Our study also provided evidence that the expression of PeWNK9 was significantly increased after all abiotic stress treatments. Similarly, the OsWNK1 gene was up-regulated after drought and cold stress and downregulated after salt stress Kumar et al. These results suggest that these proteins have similar functions and are predominantly involved in abiotic stress response.
In addition, our co-expression network analysis also revealed the relationship between abiotic stress genes and PeWNK genes. In the present study, we identified 41 WNK genes in five Bambusoideae species and analyzed the conserved motifs, domains, cis -acting elements, and tissue-specific expression studies. Transcriptome analysis of different abiotic stresses and co-expression analysis also revealed that PeWNK8 and PeWNK9 are involved in abiotic stress response. Thus, these genes can be used as good candidates for the production of genetically modified and economically important bamboo plants.
Conserved domains, motif and secondary structural arrangements were highlighted. The phosphorylation sites were mentioned in the yellow background. Common use cases Typos, corrections needed, missing information, abuse, etc. Our promise PeerJ promises to address all issues as quickly and professionally as possible. We thank you in advance for your patience and understanding. You can also choose to receive updates via daily or weekly email digests. If you are following multiple publications then we will send you no more than one email per day or week based on your preferences.
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Please enable Javascript to view PeerJ. Twitter Facebook Email. Share Twitter Facebook Email. Genome-wide identification and evolution of WNK kinases in Bambusoideae and transcriptional profiling during abiotic stress in Phyllostachys edulis. View article. Identification of WNK genes from P. Analysis of Cis -acting element We retrieved the upstream sequence region 2 Kb of the WNK genes from the genome database to analyse the cis -acting elements.
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Usage since published - updated daily. Arabidopsis RAP2. In soybean, ethylene treatment significantly enhanced the expression of GmERF3 , and the overexpression of GmERF3 in tobacco improved the salt and drought tolerance of transgenic lines Zhang et al. Therefore, we can conclude that the ethylene signalling pathway is involved in the response of JrERF s to drought stress.
The expression of JrERF11 reached the peak at 24 h 5. PbERF is involved in the regulation of genes related to plant hormones Pei et al. S3 , could be induced by drought stress and may function positively in drought stress Cao et al. Based on these findings, it can be speculated that JrERF11 is a potential useful gene for drought tolerance and its function should be further investigated. We found that the JrERF s were highly conserved and belonged to six groups. JrERF11 is the most prominently expressed gene and worthy of further study.
The result of our study can provide solid foundation for further investigation of JrERF s under multiple abiotic stresses and for exploring the molecular mechanism underlying abiotic stress responses in walnut and other woody plants. Common use cases Typos, corrections needed, missing information, abuse, etc. Our promise PeerJ promises to address all issues as quickly and professionally as possible. We thank you in advance for your patience and understanding.
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Twitter Facebook Email. Share Twitter Facebook Email. Genome-wide identification and expression analysis of ethylene responsive factor family transcription factors in Juglans regia. View article. In statin nonusers, C allele homozygotes at rs had a large absolute reduction in HbA 1c 0. We have identified clinically important genetic effects at genome-wide levels of significance, and important drug-drug-gene interactions, which include commonly prescribed statins.
With increasing availability of genetic data embedded in clinical records these findings will be important in prescribing glucose-lowering drugs. Sulfonylureas are potent glucose-lowering drugs that reduce HbA 1c by an average of 1. Despite an increasing trend to use more modern, expensive treatments, sulfonylureas remain commonly prescribed in the U.
Due to their very low cost, they are extensively used in low- and middle-income countries. It is likely that a combination of genetic and nongenetic modifying factors underlies the clinical variability of glycemic response to sulfonylureas.
While many clinical risk factors such as baseline HbA 1c , sex, duration of diabetes, and dose are associated with glycemic response to sulfonylureas 5 — 7 , modulatory genetic factors remain largely unexplored, with the exception of a few proof of concept studies with use of a candidate gene approach 8 — There have been no similar estimates for sulfonylurea response, and to date, no genome-wide association studies GWAS of glycemic response to sulfonylurea treatment have been reported, so the genetic contribution to how patients respond to sulfonylureas and clinical implication of this genetic variation have not been systematically studied.
Based on these findings we then explore the impact of interacting drugs and identify clinically important genotype-dependent statin-sulfonylurea interactions for this important class of diabetes therapies. List of abbreviations used throughout this article and their corresponding explanations are shown in Supplementary Table 1. Included participants had a clinical diagnosis of type 2 diabetes and were treated with sulfonylureas as monotherapy or as an add-on to metformin.
This study was approved by respective research ethics review boards, and participants provided written informed consent. Clinical, prescription, and biochemical data were retrieved from the electronic medical record systems. They were stably treated with sulfonylureas for at least 6 months with no other glucose-lowering drug started or stopped within the study period.
Baseline HbA 1c was defined as the HbA 1c measure closest to sulfonylurea initiation and within 6 months before and 7 days after this date. The treatment HbA 1c was the HbA 1c measure closest to 12 months after initiation of sulfonylureas between 6 and 15 months. In all the studies, covariates were selected based on previous reports and univariate association between the outcome variable HbA 1c reduction and explanatory variables.
The best fit linear regression model was determined using stepwise backward elimination. Accordingly, baseline HbA 1c , sex, age at diagnosis, baseline BMI, average daily dose, time between baseline HbA 1c and treatment HbA 1c , and drug group sulfonylurea monotherapy or sulfonylurea added to metformin were considered in the final model as available in each cohort Supplementary Table 3. Average daily dose was calculated as the mean daily dose of prescriptions filled during the study period mean of percentage of each sulfonylurea divided by maximum prescribable according to the British National Formulary.
Baseline weight was the measure nearest to the sulfonylurea start date index date and within days on either side of the index date. For each respective cohort genome-wide genotyping was performed on a variety of arrays as illustrated in Supplementary Table 3.
Genotyping data for each platform were individually cleaned by each study center. Standard postgenotyping quality control procedures were applied to each data set Supplementary Fig.
Genome-wide association analyses were carried out separately by respective study centers. Prior to meta-analysis, we performed post-GWAS harmonization and quality control of GWAS results from each cohort to track possible errors in the study-specific analyses.
We used the standard protocol accompanied by the EasyQC R package Meta-analysis was then performed with use of an inverse variance—weighted fixed-effects model, implemented in GWAMA v2.
Heterogeneity was assessed with the I 2 metric from the complete study-level meta-analysis. We used the commonly accepted threshold of 5.
The CMplot package 21 in R was used to generate Manhattan and quantile-quantile plots. Regional plots around genome-wide or suggestive genes were visualized using LocusZoom This method is a valid approach for estimating heritability in studies in which acquisition of data of family members with the same diagnosis who have received the same medication and were assessed with use of the same treatment outcome is not feasible.
Participants received a single dose of 5 mg glipizide followed by measurement of glucose and insulin levels at 30, 60, 90, , , and min. This was used to construct phenotypes of acute glipizide response. The association of rs and rs with glipizide response was assessed with linear regression with baseline glucose, age, sex, and the first 10 PCs as a covariate see Supplementary Notes.
Given we have identified a genetic variant in the SLCO1B1 a gene encoding hepatic transporter of statins associated with glycemic response to sulfonylureas, we checked for interaction between SLCO1B1 rs and statin use in a drug-drug-gene interaction model using linear regression, with HbA 1c reduction as the dependent variable. Statin-treated case subjects were recipients of sulfonylureas who were also prescribed statins for at least the 3 months prior to the measurement of treatment HbA 1c.
Statin untreated control subjects were those recipients of sulfonylureas who did not receive a statin prescription for at least 1 year prior to measurement of the treatment HbA 1c. Expression quantitative trait loci eQTL analysis seeks to identify genetic variants that affect the expression of one or more genes: a gene-SNP pair for which the expression of the gene is associated with the allelic configuration of the SNP is referred to as an eQTL.
The human liver eQTL lookups were carried out using data from a previous study performed by the group of F. In brief, this eQTL study was performed with 1, liver samples, combined from four data sets The human whole blood eQTL lookup was performed with use of data from the DIRECT consortium in a total of 3, subjects at high risk of developing type 2 diabetes or with recently diagnosed type 2 diabetes A detailed explanation of the eQTL analysis has previously been published 26 , and summary statistics are available DOI: Uptake studies were initiated after removal of 0.
For inhibition studies, the same methods above were used, where 3 H-glyburide was used as substrate and various concentrations of atorvastatin Cayman Chemical or simvastatin Cayman Chemical were added together with 3 H-glyburide. These cell lines were used to determine the uptake of 3 H-glyburide, 3 H-glipizide, and 3H-esterone sulfate as positive control. In brief, each well was transfected with ng DNA vector with 0. Uptake studies were then performed after 48 h with the methods described above and in triplicate wells.
Summary-level data that underlie the results reported in this article are available upon request to the corresponding author. This suggests that approximately one-third of the total variance of glycemic response to sulfonylureas is due to the additive effects of common variants.
Meta-GWAS identified two genome-wide significant variants, rs and rs, both on chromosome 12 Fig. Manhattan plot of genome-wide results from single marker association with glycemic response to sulfonylureas with use of an additive genetic model in a meta-analysis consisting of 5, individuals with type 2 diabetes on sulfonylureas. Regional association plots around genome-wide significant SNPs, rs left and rs right locus at chromosome 12, for the meta-GWAS. The purple diamonds in both plots indicate the top SNPs in the locus.
Indeed, some recent studies have also revealed that the expression levels of certain homoeologous genes are altered under heat tolerance, water stress, and iron deficiency in polyploid wheat 48 , 49 , Hence, homoeolog expression bias of pods and seeds of Raphanobrassica under different stresses still remains to be studied. ELD has also been widely explored in many resynthesized hybrids 13 , 15 , 17 , 51 , The parental genome toward which ELD of the synthetic hybrid biases is consistent with the similarity of phenotypes between the hybrid and parents.
For example, in our study, ELD of pods and seeds of R r R r C r C r showing preference toward CC is consistent with the fact that phenotypes of the whole silique of Raphanobrassica are similar to those of B. Hence, we could infer the ELD of the resynthesized hybrid by the similarity of the phenotypes between the progenitors and the hybrid.
In addition, there is different ELD biased expression in different organs within the same organism. For example, one previous study revealed that the gene in immature leaves of Raphanobrassica displays genome-wide ELD bias toward RR, which is different from that of the pods and seeds in the present study Intrigued, the ELD of different developmental stages of pods and seeds of Raphanobrassica still remains to be explored to comprehensively understand the relationships of global gene expression patterns between the hybrid and its two diploid progenitors.
Collectively, transcriptome shock was observed in the silique of Raphanobrassica due to the incorporation and interaction of the two parental genomes, which might lead to the split of the silique into two parts. The upper and lower sections of siliques of the hybrid exhibit expression profile differences, and the related genes are involved in different biological processes. Many more genes in the silique of Raphanobrassica exhibit homoeolog expression bias and expression level dominance toward B.
In conclusion, our mRNA transcriptome profiles are consistent with the observed phenotypes and unravel the tight correlation between the phenotypes and global gene expression patterns in the hybrid and its parents. Our results reported here provide a good reference to study plant polyploidy and mine potential candidate genes responsible for specific phenotypes. However, whether the phenotypes are tightly correlated with other multiomics data in the synthesized hybrid and its parents remains to be explored.
The diploid maternal R. All of the plant materials were planted in Wuhan, China. Whole pods Rsi and Csi , seeds Rse and Cse of siliques of the diploid progenitors, three sections of the whole pods RCsiu, RCsim, and RCsil and all seeds in the two sections of the siliques RCseu and RCsel of the hybrid, with three biological replicates of each sample, were obtained at 35 DAF for total mRNA isolation and sequencing library construction.
The aforementioned 27 sequencing libraries were sequenced on the Illumina HiSeq platform. The total clean reads of R. We also mapped the clean reads of R. The novel gene loci were predicted by StringTie 55 and annotated by the Pfam database For convenience, we considered that most of the homoeologs remained in a one-to-one relationship after polyploidization within the subgenomes of R r R r C r C r , although the homoeologous relationships are not necessarily one-to-one Based on this, we adopted the BBH method to infer homoeologs 61 , although this method has inherent drawbacks Thus, as shown in Fig.
In the process of homoeolog expression bias and ELD analyses, we only paid attention to the genes that were expressed in at least one progenitor and where both homoeologs were expressed in Raphanobrassica. C r C r in the process of homoeolog expression bias according to previously described methods Furthermore, twelve possible bins were classified according to Yoo et al. Moreover, only the first transcript was used when the gene had more than one transcript.
The expression level of mRNA was detected in the nine tissues of R. Sequencing data of R. Brenchley, R. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature , — Wang, M. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Chalhoub, B. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science , — Li, P. Genome-wide analysis of changes in miRNA and target gene expression reveals key roles in heterosis for Chinese cabbage biomass.
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