scholarly journals Genome-wide RNAi ionomics screen reveals new genes and regulation of human trace element metabolism

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Mikalai Malinouski ◽  
Nesrin M. Hasan ◽  
Yan Zhang ◽  
Javier Seravalli ◽  
Jie Lin ◽  
...  
Keyword(s):  
Trace Element ◽  
New Genes ◽  
Genome Wide ◽  
Trace Element Metabolism

scholarly journals Interrelationships in trace-element metabolism in metal toxicities in Neurospora crassa

1962 ◽  
Vol 85 (3) ◽  
pp. 486-491 ◽  
Author(s):  
KS SASTRY ◽  
PR ADIGA ◽  
V VENKATASUBRAMANYAM ◽  
PS SARMA
Keyword(s):  
Neurospora Crassa ◽  
Trace Element ◽  
Trace Element Metabolism

A genome‐wide association study identifies new genes associated with developmental dysplasia of the hip

2019 ◽  
Vol 95 (3) ◽  
pp. 345-355 ◽  
Author(s):  
Wenjin Yan ◽  
Zheng Hao ◽  
Shuyan Tang ◽  
Jin Dai ◽  
Liming Zheng ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Developmental Dysplasia ◽  
Genome Wide Association ◽  
New Genes ◽  
Genome Wide ◽  
A Genome ◽  
Dysplasia Of The Hip

scholarly journals Genome-wide association analysis of chickpea germplasms differing for salinity tolerance based on DArTseq markers

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260709
Author(s):  
Shaimaa Mahmoud Ahmed ◽  
Alsamman Mahmoud Alsamman ◽  
Abdulqader Jighly ◽  
Mohamed Hassan Mubarak ◽  
Khaled Al-Shamaa ◽  
...  
Keyword(s):  
Association Analysis ◽  
Salinity Tolerance ◽  
Field Experiments ◽  
Agricultural Research ◽  
Gene Annotation ◽  
Genome Wide Association ◽  
Grain Legume ◽  
Genome Wide Association Analysis ◽  
New Genes ◽  
Genome Wide

Soil salinity is significant abiotic stress that severely limits global crop production. Chickpea (Cicer arietinum L.) is an important grain legume that plays a substantial role in nutritional food security, especially in the developing world. This study used a chickpea population collected from the International Center for Agricultural Research in the Dry Area (ICARDA) genebank using the focused identification of germplasm strategy. The germplasm included 186 genotypes with broad Asian and African origins and genotyped with 1856 DArTseq markers. We conducted phenotyping for salinity in the field (Arish, Sinai, Egypt) and greenhouse hydroponic experiments at 100 mM NaCl concentration. Based on the performance in both hydroponic and field experiments, we identified seven genotypes from Azerbaijan and Pakistan (IGs: 70782, 70430, 70764, 117703, 6057, 8447, and 70249) as potential sources for high salinity tolerance. Multi-trait genome-wide association analysis (mtGWAS) detected one locus on chromosome Ca4 at 10618070 bp associated with salinity tolerance under hydroponic and field conditions. In addition, we located another locus specific to the hydroponic system on chromosome Ca2 at 30537619 bp. Gene annotation analysis revealed the location of rs5825813 within the Embryogenesis-associated protein (EMB8-like), while the location of rs5825939 is within the Ribosomal Protein Large P0 (RPLP0). Utilizing such markers in practical breeding programs can effectively improve the adaptability of current chickpea cultivars in saline soil. Moreover, researchers can use our markers to facilitate the incorporation of new genes into commercial cultivars.

scholarly journals A Tool to Build Up-To-Date Gene Annotations for Affymetrix Microarrays

2017 ◽  
Vol 3 (2) ◽  
pp. 38 ◽  
Author(s):  
Vladislava Milchevskaya ◽  
Grischa Tödt ◽  
Toby James Gibson
Keyword(s):  
Statistical Power ◽  
Gene Annotation ◽  
Clinical Diagnostics ◽  
Specific Gene ◽  
Microarray Probe ◽  
New Genes ◽  
Affymetrix Microarrays ◽  
Genome Wide ◽  
Definition Of ◽  
Genome Annotations

Genome-wide expression profiling and genotyping is widely applied in functional genomics research, ranging from stem cell studies to cancer, in drug response studies, and in clinical diagnostics. The Affymetrix GeneChip microarrays represent the most popular platform for such assays. Nevertheless, due to rapid and continuous improvement of the knowledge about the genome, the definition of many of the genes and transcripts change, and new genes are discovered. Thus the original probe information is out-dated for a number of Affymetrix platforms, and needs to be re-defined. It has been demonstrated, that accurate probe set definition improves both coverage of the gene expression analysis and its statistical power. Therefore we developed a method that incorporates the most recent genome annotations into the annotation of the microarray probe sets, using tools from the next generation sequencing. Additionally our method allows to quickly build project specific gene annotation models, as well as for comparison of microarray to RNAseq data.

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