Ontology highlight
ABSTRACT:
PROVIDER: PRJNA664608 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12678722.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 1 of 1 |
Similar Datasets
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
Project description:We performed genotyping of Neuroblastoma Primary tumors using Illumina HumanHap 550 - v1,v3,v3duo and 610 Quad genotyping beadchips.
2011-09-15 | GSE19385 | GEO
Project description:Development of wheat (Triticum aestivum L.) grain mainly depends on the processes of starch synthesis and storage protein accumulation, which are critical for grain yield and quality. However, the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear. Here, we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes. We found that the chromatin accessibility changes are tightly associated with differential expressions and the proportion of distal ACRs were increased gradually during grain development. Specific transcription factor (TF) binding sites were enriched at different stages, and were diversified among the 3 subgenomes. We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles. Overall, our findings have provided numerous resources and illustrated the regulatory network during wheat grain development, which would shed lights on the improvement of wheat yields and qualities.
2023-02-15 | GSE214737 | GEO
Project description:Using high-throughput RNA sequencing, we developed a spatiotemporal transcriptome atlas for seed development of eight maize inbred lines based on 144 samples from the middle to late stages of grain development. A total of 26,747 genes with FPKM value more than 1 at least one sample were found to be involved in programming grain development. Global comparisons of genes expression highlighted the fundamental transcriptomic reprogramming and the phases of development. Coexpression analysis provided further insight into the dynamic reprogramming of the transcriptome by revealing functional transitions during maturation. Combined with grain moisture content and grain dehydration rate of different developmental time points of eight maize inbred lines, we captured a large number of genes related to grain moisture content and grain dehydration rate, which should help elucidate key mechanisms and regulatory networks that underlie grain dehydration during maize grain development. These results provide a comprehensive understanding of which biological processes are involved in the regulation of moisture variety of maize grain, the general principles of which provide a new perspective on improving maize grain dehydration characteristics. Meanwhile, this study provides a valuable resource for understanding the genetic regulation of maize grain development.
2022-10-01 | GSE158816 | GEO
Project description:Bread aroma is the principal characteristic perceived by the consumer yet it is mostlydisregarded in the product chain. The main aim of this study was to evaluate the potential toinclude bread aroma as a new target criterion into the wheat product chain. The objectivesof our study were to (i) quantify the influence of genetic versus environmental factors onthe bread aroma and quality characteristics, (ii) evaluate whether bread baked from modernwheat varieties differ in terms of aroma from those baked from old varieties and (iii) comparegenomic and metabolomic approaches for their efficiency to predict bread aroma and qualitycharacteristics in a wheat breeding program. Agronomic characters as well as bread aroma andquality traits were assessed for 18 old and 22 modern winter wheat varieties evaluated at up tothree locations in Germany. Metabolite profiles of all 120 flour samples were collected using a7200 GC-QTOF. Considerable differences in the adjusted entry means for all examined breadaroma and quality characters were observed. For aroma, which was rated on a scale from 1 to9, the adjusted entry means varied for the 40 wheat varieties between 3 and 8. In contrast,the aroma of bread prepared from old and modern wheat varieties did not differ significantly(P<0.05). Bread aroma was not significantly (P<0.05) correlated with grain yield, whichsuggested that it is possible to select for the former character in wheat breeding programswithout reducing the gain of selection for the latter. Finally, we have shown that bread aromacan be better predicted using a combination of metabolite and SNP genotyping profiles insteadof the SNP genotyping profile only. In conclusion, we have illustrated possibilities to increasethe quality of wheat for consumers in the product chain.
2019-11-12 | MTBLS1187 | MetaboLights