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The basic leucine zipper (bZIP) protein transcription factors are known to modulate development, plant growth, metabolic response, and resistance to several biotic and abiotic stressors and have been widely studied in the model plant Arabidopsis thaliana. However, no comprehensive information about the bZIP transcription factor family in Artemisia annua has been explored to date. In this genome-wide study, we identified 61 bZIP TFs after removing false positives and incomplete sequences from Artemisia annua. Seven highly expressed homolog AabZIP TF genes under UV-B and differential light conditions in different tissues were identified from the publicly available microarray dataset as having their cis-regulatory elements involved in, flavonoids biosynthesis, seed-specific gene regulation, stress responses, and metabolic regulation. In-silico analysis and electrophoretic mobility shift assay (EMSA) confirmed the interaction of AabZIP19 TF over the AaPAL1 promoter in order to regulate the phenolics and flavonoid biosynthesis via the phenylpropanoid pathway. Further, RT-PCR analysis has been carried out to validate the transcript levels of selected AabZIP genes under white light, red light, blue light (45 min), and UV-B exposure (12 and 24 h). These genes have their highest expression levels under UV-B and blue light exposure, in contrast with white light. Therefore, the detection of ROS through staining confirms the accumulation of superoxide radicals and H2O2, and in addition to reducing ROS accumulation under UV-B and blue light irradiation, total phenols and flavonoids are significantly enhanced. This study laid the groundwork for deciphering the possible role of AabZIP TFs under different light stress-responsive conditions and in the regulation of secondary metabolism. [ABSTRACT FROM AUTHOR]

Key message: Genome-wide identification, classification, functional characterization and expression analysis of Auxin Responsive Factor (ARF) gene family in wheat reveal their attributes and role during leaf rust infection. Auxins are important plant growth regulators that also impact plant-pathogen interaction. Auxin responsive factors (ARF) are plant specific transcription factors that control responses to auxins. Whole genome investigation of ARF gene family is limited in allohexaploid wheat (Triticum aestivum L.). Comprehensive study of this gene family was carried out by employing the currently available reference genome sequence of wheat. In total, 27 ARF genes were identified and located on the wheat genome as well as were positioned on wheat chromosome arms. Additionally, examination of the predicted genes unveiled a decent degree of relatedness within and among the phylogenetic clades. Leaf rust, caused by the obligate biotrophic fungal pathogen Puccinia triticina, is responsible for drastic loss of wheat crop worldwide reducing grain yield by 10–90%. Expression profiling of ARF genes in retort to leaf rust infection indicated their differential regulation during this plant-pathogen interaction. Highest expression of ARF genes were observed at 12 hpi that was maintained up to 72 hpi during incompatible interaction, whereas the high expression levels receded at 48 hpi during compatible interactions. Few of the identified ARF genes were likely to be post-transcriptionally regulated by microRNAs. Many light and stress responsive elements were detected in the promoter regions of ARF genes. Microsynteny analysis showed the conservation of ARF genes within the members of the Poaceae family. This study provides fundamental details for understanding the different types of ARF genes in wheat and there putative roles during leaf rust–wheat interaction. [ABSTRACT FROM AUTHOR]

Purpose: To synthesise data from genome-wide studies reporting molecular signature of eutopic endometrium through the phases of the menstrual cycle in endometriosis. Methods: Extraction of data from publications reporting genetic signatures characterising endometrium associated with endometriosis. The nomenclature of extracted differentially expressed transcripts and proteins was adopted according to the HUGO Gene Nomenclature Committee (HGNC). Loci were further sorted according to the different phases of the menstrual cycle, i.e. menstrual (M), proliferative (P), secretory (S), early-secretory (ES), mid-secretory (MS), late-secretory (LS), and not specified (N/S) if the endometrial dating was not available. Enrichment analysis was performed using the DAVID bioinformatics tool. Results: Altered molecular changes were reported by 21 studies, including 13 performed at the transcriptomic, 6 at proteomic, and 2 at epigenomic level. Extracted data resulted in a catalogue of total 670 genetic causes with available 591 official gene symbols, i.e. M = 3, P = 188, S = 81, ES = 82, MS = 173, LS = 36, and N/S = 28. Enriched pathways included oestrogen signalling pathway, extracellular matrix organization, and endothelial cell chemotaxis. Our study revealed that knowledge of endometrium biology in endometriosis is fragmented due to heterogeneity of published data. However, 15 genes reported as dysregulated by at least two studies within the same phase and 33 significantly enriched GO-BP terms/KEGG pathways associated with different phases of the menstrual cycle were identified. Conclusions: A multi-omics insight into molecular patterns underlying endometriosis could contribute towards identification of endometrial pathological mechanisms that impact fertility capacities of women with endometriosis. [ABSTRACT FROM AUTHOR]

MYB is one of the most abundant families of plant transcription factors (TFs), and is involved in plant growth and development regulation, abiotic stress tolerance, hormone signal transduction, and disease resistance. Previously, few genome-wide assays have been conducted in Lotus japonicas and Medicago truncatula. Here, with the recent release of the genome sequences, we performed genome-wide study of MYB TFs in both, including family characterization, evolution and expression analysis. In this study, we totally identified 104 and 166 MYB genes in L. japonicas and M. truncatula, respectively. All these MYB genes were categorized into 261 R2R3-MYBs, 7 R1R2R3-MYBs and 2 atypical MYB genes. This result showed that the majority (96.7%) of them belong to the R2R3-MYB subfamily in both species. Based on phylogenetic analysis, MYB transcription factors were divided into 14 subgroups. MYB genes in four typical branches indicated species-specific expansions in M. truncatula. The exon numbers and conserved motifs associated with MYB domains were also characterized. Furthermore, gene expression analysis performed in various organs showed diverged expression profiles of most MYB genes, suggesting their potential roles in regulating organ growth and development in L. japonicas and M. truncatula. [ABSTRACT FROM AUTHOR]

The genetics of coat color have been the focus of investigation for decades because beyond its aesthetic values, coat color is associated with thermo-tolerance, production and health traits. Despite the fascinating coat color phenotypes observed in Ethiopian cattle populations, up to now, there are no studies performed to identify and characterize polymorphisms associated with such variation at the genome level. In an attempt to identify and map the genetic basis of coat color variation in Ethiopian cattle, a genome-wide association study (GWAS), selection signatures test and network analysis were performed in 187 cattle populations genotyped on Illumina high-density chip. Loci significant at the genome-wide level (P ≤ 8.29 × 10) and show selection signals ( F − 5SNP window = 0.13) were mainly localized on BTA22 (31.53-31.99) within the MITF gene. Network and functional annotation clustering analyses revealed that the candidate genes are involved in important pathways including melanogenesis. The results of the present study suggest a role of the MITF gene and its interaction with other genes in determining the spotting patterns observed in the Begait and Fogera cattle populations. [ABSTRACT FROM AUTHOR]

While primary immune defects are generally considered to lead to severe and easily recognized disease in infants and children, a number of genetic defects impairing B cell function may not be clinically apparent or diagnosed until adult life. The commonest of these is common variable immune deficiency, the genetic origins of which are beginning to be at least partially understood. CVID affects ≈1/25,000 Caucasians and is characterized by a marked reduction in serum IgG, almost always in serum IgA, and reduced serum IgM in about half of all cases; these defects continue to provide an opportunity to investigate the genes necessary for B cell function in humans. Recently, a small number of genes necessary for normal B cell function have been identified in consanguineous families leading to varying degrees of hypogammaglobulinemia and loss of antibody production. In other studies, whole-exome sequencing and copy number variation, applied to large cohorts, have extended research into understanding both the genetic basis of this syndrome and the clinical phenotypes of CVID. [ABSTRACT FROM AUTHOR]

Biomedical researchers usually test the null hypothesis that there is no difference of the population mean of pharmacokinetics (PK) parameters between genotypes by the Kruskal–Wallis test. Although a monotone increasing pattern with a number of alleles is expected for PK-related genes, the Kruskal–Wallis test does not consider a monotonic response pattern. For detecting such patterns in clinical and toxicological trials, a maximum contrast method has been proposed. We show how that method can be used with pharmacogenomics data to a develop test of association. Further, using simulation studies, we compare the power of the modified maximum contrast method to those of the maximum contrast method and the Kruskal–Wallis test. On the basis of the results of those studies, we suggest rules of thumb for which statistics to use in a given situation. An application of all three methods to an actual genome-wide pharmacogenomics study illustrates the practical relevance of our discussion.The Pharmacogenomics Journal (2009) 9, 137–146; doi:10.1038/tpj.2008.17; published online 23 December 2008 [ABSTRACT FROM AUTHOR]

We recently reported a joint analysis of genome-wide association (GWA) data on 958 sporadic amyotrophic lateral sclerosis (ALS) cases and 932 controls from Ireland and the publicly available data sets from the United States and the Netherlands. The strongest pooled association was rs10260404 in the dipeptidyl-peptidase 6 (DPP6) gene. Here, we sought confirmation of joint analysis signals in both an expanded Irish and a Polish ALS cohort. Among 287 522 autosomal single-nucleotide polymorphisms (SNPs), 27 were commonly associated on joint analysis of the Irish, US and Dutch GWAs. These 27 SNPs were genotyped in an expanded Irish cohort (312 patients with SALS; 259 controls) and an additional Polish cohort (218 patients; 356 controls). Eleven SNPs, including rs10260404, reached a final P-value below 0.05 in the Irish cohort. In the Polish cohort, only one SNP, rs6299711, showed nominal association with ALS. Pooling of data for 1267 patients with ALS and 1336 control subjects did not identify any association reaching Bonferroni significance (P<1.74 × 10−7). The present strategy did not reveal any consistently associated SNP across four populations. The result for DPP6 is surprising, as it has been replicated elsewhere. We discuss the possible interpretations and implications of these findings for future ALS GWA studies both within and between populations.European Journal of Human Genetics (2009) 17, 213–218; doi:10.1038/ejhg.2008.194; published online 5 November 2008 [ABSTRACT FROM AUTHOR]