E-GEOD-56297
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ABSTRACT:
PROVIDER: E-GEOD-56297 | ExpressionAtlas | 2019-05-15
REPOSITORIES: ExpressionAtlas
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Project description:Genetic/genome diversity underlying variation in seed oil composition and content among soybean varieties is largely attributed to differences in transcript sequences and/or transcript accumulation of oil production related genes in seeds. Discovery and analysis of sequence and expression variations in these genes will accelerate soybean oil quality improvement. In an effort to identify these variations, we sequenced the transcriptomes of soybean seeds from nine lines varying in oil composition and/or total oil content. Our results showed that 69,338 distinct transcripts from 32,885 annotated genes were expressed in seeds. A total of 8,037 transcript expression polymorphisms and 50,485 transcript sequence polymorphisms (48,792 SNPs and 1,693 small Indels) were identified among the lines. Effects of the transcript polymorphisms on their encoded protein sequences and functions were predicted. The studies also provided independent evidence that the lack of FAD2-1A gene activity and a non-synonymous SNP in the coding sequence of FAB2C caused elevated oleic acid and stearic acid levels in soybean lines M23 and FAM94-41, respectively. As a proof-of-concept, we developed an integrated RNA-seq and bioinformatics approach to identify and functionally annotate transcript polymorphisms, and demonstrated its high effectiveness for discovery of genetic and transcript variations that result in altered oil quality traits. The collection of transcript polymorphisms coupled with their predicted functional effects will be a valuable asset for further discovery of genes, gene variants, and functional markers to improve soybean oil quality. transcriptome comparison of nine different soybean varieties
2016-01-13 | E-GEOD-56297 | biostudies-arrayexpress
Project description:Genetic/genome diversity underlying variation in seed oil composition and content among soybean varieties is largely attributed to differences in transcript sequences and/or transcript accumulation of oil production related genes in seeds. Discovery and analysis of sequence and expression variations in these genes will accelerate soybean oil quality improvement. In an effort to identify these variations, we sequenced the transcriptomes of soybean seeds from nine lines varying in oil composition and/or total oil content. Our results showed that 69,338 distinct transcripts from 32,885 annotated genes were expressed in seeds. A total of 8,037 transcript expression polymorphisms and 50,485 transcript sequence polymorphisms (48,792 SNPs and 1,693 small Indels) were identified among the lines. Effects of the transcript polymorphisms on their encoded protein sequences and functions were predicted. The studies also provided independent evidence that the lack of FAD2-1A gene activity and a non-synonymous SNP in the coding sequence of FAB2C caused elevated oleic acid and stearic acid levels in soybean lines M23 and FAM94-41, respectively. As a proof-of-concept, we developed an integrated RNA-seq and bioinformatics approach to identify and functionally annotate transcript polymorphisms, and demonstrated its high effectiveness for discovery of genetic and transcript variations that result in altered oil quality traits. The collection of transcript polymorphisms coupled with their predicted functional effects will be a valuable asset for further discovery of genes, gene variants, and functional markers to improve soybean oil quality.
2016-01-13 | GSE56297 | GEO
Project description:Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content
| PRJNA242863 | ENA
Project description:RNA-seq analysis of soybean root transcriptomes with high (Conrad and AC Colombe) and low (AC Glengarry and Pagoda) isoflavonoid content
2017-02-01 | E-MTAB-4929 | biostudies-arrayexpress
Project description:Two soybean near-isogenic lines (NILs) differing in seed protein content were genotyped to determine differential genetic introgressions from the wild relative Glycine soja. The CGH comparison reveals loci that are differentially introgressed between the two lines.
2013-02-28 | GSE44725 | GEO
Project description:Microarray hybridization was used to assess acclimation responses to four UV regimes by near isogenic Zea mays lines varying in flavonoid content. Keywords: other
2003-08-04 | GSE573 | GEO
Project description:Drought-responsive genes in soybean leaves were successfully identified using Affymetrix Soybean Gene 1.0 ST arrays on leaves samples of reproductive-stage soybean plants. R1 soybean plants planted in pots were imposed drought by withholding water for 5 days until the soil moisture content dropped to 5%, and 3rd trifoliates (now at the R2 stage) were collected for expression profiling. Soybean plants were grown in pots. When the plants reached the R1 stage (started flowering), drought treatment was imposed by withholding water. The soil moisture content was monitored during the process until the 5th day of water withholding, when soil moisture content reached 5%. The 3rd trifoliate (counting from shoots), now at the R2 stage, was collected for total RNA extraction, while other 3rd trifoliates of similar chlorophyl index were collected for leaves water content determination to identify the severity of the stress. Total RNA from 3rd trifoliates were used for expression profiling using Affymetrix Soybean Gene 1.0 ST arrays. Four biological repeats per treatment were performed, three biological repeats were chosen for expression profiling.
2012-11-10 | E-GEOD-40604 | biostudies-arrayexpress
Project description:Two soybean near-isogenic lines (NILs) differing in seed protein content were genotyped to determine differential genetic introgressions from the wild relative Glycine soja. The CGH comparison reveals loci that are differentially introgressed between the two lines. Comparison of HiPro (LD0-15154) and LoPro (LD0-15146) soybean NILs; the reported values show the log2 ratio of the normalized HiPro hybridization signal (Cy3) over the normalized LoPro hybridization signal (Cy5)
2013-02-28 | E-GEOD-44725 | biostudies-arrayexpress
Project description:Soybean is a rich source of protein and oil and a primary feedstock for biodiesel production. Previous research on soybean indicated that protein, oil and yield are controlled quantitatively in soybean seeds. However, genetic mechanisms controlling seed composition and yield in soybean remain unknown. We used Affymetrix Soybean GeneChips® to identify genes that are differentially expressed between developing seeds of the Minsoy and Archer soybean varieties, which differ in seed weight, yield, protein content and oil content. Some of the differentially expressed genes identified in this study may play important roles in controlling these traits.
2015-04-29 | GSE21598 | GEO
Project description:Microarray hybridization was used to assess acclimation responses to four UV regimes by near isogenic Zea mays lines varying in flavonoid content.
2010-06-05 | E-GEOD-573 | biostudies-arrayexpress