Ontology highlight
ABSTRACT:
PROVIDER: PRJNA589345 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Evaluation of transcripts from soybean seed tissue during seed fill for a pair of near-isogenic lines contrasting in seed protein and oil and carrying an introgression at the linkage group I protein QTL region. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Yung-Tsi Bolon. The equivalent experiment is GM11 at PLEXdb.]
2011-11-22 | GSE33408 | GEO
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:Evaluation of transcripts from soybean seed tissue during seed fill for a pair of near-isogenic lines contrasting in seed protein and oil and carrying an introgression at the linkage group I protein QTL region. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Yung-Tsi Bolon. The equivalent experiment is GM11 at PLEXdb.] genotype: LoProt - time: 25-50(3-replications); genotype: LoProt - time: >50-100(3-replications); genotype: LoProt - time: >100-200(3-replications); genotype: LoProt - time: >200-300(3-replications); genotype: HiProt - time: 25-50(3-replications); genotype: HiProt - time: >50-100(3-replications); genotype: HiProt - time: >100-200(3-replications); genotype: HiProt - time: >200-300(3-replications)
2011-11-22 | E-GEOD-33408 | 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. The soybean plants of two soybean varieties Minsoy and Archer and two recombinant inbred lines from the cross that are similar in maturity but differ in yield were grown in St Paul, Minnesota during the summers of 2007 and 2008. In 2007, each line was planted as a single row. In 2008, a randomized complete block (RCB) design was used and each line had 3 replicates planted 1-2 weeks apart. Within each replicate, two rows per line were planted. Seeds were harvested at three developmental stages, namely, seed length = 2 mm, 3.5 mm, and 5-6 mm, which correspond approximately to soybean reproductive stages R4, R5 and early R6, respectively. In 2007 three independent samples were collected for each line and developmental stage. In 2008, two seed samples (one from each row) were collected for each line at each stage within each replicate. The pairs of seed samples were then pooled. Thus, three sets of independent tissue samples were collected for RNA extraction and hybridization on Affymetrix microarrys.
2015-04-29 | E-GEOD-21598 | biostudies-arrayexpress
Project description:Japanese cedar (Cryptomeria japonica) is an allogamous coniferous species that relies on wind-mediated pollen and seed dispersal, and it is one of the most important forestry tree species in Japan. For accelerating breeding, we collected massive SNPs based on ESTs from several organs using NGS, and thus carried out QTL, GWAS and GS based on high-density linkage maps.
2018-05-07 | GSE95618 | GEO
Project description:Japanese cedar (Cryptomeria japonica) is an allogamous coniferous species that relies on wind-mediated pollen and seed dispersal, and it is one of the most important forestry tree species in Japan. For accelerating breeding, we collected massive SNPs based on ESTs from several organs using NGS, and thus carried out QTL, GWAS and GS based on high-density linkage maps.
2018-05-07 | GSE95616 | GEO
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: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:Soybean (Glycine max (L.)) originated in China more than 5000 years ago, and the country is currently the third largest producer of soybeans in the world (Hymowitz et al., 2015). Based on a wild soybean Chromosome Segment Substitution Line (CSSL) population were constructed by crossing with the cultivar Suinong14 and ZYD00006 (the donor parent, a wild soybean variety) (Xin et al. 2016). A high-oil, low-protein (LPHO) and a high-protein, low-oil (HPLO) lines were screened out. In this study, a global interstitial microorganisms map were constructed, including Rhizosphere microorganisms, Phyllosphere microorganisms, Stem-interstitial microorganisms and interstitial microorganisms at the seeds developmental stage of early maturity stage (EM), mid-seed maturity stage (MM), late maturing stage (LM) and dry seed stage (DS). Whether the interstitial microorganisms may affect the growth of soybeans and the protein and oil content, as well as whether metabolites related to protein and oil content affect the surface and interior of soybeans in terms of beneficial microbial enrichment. To address these questions, we performed transcriptome sequencing, metabolomics, and microbial diversity analyses and examined significantly different microbial enrichment in LPHO/HPLO lines to screen out beneficial microbes associated with influencing soybean growth and affecting the protein and oil content. This finding will provide new ideas for further research on microorganisms affecting the protein and oil content of soybean seeds.
2024-11-13 | MTBLS9424 | MetaboLights