk of all prostate cancers but increased risk of high-grade prostate cancer in the finasteride arm. The aim of the present analysis was to identify genotypes that modify the effect of finasteride using case-only methods for estimating gene-treatment interactions. Methods: Germline genetic data from 1157 prostate cancer cases in the Prostate Cancer Prevention Trial (PCPT, NCT00288106) were analyzed by case-only methods. Genotypes included 357 single nucleotide polymorphisms (SNPs) from 83 candidate genes in androgen metabolism, inflammation, circadian rhythm and other pathways. Univariate case-only analysis was conducted to evaluate whether individual SNPs modified the finasteride effect on the risk of high-grade and low-grade prostate cancer. Case-only classification trees and random forests, which are powerful machine learning methods with resampling-based controls for model complexity, were employed to identify a predictive...

Transcriptomic Profiles of Brain Provide Insights into Molecular Mechanism of Feed Conversion Efficiency in Crucian Carp (Carassius auratus).

Feed efficiency is an economically crucial trait for cultured animals, however, progress has been scarcely made in the genetic analyses of feed conversion efficiency (FCE) in fish because of the difficulties in measurement of trait phenotypes. In the present investigation, we present the first application of RNA sequencing (RNA-Seq) combined with differentially expressed genes (DEGs) analysis for identification of functional determinants related to FCE at the gene level in an aquaculture fish, crucian carp (Carassius auratus). Brain tissues of six crucian carp with extreme FCE performances were subjected to transcriptome analysis. A total of 544,612 unigenes with a mean size of 644.38 bp were obtained from Low- and High-FCE groups, and 246 DEGs that may be involved in FCE traits were identified in these two groups. qPCR confirmed that genes previously identified as up- or down-regulated by RNA-Seq were effectively up- or down-regulated under the studied conditions. Thirteen key genes, whose functions are associated with metabolism (Dgkk, Mgst3 and Guk1b), signal transduction (Vdnccsa1b, Tgfα, Nr4a1 and Tacr2) and growth (Endog, Crebrtc2, Myh7, Myh1, Myh14 and Igfbp7) were identified according to GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations. Our novel findings provide useful pathway information and candidate genes for future studies of genetic mechanisms underlying FCE in crucian carp.

659: Genetic variation and recurrent prematurity among women receiving 17-alpha hydroxyprogesterone caproate for the prevention of recurrent preterm birth

17-alpha-hydroxyprogesterone caproate (17P) reduces recurrent preterm birth (PTB) in some, but not all, women. We hypothesized that genetic polymorphisms affect variable response to 17P for the prevention of recurrent PTB. Prospective cohort of women with ≥1 prior singleton SPTB 16-36 weeks, recruited prospectively from a PTB prevention clinic over a 3 year period at a single tertiary referral center. This planned nested cohort analysis included the subset of women who received weekly 17P. Women were classified as a 17P responder or non-responder based on the difference in delivery GA between their 17P-treated and 17P untreated pregnancy. Non-responders were those delivering <3 weeks of the GA of their earliest prior PTB, and responders delivered ≥ 3 weeks later with 17P. Women were genotyped for single nucleotide polymorphisms (SNPs) from candidate genes in immunomodulatory, steroid hormone, and collagen pathways using the Illumina Infinium Global Screening Array. Logistic regression models evaluated the association between genotype (additive inheritance), clinical variables, and 17P responder status, using Plink v. 1.9. We adjusted models a priori for black race and 3rd trimester vaginal bleeding. 175 women met inclusion criteria; 27 (15%) were non-responders. The GA of each participant’s earliest PTB differed by responder status (median 26 wks for responders vs. 35 wks for non-responders, p<0.001), and responders achieved a median +11 wks longer with 17P, versus +1 wk for non-responders (p<0.001). Non-responders were more likely to have vaginal bleeding in the third trimester (25.9% vs. 10.8%, p=0.03). Similar proportions of responders and non-responders were black, had multiple previous PTB, smoked, and had a short cervix <20mm. All SNPs met quality control filters. We evaluated 18 SNPs in 9 genes (PGR, CYP3A5, IL6ST, NOS2, FLT1, COL5A1, MMP9, COL9A1, ESR2) and did not find any significant associations between maternal genotype and 17P response status (Table). Maternal genotype was not associated with non-response to 17P in this high-risk cohort of women with at least one prior SPTB. Pregnancy outcomes in women receiving 17P remain difficult to predict using clinical and genetic data.

Association of genetic variants with fatigue in patients with malignant glioma.

Fatigue is a consistently reported, severe symptom among patients with gliomas throughout the disease trajectory. Genomic pathways associated with fatigue in glioma patients have yet to be identified. Clinical factors (performance status, tumor details, age, gender) were collected by chart review on glioma patients with fatigue ("I have lack of energy" on Functional Assessment of Cancer Therapy-Brain), as well as available genotyping data. Candidate genes in clock and inflammatory pathways were identified from a literature review, of which 50 single nucleotide polymorphisms (SNPs) in 7 genes were available. Clinical factors and SNPs identified by univariate analyses were included in a multivariate model for moderate-severe fatigue. The study included 176 patients (median age = 47 years, 67% males). Moderate-severe fatigue was reported by 43%. Results from multivariate analysis revealed poor performance status and 2 SNPs were associated with fatigue severity. Moderate-severe fatigue was more common in patients with poor performance status (OR = 3.52, P < .01). For each additional copy of the minor allele in rs934945 (PER2) the odds of fatigue decreased (OR = 0.51, P < .05). For each additional copy of the minor allele in rs922270 (ARTNL2) the odds of fatigue increased (OR = 2.38, P < .01). Both of these genes are important in the circadian clock pathway, which has been implicated in diurnal preference, and duration and quality of sleep. No genes in the inflammatory pathway were associated with fatigue in the current study. Identifying patients at highest risk for fatigue during treatment allows for improved clinical monitoring and enrichment of patient selection for clinical trials.

Shikonin changes the lipopolysaccharide-induced expression of inflammation-related genes in macrophages.

We aimed to find candidate molecules possibly involved in the anti-inflammatory activity of shikonin (active compound of "Shikon") by analyzing its effects on gene expression of lipopolysaccharide (LPS)-treated THP-1 macrophages. Polysome-associated mRNAs (those expected to be under translation: translatome) from cells treated with LPS alone (LPS: 5µg/mL), shikonin alone (S: 100nM), or LPS plus shikonin (LPS&S) for 3h were analyzed by DNA microarray followed by detection of enriched pathways/gene ontologies using the tools of the STRING database. Candidate genes in enriched pathways in the comparison of LPS&S cells vs. LPS cells were analyzed by reverse-transcription quantitative real-time PCR (RT-qPCR; 1, 2, and 3 h). DNA microarray showed shikonin significantly influences gene expression. Gene expression changes between LPS&S cells and LPS cells were compared to detect relevant proteins and/or mRNAs underlying its anti-inflammatory effects: shikonin downregulated pathways which were upregulated in LPS cells, for example, 'innate immune response'. Within changed pathways, three genes were selected for RT-qPCR analyses as key candidates influencing inflammatory responses: CYBA (component of the superoxide-generating Nox2 enzyme), GSK3B (controller of cell responses after toll-like receptor stimulation), and EIF4E (a key factor of the eukaryotic translation initiation factor 4F complex that regulates abundance of other proteins involved in immune functions). All three mRNAs were decreased at 2 h, and CYBA continued low at 3 h relative to LPS cells. Given that shikonin decreased the expression of CYBA gene of Nox2, in addition to the direct inhibition of the Nox2 activity that we have previously shown, it is suggested that one of its anti-inflammatory mechanisms could be attenuation of oxidative stress.

Regulating the Regulators in Attention-Deficit/Hyperactivity Disorder: A Genetic Association Study of microRNA Biogenesis Pathways.

Attention-deficit/hyperactivity disorder (ADHD) is one of the most prevalent complex psychiatric disorders in children as well as adults. ADHD impacts not only the affected individuals but also their families and social and professional networks. The clinical and diagnostic criteria for ADHD remain imprecise, in part, due to lack of robust biomarkers. ADHD comprises multiple subsets of diseases that present a shared set of downstream clinical findings, while displaying extensive molecular heterogeneity. This calls for innovation in diagnostic strategies that can help establish an ADHD diagnosis unequivocally as well as guiding precision medicine in this common mental health disorder. No study has examined, to the best of our knowledge, the upstream regulation of miRNAs that impact the downstream final ADHD phenotype. The latter focus on putative genetic biomarkers that regulate the regulators and can be tested empirically, for example, through genetic association analyses of the biogenesis pathways for miRNAs that impact the ADHD phenotype. Hence, we report here polymorphic variation in 10 miRNA biogenesis pathway candidate genes, including RNASEN, DGCR8, XPO5, RAN, DICER1, TARBP2, AGO1, AGO2, GEMIN3, and GEMIN4, in a large sample from the Eastern Mediterranean region (N = 355; 191 cases and 164 controls). We found that AGO1 rs595961 was significantly associated with ADHD susceptibility (p < 0.05). While polymorphic variation in other miRNA biogenesis pathway genes did not display a significant association in the present sample, the observations reported herein on miRNA biogenesis variation offer a new avenue of research for innovation in biomarker discovery concerning ADHD and other complex psychiatric diseases with major global health burden.

XPG Asp1104His, XRCC2 Rs3218536 A/G and RAD51 135G/C Gene Polymorphisms and Colorectal Cancer Risk: A Meta-Analysis

Background:DNA repair mechanisms are crucial for sustaining DNA integrity and preventing carcinogenesis. The xeroderma pigmentosum group G (XPG), X-ray repair cross complementing group 2 (XRCC2) and RAD51 are candidate genes for DNA repair pathways.Methods:We performed a meta-analysis of 26 studies that assessed the impact of XPG Asp1104His, XRCC2 rs3218536 A/G and RAD51 135G/C polymorphisms on colorectal cancer (CRC) risk. This study included 10288 CRC patients and 11885 controls, and odds ratio (OR) with its 95% confidence interval (CI) were used to calculate the strength of association.Results:The results of overall meta-analysis suggested an association between the XPG Asp1104His polymorphism and CRC susceptibility in allele (OR=1.06; 95% CI=1.01-1.12) and heterozygote model (OR=1.16; 95%CI=1.02-1.31). In the subgroup analysis based on ethnicity and source of control, we found significantly increased CRC cancer risk in Asians (OR=1.12, 95%CI=1.04-1.21) and in hospital-based (OR=1.22, 95%CI=1.08-1.38) populations. Moreover, the RAD51 135 G/C polymorphism increased the risk of CRC in total using allele (OR=1.21) and recessive models (OR=1.62). However, XRCC2 rs3218536 A/G was not associated with the risk of CRC in total or in subgroups.Conclusions:According to the results of our meta-analysis, the XPG Asp1104His and RAD51 135 G/C polymorphisms might influence colorectal cancer risk.

Identifying High-Risk CLL to Predict Early Relapse after FCR Based Treatment Using Whole Genome Sequencing: First Results from the Genomics England CLL Pilot

BackgroundChemo-immunotherapy (CIT) with fludarabine, cyclophosphamide, and rituximab (FCR) is the standard of care in frontline treatment of CLL. With this approach, 25% of patients relapse within 24 months, whereas approximately one third of patients with hypermutated immunoglobulin heavy chains (IgHV) achieve a functional cure (Hallek et al. Lancet. 2010; Tam et al. Blood, 2014, Fischer et al, Blood 2015; Philip A. Thompson et al. Blood 2016). So far, mutations and/or deletions of TP53 remain the only predictive marker screened for in routine clinical practice, accounting for only one third of patients relapsing early after CIT. Recent next-generation sequencing (NGS) studies have revealed novel candidate predictors of early relapse including somatic mutations in RPS15 (Landau et al. Nature, 2015) and SAMHD1 (Clifford et al., submitted). Taken together with TP53disruption, these only occur in a subset of high-risk patients. Here, we present a comprehensive analysis of high-risk patients using Whole Genome Sequencing (WGS).Patients and MethodsUsing WGS we investigated 149 CLL patients from 5 national UK clinical trials: CLEAR (n=8), RIAltO (n=45), CLL 210 (n=22), ARCTIC (n=32) and AdMIRe (n=42). The two first line FCR-based clinical trials (ARCTIC and AdMIRe) were studied in most detail: 56 patients relapsed within 24 months; this group of patients will be referred to as high risk patients. Leukemia samples (peripheral blood) and germline samples (saliva) were collected for each patient. We performed WGS on the HiSeqX (Illumina). After read alignment, we detected somatic variants using Strelka 2.4.7 for small variants detection (SNV and InDels), Manta 0.28.0 for Structural variant (SV) detection, and Canvas 1.3.1 for Copy number variant (CNV) detection (Illumina). Non-coding regions were annotated with information from primary CLL, CLL cell lines and B-cell ENCODE databases. We interrogated the data at a gene scale and global level in order to identify patterns of early relapsing patients. Operative mutational signatures were analysed according to Alexandrov et al. (Nature, 2013). Putative regions of kataegis were calculated based on Lawrence et al. (Nature, 2013) and Alexandrov et al. (Nature, 2013).ResultsThe mean coverage for CLL tumour and germline samples was 105.2X and 33.7X, respectively. The analysis of the whole cohort highlighted 1,723,603 somatic SNVs (mean= 11,570/sample) and 555,179 InDels (mean= 3,726/sample). Somatic SNVs spectrum consisted mainly of C>T/G>A mutations (30% of total SNVs reported) as previously described. The analysis of 13,490 somatic functional SNVs and InDels revealed novel candidate genes as most commonly mutated in the cohort. In high-risk patients, we noticed an enrichment of mutations in known genes such as TP53, genes of the NF-κB pathway and novel candidate genes previously reported in other cancers. A specific analysis of the functional coding mutations of known CLL driver genes revealed ATM, SF3B1 and IGLL5 as most commonly mutated genes in FCR responders compared to TP53, RPS15 and EGR2 in high risk patients. In depth analysis of somatic non-coding regions also identified potential new candidate regions associated with early relapse. Next, we investigated 52,871 CNAs (mean= 380/sample) and 29,080 SVs (mean= 195/sample) and identified as expected del13q, del17p, del11q and tri12 as the most frequent aberrations. In addition, we identified SVs across genes of interest in CLL, for instance TP53, ATM and BIRC3. Finally, we performed global genome analyses with investigation of mutational signatures and kataegis analyses highlighting hypermutated candidate regions, including the previously described IGLL5gene.ConclusionHere we present initial analysis of WGS data on 149 CLL patients from 5 UK clinical trials. Different patterns of mutations between low and high risk clinical groups are suggested. More detailed analysis with greater numbers of samples is ongoing and will determine the true clinical significance of these preliminary findings. The possibility of using WGS to aid clinical decision-making is becoming a realistic goal. DisclosuresBecq:Illumina: Employment. He:Illumina: Employment. Pettitt:Celgene: Speakers Bureau; Gilead: Research Funding, Speakers Bureau; Roche: Research Funding, Speakers Bureau; Infinity: Research Funding. Hillmen:Pharmacyclics: Research Funding; Janssen: Honoraria, Research Funding; Roche: Honoraria, Research Funding; Gilead: Honoraria, Research Funding; Abbvie: Research Funding. Bentley:Illumina: Employment. Schuh:Gilead: Consultancy, Honoraria, Research Funding; Roche, Janssen, Novartis, Celgene, Abbvie: Consultancy, Honoraria.

Association of Variants in Candidate Genes with Lipid Profiles in Women with Early Breast Cancer on Adjuvant Aromatase Inhibitor Therapy

Aromatase inhibitors can exert unfavorable effects on lipid profiles; however, previous studies have reported inconsistent results. We describe the association of single-nucleotide polymorphisms (SNP) in candidate genes with lipid profiles in women treated with adjuvant aromatase inhibitors. We conducted a prospective observational study to test the associations between SNPs in candidate genes in estrogen signaling and aromatase inhibitor metabolism pathways with fasting lipid profiles during the first 3 months of aromatase inhibitor therapy in postmenopausal women with early breast cancer randomized to adjuvant letrozole or exemestane. We performed genetic association analysis and multivariable linear regressions using dominant, recessive, and additive models. A total of 303 women had complete genetic and lipid data and were evaluable for analysis. In letrozole-treated patients, SNPs in CYP19A1, including rs4646, rs10046, rs700518, rs749292, rs2289106, rs3759811, and rs4775936 were significantly associated with decreases in triglycerides by 20.2 mg/dL and 39.3 mg/dL (P < 0.00053), respectively, and with variable changes in high-density lipoprotein (HDL-C) from decreases by 4.2 mg/dL to increases by 9.8 mg/dL (P < 0.00053). Variants in CYP19A1 are associated with decreases in triglycerides and variable changes in HDL-C in postmenopausal women on adjuvant aromatase inhibitors. Future studies are needed to validate these findings, and to identify breast cancer survivors who are at higher risk for cardiovascular disease with aromatase inhibitor therapy.

The adaptive potential of subtropical rainbowfish in the face of climate change: heritability and heritable plasticity for the expression of candidate genes.

Whilst adaptation and phenotypic plasticity might buffer species against habitat degradation associated with global climate change, few studies making such claims also possess the necessary and sufficient data to support them. Doing so requires demonstration of heritable variation in traits affecting fitness under new environmental conditions. We address this issue using an emerging aquatic system to study adaptation to climate change, the crimson‐spotted rainbowfish (Melanotaenia duboulayi), a freshwater species from a region of eastern Australia projected to be affected by marked temperature increases. Captive born M. duboulayi of known pedigree were used to assess the long‐term effects of contemporary and 2070‐projected summer temperatures on the expression of genes previously identified in a climate change transcriptomics (RNA‐Seq) experiment. Nearly all genes responded to increasing temperature. Significant additive genetic variance explained a moderate proportion of transcriptional variation for all genes. Most genes also showed broad‐sense genetic variation in transcriptional plasticity. Additionally, molecular pathways of candidate genes co‐occur with genes inferred to be under climate‐mediated selection in wild M. duboulayi populations. Together, these results indicate the presence of existing variation in important physiological traits, and the potential for adaptive responses to a changing thermal environment.

Genome-wide association and high-resolution phenotyping link Oryza sativa panicle traits to numerous trait-specific QTL clusters.

Rice panicle architecture is a key target of selection when breeding for yield and grain quality. However, panicle phenotypes are difficult to measure and susceptible to confounding during genetic mapping due to correlation with flowering and subpopulation structure. Here we quantify 49 panicle phenotypes in 242 tropical rice accessions with the imaging platform PANorama. Using flowering as a covariate, we conduct a genome-wide association study (GWAS), detect numerous subpopulation-specific associations, and dissect multi-trait peaks using panicle phenotype covariates. Ten candidate genes in pathways known to regulate plant architecture fall under GWAS peaks, half of which overlap with quantitative trait loci identified in an experimental population. This is the first study to assess inflorescence phenotypes of field-grown material using a high-resolution phenotyping platform. Herein, we establish a panicle morphocline for domesticated rice, propose a genetic model underlying complex panicle traits, and demonstrate subtle links between panicle size and yield performance.

Circulating n-3 fatty acids and trans-fatty acids, PLA2G2A gene variation and sudden cardiac arrest.

Whether genetic factors influence the associations of fatty acids with the risk of sudden cardiac arrest (SCA) is largely unknown. To investigate possible gene-fatty acid interactions on SCA risk, we used a case-only approach and measured fatty acids in erythrocyte samples from 1869 SCA cases in a population-based repository with genetic data. We selected 191 SNP in ENCODE-identified regulatory regions of fifty-five candidate genes in fatty acid metabolic pathways. Using linear regression and additive genetic models, we investigated the association of the selected SNP with erythrocyte levels of fatty acids, including DHA, EPA and trans-fatty acids among the SCA cases. The assumption of no association in non-cases was supported by analysis of publicly available datasets containing over 8000 samples. None of the SNP-fatty acid associations tested among the cases reached statistical significance after correction for multiple comparisons. One SNP, rs4654990 near PLA2G2A, with an allele frequency of 0·33, was nominally associated with lower levels of DHA and EPA and higher levels of trans-fatty acids. The strongest association was with DHA levels (exponentiated coefficient for one unit (1% of total fatty acids), 0·90, 95% CI 0·85, 0·97; P=0·003), indicating that for subjects with a coded allele, the OR of SCA associated with one unit higher DHA is about 90% what it is for subjects with one fewer coded allele. These findings suggest that the associations of circulating n-3 and trans-fatty acids with SCA risk may be more pronounced in carriers of the rs4654990 G allele.

Endothelin-1 Pathway Polymorphisms and Outcomes in Pulmonary Arterial Hypertension.

Pulmonary arterial hypertension (PAH) is a progressive fatal disease. Variable response and tolerability to PAH therapeutics suggests that genetic differences may influence outcomes. The endothelin pathway is central to pulmonary vascular function, and several polymorphisms and/or mutations in the genes coding for endothelin (ET)-1 and its receptors correlate with the clinical manifestations of other diseases. To examine the interaction of ET-1 pathway polymorphisms and treatment responses of patients with PAH treated with ET receptor antagonists (ERAs). A total of 1,198 patients with PAH were prospectively enrolled from 45 U.S. and Canadian pulmonary hypertension centers or retrospectively from global sites participating in the STRIDE (Sitaxsentan To Relieve Impaired Exercise) trials. Comprehensive objective measures including a 6-minute-walk test, Borg dyspnea score, functional class, and laboratory studies were completed at baseline, before the initiation of ERAs, and repeated serially. Single-nucleotide polymorphisms from ET-1 pathway candidate genes were selected from a completed genome-wide association study performed on the study cohort. Patient efficacy outcomes were analyzed for a relationship between ET-1 pathway polymorphisms and clinical efficacy using predefined, composite positive and negative outcome measures in 715 European descent samples. A single-nucleotide polymorphism (rs11157866) in the G-protein alpha and gamma subunits gene was significantly associated, accounting for multiple testing, with a combined improvement in functional class and 6-minute-walk distance at 12 and 18 months and marginally significant at 24 months. ET-1 pathway associated polymorphisms may influence the clinical efficacy of ERA therapy for PAH. Further prospective studies are needed.

Characterization of the Transcriptome of the Xerophyte Ammopiptanthus mongolicus Leaves under Drought Stress by 454 Pyrosequencing.

Background Ammopiptanthus mongolicus (Maxim. Ex Kom.) Cheng f., an endangered ancient legume species, endemic to the Gobi desert in north-western China. As the only evergreen broadleaf shrub in this area, A. mongolicus plays an important role in the region’s ecological-environmental stability. Despite the strong potential of A. mongolicus in providing new insights on drought tolerance, sequence information on the species in public databases remains scarce. To both learn about the role of gene expression in drought stress tolerance in A. mongolicus and to expand genomic resources for the species, transcriptome sequencing of stress-treated A. mongolicus plants was performed.ResultsUsing 454 pyrosequencing technology, 8,480 and 7,474 contigs were generated after de novo assembly of RNA sequences from leaves of untreated and drought-treated plants, respectively. After clustering using TGICL and CAP3 programs, a combined assembly of all reads produced a total of 11,357 putative unique transcripts (PUTs). Functional annotation and classification of the transcripts were conducted by aligning the 11,357 PUTs against the public protein databases and nucleotide database (Nt). Between control and drought-treated plants, 1,620 differentially expressed genes (DEGs) were identified, of which 1,106 were up-regulated and 514 were down-regulated. The differential expression of twenty candidate genes in metabolic pathways and transcription factors families related to stress-response were confirmed by quantitative real-time PCR. Representatives of several large gene families, such as WRKY and P5CS, were identified and verified in A. mongolicus for the first time.ConclusionsThe additional transcriptome resources, gene expression profiles, functional annotations, and candidate genes provide a more comprehensive understanding of the stress response pathways in xeric-adapted plant species such as A. mongolicus.

Transcriptional responses of Norway spruce (Picea abies) inner sapwood against Heterobasidion parviporum.

The white-rot fungus Heterobasidion parviporum Niemelä & Korhonen establishes a necrotrophic interaction with Norway spruce (Picea abies (L.) H.Karst.) causing root and butt rot and growth losses in living trees. The interaction occurs first with the bark and the outer sapwood, as the pathogen enters the tree via wounds or root-to-root contacts. Later, when the fungus reaches the heartwood, it spreads therein creating a decay column, and the interaction mainly occurs in the inner sapwood where the tree creates a reaction zone. While bark and outer sapwood interactions are well studied, little is known about the nature of the transcriptional responses leading to the creation of a reaction zone. In this study, we sampled bark and sapwood both proximal and distal to the reaction zone in artificially inoculated and naturally infected trees. We quantified gene expression levels of candidate genes in secondary metabolite, hormone biosynthesis and signalling pathways using quantitative polymerase chain reaction. An up-regulation of mainly the phenylpropanoid pathway and jasmonic acid biosynthesis was found at the inoculation site, when inoculations were compared with wounding. We found that transcriptional responses in inner sapwood were similar to those reported upon infection through the bark. Our data suggest that the defence mechanism is induced due to direct fungal contact irrespective of the tissue type. Understanding the nature of these interactions is important when considering tree breeding-based resistance strategies to reduce the spread of the pathogen between and within trees.

Genetic association of key Th1/Th2 pathway candidate genes, IRF2, IL6, IFNGR2, STAT4 and IL4RA, with atopic asthma in the Indian population.

Asthma is a complex, multifactorial disease resulting due to dysregulated immune responses. Genetic factors contribute significantly to asthma pathogenesis, and identification of these factors is one of the major goals in understanding the disease. Th1/Th2 helper differentiation has a critical role in modulating the phenotypes associated with atopic asthma. This study was aimed at identifying genetic modifiers of asthma in selected genes involved in T helper differentiation. A total of 354 single-nucleotide polymorphisms (SNPs) in 33 candidate genes were genotyped in a case-control cohort (cases=147, controls=199) and families (n=247) using Illumina's Golden Gate Assay. Five SNPs, rs3733475A/C (IRF2), rs2069832A/G (IL6), rs2012075G/A (IFNGR2) and rs1400656G/A (STAT4) and rs1805011C/A (IL4RA) were found to be associated with asthma in family based as well as in case-control analyses (P=0.002, P=0.001, P=0.004, P=0.003 and P=0.001, respectively). Interestingly, the minor alleles at these loci showed a protective effect. A five loci haplotype, TAACG, in IRF2 gene, was significantly associated with asthma in families (P=1.1 × 10(-6)) and in case-control cohort (P=0.01). In conclusion, our studies led to identification of some key candidate genes, namely IRF2, IL6, IFNGR2, STAT4 and IL4RA that modulate genetic susceptibility to asthma in the Indian population. Also, this is the first report of independent association of IL6 gene polymorphism with atopic asthma.