Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1271734 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33821600_1.fastq.gz | Fastqsanger.gz | |||
| SRR33821600_2.fastq.gz | Fastqsanger.gz | |||
| SRR33821601_1.fastq.gz | Fastqsanger.gz | |||
| SRR33821601_2.fastq.gz | Fastqsanger.gz | |||
| SRR33821602_1.fastq.gz | Fastqsanger.gz |
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Project description:Waxy starch has an important influence on bread dough and the qualities of breads. Generally, grain weight and yield in waxy wheat (Triticum aestivum L.) are significantly lower than in bread wheat. In this study, we performed the first proteomic and phosphoproteomic analyses of starch granule-binding proteins by comparing the waxy wheat cultivar Shannong 119 and the bread wheat cultivar Nongda 5181. The waxy and non-waxy wheats had similar starch granule morphological features and developmental patterns, and similar amylopectin quality in the grain. These results indicate that reduced amylose content does not affect amylopectin synthesis, but it causes significant reduction of total starch biosynthesis, grain size, weight and yield. Two-dimensional differential in-gel electrophoresis identified 40 differentially expressed protein (DEP) spots in waxy and non-waxy wheats, which belonged mainly to starch synthase (SS) I, SS IIa and granule-bound SS I. Most DEPs involved in amylopectin synthesis showed a similar expression pattern during grain development, suggesting relatively independent amylose and amylopectin synthesis pathways. Phosphoproteome analysis of starch granule-binding proteins, using TiO2 microcolumns and LC-MS/MS, showed that the total number of phosphoproteins and their phosphorylation levels in ND5181 were significantly higher than in SN119, but proteins controlling amylopectin synthesis had similar phosphorylation levels. Dynamic transcriptional expression profiling of starch biosynthesis-related genes indicated similar transcriptional expression profiles in both cultivars. Our results revealed that phosphorylation modifications played critical roles in amylose and amylopectin biosynthesis, but the lack of amylose did not affect the expression and phosphorylation of the starch granule-binding proteins involved in amylopectin biosynthesis.
2017-10-30 | PXD002805 | Pride
Project description:Waxy starch has an important influence on the qualities of breads. Generally, grain weight and yield in waxy wheat (Triticum aestivum L.) are significantly lower than in bread wheat. In this study, we performed the first proteomic and phosphoproteomic analyses of starch granule-binding proteins by comparing the waxy wheat cultivar Shannong 119 and the bread wheat cultivar Nongda 5181. These results indicate that reduced amylose content does not affect amylopectin synthesis, but it causes significant reduction of total starch biosynthesis, grain size, weight and grain yield. Two-dimensional differential in-gel electrophoresis identified 40 differentially expressed protein (DEP) spots in waxy and non-waxy wheats, which belonged mainly to starch synthase (SS) I, SS IIa and granule-bound SS I. Most DEPs involved in amylopectin synthesis showed a similar expression pattern during grain development, suggesting relatively independent amylose and amylopectin synthesis pathways. Phosphoproteome analysis of starch granule-binding proteins, using TiO2 microcolumns and LC-MS/MS, showed that the total number of phosphoproteins and their phosphorylation levels in ND5181 were significantly higher than in SN119, but proteins controlling amylopectin synthesis had similar phosphorylation levels. Our results revealed the lack of amylose did not affect the expression and phosphorylation of the starch granule-binding proteins involved in amylopectin biosynthesis.
2017-01-17 | PXD000646 | Pride
Project description:In Poland, conducted for years porcine breeding works focused on improving meat content in the carcass without undertaken to accomplish the more effectiveness of fattening indicators that impact on feed efficiency. At present, feeding and feed conversion became important factors that are especially evident in the countries where the production of fattening pigs is conducted in large farms. In the present study, was attempted to indicate pituitary candidate genes depending on feed conversion ratio (FCR) in native Polish pig breed, Złotnicka White. The whole pituitary transcriptome was sequenced using next-generation sequencing technology. The obtained results show the differences in gene expression for pathways associated with hormonal regulation and also with Notch and Wnt signaling. Moreover, it was observed that worse FCR in Złotnicka pigs was associated with a higher fat level in a carcass and a significant higher level of prolactin expression in the pituitary.
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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.
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Project description:Background The composition of intramuscular fat depends on genetic and environmental factors, including the diet. In pigs, we identified a haplotype of three SNP mutations in the steaoryl-coA desaturase (SCD) gene promoter associated with higher content of monounsaturated fatty acids in intramuscular fat. The second of these three SNPs (rs80912566, C>T) affected a putative retinol response element in the SCD promoter. The effect of dietary vitamin A restriction over intramuscular fat content is controversial in pigs as it seems to depend on the genetic line and the duration of the restriction. This study aims to investigate changes in the muscle transcriptome in SCD rs80912566_TT and CC pigs fed with and without vitamin A supplement during the fattening period. Results Vitamin A did not affect carcass fattening traits and fatty acid composition in muscle, but we observed an interaction between vitamin A and SCD genotype on the desaturation of muscle fatty acids. The diet without vitamin A supplement tended to enlarge the compositional differences between genotypes. The interaction between diet and genotype was also evident at the transcriptome level, the highest number of differentially expressed genes were detected between SCD rs80912566_TT pigs fed with the two diets. Conclusions Restricting dietary vitamin A during the fattening period did not improve intramuscular fat content despite relevant changes in muscle gene expression, both in coding and non-coding genes. Despite this, there was a significant interaction between the SCD genotype and the dietary vitamin A, which affected the quality of the meat through a change in the saturation index of intramuscular fat and activated general pathways of retinol response in a SCD genotype-dependant manner.
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Project description:Microbiome development in Danish fattening pigs
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