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- Berndt, Sonja I., et al.
(författare)
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Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:5, s. 501-U69
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Tidskriftsartikel (refereegranskat)abstract
- Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.
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- Mun, Bong-Gyu, et al.
(författare)
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Profile and time-scale dynamics of differentially expressed genes in transcriptome of Populus davidiana under drought stress
- 2017
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Ingår i: Plant Molecular Biology Reporter. - : Springer. - 0735-9640 .- 1572-9818. ; 35:6, s. 647-660
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Tidskriftsartikel (refereegranskat)abstract
- The genus Populus contains 25–35 species of deciduous flowering plants in the family Salicaceae. It has evolved to overcome various environmental stresses including drought stress through changes in physiological processes such a stomatal movement, photosynthesis, stress signaling, defense responses, and overall growth rate. In this study, we performed RNA-seq-based transcriptome profiling of Populus davidiana in response to drought stress induced by 10% PEG at two time points (6 and 12 h). We generated over 527 million reads by applying Populus trichocarpa as reference genome. Assembly of the reads yielded 32,650 genes and 75,820 transcripts; of these, after quantile normalization, a total of 997 genes were identified with dynamic expression over time, classifying them into nine different clusters. Among them, 550 genes responded significantly to drought stress treatment after 6 h (108 genes up-regulated and 201 genes down-regulated) and 12 h (161 up-regulated and 80 down-regulated) respectively, with at least twofold change in their expression. Based on analysis of these genes, we found several differentially expressed genes (DEGs) involved in cellular transport, transcriptional regulation, protein modification, regulation of cellular redox state, and those involved in response to other stresses. We also validated RNA-seq-mediated transcriptome data by RT-qPCR analysis of eight randomly selected DEGs. It showed significantly high correlation coefficient (0.95) suggesting high reliability of RNA-seq analysis. This study presents the first RNA-seq mediated transcriptome profile of P. davidiana in response to drought stress, providing critical information necessary for understanding the mechanisms underpinning drought stress tolerance in forest trees and other plant species.
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- Sharma, Arti, et al.
(författare)
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Comprehensive analysis of plant rapid alkalization factor (RALF) genes
- 2016
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Ingår i: Plant physiology and biochemistry (Paris). - : Elsevier. - 0981-9428 .- 1873-2690. ; 106, s. 82-90
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Tidskriftsartikel (refereegranskat)abstract
- Receptor mediated signal carriers play a critical role in the regulation of plant defense and development. Rapid alkalization factor (RALF) proteins potentially comprise important signaling components which may have a key role in plant biology. The RALF gene family contains large number of genes in several plant species, however, only a few RALF genes have been characterized to date. In this study, an extensive database search identified 39, 43, 34 and 18 RALF genes in Arabidopsis, rice, maize and soybean, respectively. These RALF genes were found to be highly conserved across the 4 plant species. A comprehensive analysis including the chromosomal location, gene structure, subcellular location, conserved motifs, protein structure, protein-ligand interaction and promoter analysis was performed. RALF genes from four plant species were divided into 7 groups based on phylogenetic analysis. In silico expression analysis of these genes, using microarray and EST data, revealed that these genes exhibit a variety of expression patterns. Furthermore, RALF genes showed distinct expression patterns of transcript accumulation in vivo following nitrosative and oxidative stresses in Arabidopsis. Predicted interaction between RALF and heme ligand also showed that RALF proteins may contribute towards transporting or scavenging oxygen moieties. This suggests a possible role for RALF genes during changes in cellular redox status. Collectively, our data provides a valuable resource to prime future research in the role of RALF genes in plant growth and development.
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