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Identification of transcriptome SNPs for assessing allele specific gene expression within a super-hybrid rice Xieyou9308

ABSTRACT: We identified 9325 reliable single nucleotide polymorphisms (SNPs) distributed throughout the genome, of which nearly 68% were represented in R9308 versus Xieqingzao B by CT and GA SNPs. This may indicate that DNA methylation, a heritable epigenetic mark, exists in the parents and their F1 hybrid. Of 2793 identified transcripts with consistent allelic biases, only 480 (17%) showed significant allelic biases during at least one stage, suggesting that trans effects may mediate most transcriptional differences in hybrid offspring. Approximately 67% and 62% of the 480 transcripts showed allelic expression biases towards the R9308 allele at tillering and heading stages, respectively. Transcripts with higher levels of gene expression in R9308 also exhibited R9308 allelic biases in the hybrid. In addition, 125 transcripts were identified with significant allelic expression biases at both stages, of which 74% showed allele expression biases towards the R9308 allele. R9308 alleles may tend to preserve their characteristic states of activity in the hybrid and may play an important role in hybrid vigor at both stages. The allelic expression of 355 transcripts was highly stage-specific, with divergent allelic expression patterns observed at different developmental stages. Many transcripts associated with stress resistance were differently regulated in the F1 hybrid. The results of this study would provide valuable information for further understanding molecular mechanisms of heterosis.

ORGANISM(S): Oryza sativa

PROVIDER: GSE43727 | GEO | 2014/05/16

SECONDARY ACCESSION(S): PRJNA187383

REPOSITORIES: GEO

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Identification of transcriptome SNPs for assessing allele specific gene expression within a super-hybrid rice Xieyou9308

Project description:We identified 9325 reliable single nucleotide polymorphisms (SNPs) distributed throughout the genome, of which nearly 68% were represented in R9308 versus Xieqingzao B by CT and GA SNPs. This may indicate that DNA methylation, a heritable epigenetic mark, exists in the parents and their F1 hybrid. Of 2793 identified transcripts with consistent allelic biases, only 480 (17%) showed significant allelic biases during at least one stage, suggesting that trans effects may mediate most transcriptional differences in hybrid offspring. Approximately 67% and 62% of the 480 transcripts showed allelic expression biases towards the R9308 allele at tillering and heading stages, respectively. Transcripts with higher levels of gene expression in R9308 also exhibited R9308 allelic biases in the hybrid. In addition, 125 transcripts were identified with significant allelic expression biases at both stages, of which 74% showed allele expression biases towards the R9308 allele. R9308 alleles may tend to preserve their characteristic states of activity in the hybrid and may play an important role in hybrid vigor at both stages. The allelic expression of 355 transcripts was highly stage-specific, with divergent allelic expression patterns observed at different developmental stages. Many transcripts associated with stress resistance were differently regulated in the F1 hybrid. The results of this study would provide valuable information for further understanding molecular mechanisms of heterosis. Root mRNA profiles of a super-hybrid rice Xieyou 9308 and its parents at tillering and heading stages were generated by deep sequencing, in duplicate, on Illumina Hiseq 2000 platform.

2014-05-16 | E-GEOD-43727 | biostudies-arrayexpress

Allele-specific RNA-seq of single pollen precursors

Project description:Single pollen precursors were isolated from maize anthers, covering 3 weeks of development from before meiosis through mature pollen. Starting material was staged by anther length and microscopy, and anther stages were densely sampled throughout pollen development. All samples were from an F1 hybrid between A188 and B73 inbred lines, and transcripts were associated with a specific parental allele when possible. In the "transcript_counts.csv" file, each sample is given 4 columns to separate the allele calls: '_g1' contains counts matching the B73 allele, '_g2' contains counts matching the A188 allele, 'ua' means unassigned (no SNPs were present in the transcript), and '_cf' means conflicting (the transcript had SNPs matching both alleles -- this is most likely sequencing error). Code to reproduce all figures from the main text of Nelms and Walbot (2022) can be found at https://doi.org/10.5281/zenodo.6620997

2021-10-26 | GSE175505 | GEO

F1 allele specific gene expression

Project description:By comparing mouse fibroblasts from two parental strains (Bl6 and Spretus) with fibroblasts from their first generation offspring (F1) we can detect allele specific expression of proteins. The Bl6 and Spretus lines are evolutionary distant and harbour many SNPs in their genomes which when synonomous we can detect on the protein level using mass spectrometry. By mixing SILAC labeled Bl6, Spretus and F1 offspring cell lines we can detect peptides shared between all three cell lines and also SNP peptides that are only expressed in the F1 cells and either Bl6 or Spretus cells. By comparing the abundance of the shared peptides and the SNP peptides we can quantify how much of a protein in the F1 cells that comes from the paternal or maternal allele. This data were then further compared to polysome profiling data. Azidohomoalanine labeling was used to enrich newly synthesized proteins from the three cell lines.

2015-08-18 | PXD002337 | Pride

Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Embryo data

Project description:Microarray analysis of gene expression patterns in immature ear, seedling, and embryo tissues from the maize inbred lines B73 and Mo17 identified numerous genes with variable expression. Some genes had detectable expression in only one of the two inbreds; most of these genes were detected in the genomic DNA of both inbreds, indicating that the expression differences are likely caused by differential regulation rather than by differences in gene content. Gene expression was also monitored in the reciprocal F1 hybrids B73xMo17 and Mo17xB73. The reciprocal F1 hybrid lines did not display parental effects on gene expression levels. Approximately 80% of the differentially expressed genes displayed additive expression patterns in the hybrids relative to the inbred parents. The approximately 20% of genes that display nonadditive expression patterns tend to be expressed at levels within the parental range, with minimal evidence for novel expression levels greater than the high parent or less than the low parent. Analysis of allele-specific expression patterns in the hybrid suggested that intraspecific variation in gene expression levels is largely attributable to cis-regulatory variation in maize. Collectively, our data suggest that allelic cis-regulatory variation between B73 and Mo17 dictates maintenance of inbred allelic expression levels in the F1 hybrid, resulting in additive expression patterns. Keywords: genotype comparison

2007-06-21 | GSE8179 | GEO

Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data

2007-06-21 | GSE8176 | GEO

Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Seedling data

2007-06-21 | GSE8174 | GEO

Transcription profiling of mazie inbred lines B73 and Mo17 leads to additive expression - Embryo data

2008-06-16 | E-GEOD-8179 | biostudies-arrayexpress

Transcription profiling of maize inbred lines B73 and Mo17 leads to additive expression - seedling data

2008-06-17 | E-GEOD-8174 | biostudies-arrayexpress

Transcription profiling of maize inbred lines B73 and Mo17

2008-06-16 | E-GEOD-8176 | biostudies-arrayexpress

Gene and allele specific expression during electric organ ontogeny in African weakly electric fish and hybrid

Project description:Hybridization can act as a catalyst for rapid phenotypic evolution by introducing novel allelic combinations, which can affect hybrid phenotype through changes in gene expression. The African weakly electric fish use their muscle-derived electric organ to produce electric organ discharge (EOD) for electrocommunication and electrolocation. The EOD in genus Campylomormyrus and cross-species hybrids is usually species-specific and varies during ontogeny. We compared the gene expression patterns and allele specific expression between juvenile and adult individuals in C. compressirostris (EOD duration 0.4 ms in juvenile and 0.4 ms in adult), C. rhynchophorus (EOD duration 5 ms in juvenile and 40 ms in adult) and their hybrid (EOD duration 0.4 ms in juvenile and 4 ms in adult). Differentially expressed genes between juveniles and adults were highly enriched in “membrane”, “plasma membrane” and “cytoplasm” Go Ontogeny terms. We detected several potassium channel-related genes (e.g. KCNJ2, ADCYAP1) that are potentially involved in the EOD development during ontogeny. The alleles from C. compressirostris show dominant expression in the hybrid at juvenile and adult life stages. KCNJ2 is the only gene that exhibits allelic dominance of C. rhynchophorus allele, and has an increasing expression during ontogeny in this allele. This suggests that the EOD development in hybrids could be related to the increasing allelic expression of the C. rhynchophorus allele under the scenario of overall dominance of C. compressirostris alleles. Our study sheds light in the evolution of the electric organ discharge in electric fishes and on the role of introgressive hybridization in complex phenotypic traits.

2023-08-31 | GSE240784 | GEO

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