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Affymetrix Axiom® Peanut 47K Genotyping Array

ABSTRACT: Affymetrix Axiom® Peanut 47K Genotyping Array

PROVIDER: PRJNA1221891 | ENA |

REPOSITORIES: ENA

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Affymetrix Axiom® Peanut 47K Genotyping Array

Project description:The cultivated peanut, A. hypogaea L., is a critical oil and food crop worldwide. Decoding the genetic makeup behind natural variation in kernel oil and fatty acid concentrations is crucial for molecular breeding-based nutrient quantity and quality manipulation. Herein, we recognized 87 quantitative trait loci (QTLs) in 45 genomic regions for the concentrations of oil, oleic acid, and linoleic acid, as well as the oleic acid to linoleic acid (O/L) ratio via a genome-wide association study (GWAS) involving 499 peanut accessions. Eight QTLs clarified over 15% of the phenotypic variation in peanut accessions. Among the 45 potential genes significantly related to the 4 traits, only three genes displayed annotation to the fatty acid pathway. Furthermore, on the basis of pleiotropism or linkage data belonging to the identified singular QTLs, we generated a trait-locus axis to better elucidate the genetic background behind the observed oil and fatty acid concentration association. Together, our results provide strong evidence for the genetic mechanism behind oil biosynthesis in A. hypogaea L., facilitating future advances in multiple fatty acid component generation via pyramiding of desirable QTLs This natural population consisting of 499 peanut accessions combined with high-density SNPs will provide a better choice for identifying peanut QTLs/genes in the future. Together, our results provide strong evidence for the genetic mechanism behind oil biosynthesis in peanut, facilitating future advances in multiple fatty acid component generation via pyramiding of desirable QTLs.

2025-05-05 | GSE289195 | GEO

Affymetrix axiom EUR array data for MDS fibroblasts and iPSCs

2013-11-26 | GSE52691 | GEO

High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® axiom® array.

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Affymetrix axiom EUR array data for MDS fibroblasts and iPSCs

Project description:MDS patients are characterized as the deletion in chromosome 17. We generated induced pluripotent stem cells (iPSCs) from MDS fibroblasts. We performed SNP microarray analysis using Affymetrix axiom EUR array platform. Affymetrix axiom EUR arrays were performed according to the manufacturer's directions on DNA extracted from MDS fibroblasts and iPSCs.

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Transdisciplinary Research Into Cancer of the Lung (TRICL): Affymetrix Axiom Array

Project description:Transdisciplinary Research Into Cancer of the Lung (TRICL): Affymetrix Axiom Array

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Affymetrix SNP array data for analysis of peanut agronomic traits

Project description:Peanut is one of the most important cash crops with high quality oil, high protein content, and many other nutritional elements, and grown globally. Cultivated peanut (Arachis hypogaea L.) is allotetraploid with a narrow genetic base, and its genetics and molecular mechanisms controlling the agronomic traits are poorly understood. The array SNP data was used for revaling of key candidate loci and genes associated with important agronomic traits in peanut

2022-02-22 | GSE197103 | GEO

Affymetrix SNP array data for analysis of peanut agronomic traits

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AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow.

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Exome Genotyping Study of Scripps Venous Thrombosis Registry using Axiom® Exome Genotyping Array

Project description:Younger age and VTE recurrence are more likely to be caused by genetic risk factors than secondary VTE in older patients who more likely have comorbidities. When the exome rare variant genotyping database of the Scripps VTE Registry for adults < 55 yrs old was generated and analyzed for single nucleotide polymorphisms (SNPs). Two F5 related SNPs (rs6025, factor V Leiden and rs6687813) exceeded significance (FDR (false discovery rate) p < 0.05). No other variants met genome-wide significance. When the data for the subgroup of cases with recurrent VTE that are more likely to have genetic risk factors than cases with a single VTE episode were compared to controls (N=211 controls and N=32 recurrent VTE cases), 28 SNPs, including the F5 rs6025 SNP, achieved significance (FDR p < 0.05).

2021-12-04 | GSE76016 | GEO

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2019-05-25 | GSE131764 | GEO

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