Soybean seeds proteomics analysis of parents and recombinant inbred lines
Ontology highlight
ABSTRACT:
ORGANISM(S): Glycine Max
SUBMITTER: 
Yinghong Pan
PROVIDER: PXD025909 | iProX | Mon May 10 00:00:00 BST 2021
REPOSITORIES: iProX
Similar Datasets
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: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 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:MicroRNAs (miRNAs) play an important role as regulators of gene expression. In plants they affect a wide variety of biological process like growth, development and response to biotic and abiotic stress. Glycine max is one of the most important crop worldwide due to its rich protein and oil content. Drought and salt stress are the main abiotic stresses that affect soybean. Salt stress impacts the fisiology of the plants due to the damage in the photosynthetic rate, growth and development. This work aim to identify salt-stress responsive miRNAs and their respective targets in Glycine max using high-throughput RNA sequencing technology.
2017-07-11 | GSE69570 | GEO
Project description:MicroRNAs (miRNAs) play an important role as regulators of gene expression. In plants they affect a wide variety of biological process like growth, development and response to biotic and abiotic stress. Glycine max is one of the most important crop worldwide due to its rich protein and oil content. Drought and salt stress are the main abiotic stresses that affect soybean. Salt stress impacts the fisiology of the plants due to the damage in the photosynthetic rate, growth and development. This work aim to identify salt-stress responsive miRNAs and their respective targets in Glycine max using high-throughput RNA sequencing technology.
2017-07-11 | GSE69569 | GEO
Project description:Seeds, including soybean (Glycine max), contain bioactive proteins with anti-nutritional and immunological properties that affect metabolism and assimilation of seed derived nutrients and as allergens that can induce escalating adverse immune responses. The presence of anti-nutritional proteins requires soybean protein to be processed by heat that results in energy costs and alteration of soybean protein’s physiochemical properties. Nulls for bioactive seed proteins have been isolated from the USDA soybean collection including Kunitz trypsin inhibitor (TI) and soybean agglutinin (LE) and immunodominant soybean allergen P34 proteins. Each of these nulls has the potential to partially address concerns of soybean feed/food consumption and stacked together these traits can form a basis for engineering improved soybean cultivars. A stack of cultivars of recessive nulls of TI, LE, and P34 was created in a cv Williams 82 background termed “Triple Null”. The reduction of these proteins slightly diminishes the overall protein content of the seed that was analyzed by 2D IEF/SDS gels and proteomics. P34 and Kunitz Trypsin Inhibitor nulls are frame shift mutants shown by mass spectroscopy to accumulate small amounts of authentic protein. Triple Null’s capacity for biolistic transformation was assessed showing that Triple Null can be transformed permitting stacking of transgene traits. Triple Null has possible application as a conventional feed/food source and for immunotherapy to mitigate soybean allergenic response and be leveraged as a transformation platform to stack other production or consumer traits.
2022-02-23 | PXD000967 | Pride
Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development. In soybean (Glycine max), an important edible oil crop, valuable lipids are synthesized and stored in the cotyledons during embryogenesis .This storage lipids are used as energy source of the emerging seeds, during the germination procces. Until now, there are no microRNAs related to lipid metabolism in soybean or any other plant. This work aims to describe the miRNAome of germinating seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus germinating seeds. A total of 183 familes were detected through a computational analysis of a large number of reads obtained from deep sequencing from two small RNA libraries of (i) pooled germintaing seeds stages and (ii) mature soybean seeds. We have found 39 new mirna precursors which produce 41 new mature forms. The present work also have identified isomiRNAs and mirnas offset (moRNAs). This work presents a comprehensive study of the miRNA transcriptome of soybean germinating seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in lipid consumption in development soybean seeds.
2015-05-25 | GSE38373 | GEO
Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development. In soybean (Glycine max), an important edible oil crop, valuable lipids are synthesized and stored in the cotyledons during embryogenesis .This storage lipids are used as energy source of the emerging seeds, during the germination procces. Until now, there are no microRNAs related to lipid metabolism in soybean or any other plant. This work aims to describe the miRNAome of germinating seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus germinating seeds. A total of 183 familes were detected through a computational analysis of a large number of reads obtained from deep sequencing from two small RNA libraries of (i) pooled germintaing seeds stages and (ii) mature soybean seeds. We have found 39 new mirna precursors which produce 41 new mature forms. The present work also have identified isomiRNAs and mirnas offset (moRNAs). This work presents a comprehensive study of the miRNA transcriptome of soybean germinating seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in lipid consumption in development soybean seeds. MicroRNA profiles in 2 different seed libraries (mature seeds and a pool of germinating seed stages) of Glycine max by deep sequencing (Illumina GAII).
2015-05-25 | E-GEOD-38373 | biostudies-arrayexpress
Project description:Energy densification and enrichment of monounsaturated fatty acids increases oat’s nutritional value among small grain cereals. However, optimization of oat oil traits is challenging through conventional breeding. Using the biolistic method for oat’s oil improvement, here we showed that metabolic engineering is a feasible strategy in improving the oil traits of oat. In this study, two constructs containing three genes involved in lipid biosynthesis pathway (AtWRI1, AtDGAT, and SiOLEOSIN) were transformed into oat cultivar ‘Park’ to enhance the oil composition and content in oat grain and leaves. We performed RNA-sequencing in mature seeds and boot leaves of trasngenic lines. Transgene expression contributed to a global transcriptional reprogramming in oat seeds and leaves. Endogenous DGAT, WRI1, and OLEOSIN genes were up regulated while the genes involved in fatty acid biosynthesis expressed in opposite way between oat seeds and leaves. Transcriptomic studies revealed differential gene expression mainly enriched in lipid metabolism.
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