Ontology highlight
ABSTRACT:
PROVIDER: PRJNA664608 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12678722.fastq.gz | Fastqsanger.gz |
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Project description:<p><strong>BACKGROUND:</strong> Amaranth (<em>Amaranthus spp.</em>) has high nutritional quality, with edible grain and leaves, and many agronomic advantages, making it a promising part of the solution for global food insecurity. However, we lack comprehensive metabolomic and genome sequence data for many cultivars. To support the improvement of this versatile, sustainable crop, a detailed metabolome profiling of the edible grains and leaves and genome sequencing resources is required for the widely cultivated grain amaranth cultivars such as Coral Fountain (CF), Emerald Tassels (ET), Golden Giant (GG), Hopi Red Dye (HR), and New Mexico (NM).</p><p><strong>RESULTS:</strong> Through a non-targeted high-throughput metabolic profiling using ultra-performance liquid chromatography-tandem mass spectrometry, we precisely determined the whole-grain and leaf metabolites of these five cultivars. This analysis identified 426 and 420 metabolites with known chemical structures in the grain and leaf, respectively. The five amaranth cultivars differed significantly in the levels of several nutritionally valuable compounds in grains and leaves, including sulfur amino acids, vitamins, and chlorogenic acids, as well as potentially anti-nutritive compounds, such as oxalate and raffinose family oligosaccharides. On average, the cultivars CF and ET had more favorable levels of most identified health-promoting compounds compared to GG, HR, and NM. In addition, we provide high-quality reference genome sequences for the five cultivars using the PacBio Sequel II sequencing platform with an estimated genome size of 465-483 Mb comprising 46.9-48.7% repetitive elements. We generated an iso-seq library from different amaranth plant parts and utilized it to predict the amaranth genes and annotate their function into their respective gene ontology terms.</p><p><strong>CONCLUSIONS:</strong> These resources will assist in breeding improved amaranth varieties and identifying targeted genes for trait modification and advancement through genome editing and engineering technologies.</p><p><br></p><p><strong>Leaf assays</strong> are reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS3498' rel='noopener noreferrer' target='_blank'><strong>MTBLS3498</strong></a>.</p><p><strong>Seed assays</strong> are reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS815' rel='noopener noreferrer' target='_blank'><strong>MTBLS815</strong></a>.</p>
2025-02-25 | MTBLS3498 | MetaboLights
Project description:<p><strong>BACKGROUND:</strong> Amaranth (<em>Amaranthus spp.</em>) has high nutritional quality, with edible grain and leaves, and many agronomic advantages, making it a promising part of the solution for global food insecurity. However, we lack comprehensive metabolomic and genome sequence data for many cultivars. To support the improvement of this versatile, sustainable crop, a detailed metabolome profiling of the edible grains and leaves and genome sequencing resources is required for the widely cultivated grain amaranth cultivars such as Coral Fountain (CF), Emerald Tassels (ET), Golden Giant (GG), Hopi Red Dye (HR), and New Mexico (NM).</p><p><strong>RESULTS:</strong> Through a non-targeted high-throughput metabolic profiling using ultra-performance liquid chromatography-tandem mass spectrometry, we precisely determined the whole-grain and leaf metabolites of these five cultivars. This analysis identified 426 and 420 metabolites with known chemical structures in the grain and leaf, respectively. The five amaranth cultivars differed significantly in the levels of several nutritionally valuable compounds in grains and leaves, including sulfur amino acids, vitamins, and chlorogenic acids, as well as potentially anti-nutritive compounds, such as oxalate and raffinose family oligosaccharides. On average, the cultivars CF and ET had more favorable levels of most identified health-promoting compounds compared to GG, HR, and NM. In addition, we provide high-quality reference genome sequences for the five cultivars using the PacBio Sequel II sequencing platform with an estimated genome size of 465-483 Mb comprising 46.9-48.7% repetitive elements. We generated an iso-seq library from different amaranth plant parts and utilized it to predict the amaranth genes and annotate their function into their respective gene ontology terms.</p><p><strong>CONCLUSIONS:</strong> These resources will assist in breeding improved amaranth varieties and identifying targeted genes for trait modification and advancement through genome editing and engineering technologies.</p><p><br></p><p><strong>Seed assays</strong> are reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS815' rel='noopener noreferrer' target='_blank'><strong>MTBLS815</strong></a><strong>.</strong></p><p><strong>Leaf assays</strong> are reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS3498' rel='noopener noreferrer' target='_blank'><strong>MTBLS3498</strong></a><strong>.</strong></p>
2025-02-25 | MTBLS815 | MetaboLights
Project description:Genetic changes and demography of introduction of grain amaranth to India
| PRJEB76492 | ENA
Project description:Genotyping by sequencing data for F2 mapping population in amaranth
| PRJEB30533 | ENA
Project description:Genomic and phenotypic evidence for an incomplete domestication of South American grain amaranth (Amaranthus caudatus)
| PRJEB13013 | ENA
Project description:A deeper understanding of the genetics of rice grain starch structure is crucial in tailoring grain digestibility and ensuring cooking quality to meet consumer preferences. Significant association peaks on chromosomes 6 and 7 were identified through genome-wide association study (GWAS) of debranched starch structure from grains of a 320 indica rice diversity panel using genotyping data from the high-density rice array. A systems genetics approach that interrelates starch structure data from GWAS to functional pathways from a gene regulatory network identified known and novel genes with high correlation to the proportion of amylose and amylopectin. A novel SNP in the promoter region of Granule Bound Starch Synthase I (GBSS I) was identified along with seven other SNPs to form haplotypes that discriminate samples into different phenotypic ranges of amylose. A novel GWAS peak on chromosome 7 between LOC_Os07g11020 and LOC_Os07g11520 indexed by a non-synonymous SNP mutation on exon 5 of a bHLH transcription factor was found to elevate the proportion of amylose at the expense of reduced short-chain amylopectin. Linking starch structure with starch digestibility by determining the kinetics of cooked grain amylolysis of selected haplotypes revealed strong association of starch structure with estimated digestibility kinetics. Combining all results from grain quality genomics, systems genetics, and digestibility phenotyping, we propose novel target haplotypes for fine-tuning starch structure in rice through marker-assisted breeding that can be used to alter the digestibility of rice grain, thus offering rice consumers a new diet-based intervention to mitigate the impact of nutrition-related non-communicable diseases.
2016-11-29 | GSE90576 | GEO