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Gene expression analysis at the intersection of ploidy and hybridity in maize.

ABSTRACT: Heterosis and polyploidy are two important aspects of plant evolution. To examine these issues, we conducted a global gene expression study of a maize ploidy series as well as a set of tetraploid inbred and hybrid lines. This gene expression analysis complements an earlier phenotypic study of these same materials. We find that ploidy change affects a large fraction of the genome, albeit at low levels; gene expression changes rarely exceed 2-fold and are typically not statistically significant. The most common gene expression profile we detected is greater than linear increase from monoploid to diploid, and reductions from diploid to triploid and from triploid to tetraploid, a trend that mirrors plant stature. When examining heterosis in tetraploid maize lines, we found a large fraction of the genome impacted but the majority of changes were not statistically significant at 2-fold or less. Non-additive expression was common in the hybrids, and the extent of non-additivity increased both in number and magnitude from duplex to quadruplex hybrids. Overall, we find that gene expression trends mirror observations from the phenotypic studies; however, obvious mechanistic connections remain unknown.

ORGANISM(S): Zea mays

PROVIDER: GSE25526 | GEO | 2010/11/30

SECONDARY ACCESSION(S): PRJNA133995

REPOSITORIES: GEO

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Gene expression analysis at the intersection of ploidy and hybridity in maize.

Project description:Heterosis and polyploidy are two important aspects of plant evolution. To examine these issues, we conducted a global gene expression study of a maize ploidy series as well as a set of tetraploid inbred and hybrid lines. This gene expression analysis complements an earlier phenotypic study of these same materials. We find that ploidy change affects a large fraction of the genome, albeit at low levels; gene expression changes rarely exceed 2-fold and are typically not statistically significant. The most common gene expression profile we detected is greater than linear increase from monoploid to diploid, and reductions from diploid to triploid and from triploid to tetraploid, a trend that mirrors plant stature. When examining heterosis in tetraploid maize lines, we found a large fraction of the genome impacted but the majority of changes were not statistically significant at 2-fold or less. Non-additive expression was common in the hybrids, and the extent of non-additivity increased both in number and magnitude from duplex to quadruplex hybrids. Overall, we find that gene expression trends mirror observations from the phenotypic studies; however, obvious mechanistic connections remain unknown. We examined gene expression in a ploidy series (1n to 4n) of the maize line B73 and in a variety of hybrid tetraploid lines using a complex loop design. Pooled RNA samples from 10 plants were used (2 independent RNA isolations/sample), and all comparisons were made using replicate dye swaps (16 slide sets/comparison). For the ploidy analysis, all expression changes were computed relative to the diploid as well as between 2n + 3n and 3n + 4n. For the expression analysis of hybrids, hybrid expression levels were compared to the parental expression levels as well as to mid-parent levels.

2010-11-30 | E-GEOD-25526 | biostudies-arrayexpress

Transcriptome profiling of an autopolyploidy series of Arabidopsis thaliana

Project description:Heterosis occurs where F1 offspring display superior characteristics to the parents. Heterosis is usually considered to result from crosses of genetically distinct (e.g. homozygous inbred) parents producing heterozygous F1 offspring. Most mechanistic models for heterosis require genetically heterozygous F1 hybrid offspring harbouring allelic diversity. Epigenetic or dosage models for heterosis could allow for heterosis effects in F1 offspring that display no allelic diversity with their parents. Reciprocal inter-ploidy crosses between diploid (2x) and tetraploid (4x) lines in the same genetic background generates genetically identical F1 triploids (3x). Such reciprocal F1 triploids differ according to whether the additional chromosome set is either maternally (maternal excess) or paternally inherited (paternal excess). Biomass accumulation and abiotic stress tolerance between the parental (2x and 4x) and reciprocal F1 triploid (3x) offspring of Arabidopsis thaliana accession C24 reveals a strong parental genome-dosage induced heterosis in the paternal-excess triploid F1 plants. In these F1 triploids, the circadian clock related genes CCA1 and TOC1, and the growth factors PIF4 and PIF5, display different expression levels compared to the non-heterotic maternal excess F1 triploid siblings. Whole transcriptome profiling reveals a paternal genome dosage effect on gene expression levels with strong enrichment for dysregulated abiotic stress-related genes in the paternal excess F1 triploids. This study demonstrates that heterosis can be triggered without allelic diversity in F1 triploid plants. Heterosis without heterozygosity in plants can be induced via an epigenetic “chromosome imprinting” like parental genome dosage effect requiring paternal transmission of an additional chromosome set 4 or 5 biological replicates per ploidy level, each replicate being a single two weeks old seedling

2014-08-01 | E-GEOD-52885 | biostudies-arrayexpress

Transcriptomic characterizations associated with autopolyploidization of Chinese woad (Isatis indigotica Fort.)

2015-02-01 | GSE61103 | GEO

Transcriptome profiling of an autopolyploidy series of Arabidopsis thaliana

2014-08-01 | GSE52885 | GEO

Transcriptomic characterizations associated with autopolyploidization of Chinese woad (Isatis indigotica Fort.)

Project description:The study was to obtain transcriptional data and examine gene expression of different ploidy based on RNA-Seq and bioinformatic analysis. Differentially expressed genes including both up- and down-regulated were received by pairwise contrasts of diploid, triploid and tetraploid. RNA from young plant leaves were isolated and gene expressions of different autoploidy via RNA-Seq and bioinformatic analysis were conducted

2015-02-01 | E-GEOD-61103 | biostudies-arrayexpress

Small RNA transcriptome in the Squalius alburnoides complex

Project description:The Squalius alburnoides complex (Steindachner) is one of the most intricate hybrid polyploid systems known in vertebrates. In this complex, the constant switch of the genome composition in consecutive generations, very frequently involving a change on the ploidy level, promotes repetitive situations of potential genomic shock. Previously in this complex, it was shown that in response to the increase in the genome dosage, triploid hybrids could regulate gene expression to a diploid state. In this work, we compared the small RNA profiles in the different genomic compositions interacting in the complex. Using high-throughput arrays and sequencing technologies, we were able to verify that diploid and triploid hybrids were closely related: they shared most of their sequences and their miRNA expression profiles were highly correlated. However, an overall view indicates an up-regulation of a substantial number of miRNAs in triploids. Also, the global miRNA expression in triploids was higher than predicted from an additive model. These results point to a participation of miRNAs in the cellular functional stability needed when the ploidy change.

2013-01-02 | GSE38691 | GEO

miRNA expression profile in the Squalius alburnoides complex

2013-01-02 | GSE36894 | GEO

Transcriptome Shock in an Interspecific F1 Triploid Hybrid of Oryza Revealed by RNA Sequencing

Project description:Here, we produced a set of interspecific F1 triploid hybrid plants between Oryza sativa, ssp. japonica (2nâ=â2xâ=â24, genome AA) and the tetraploid form of O. punctata (2nâ=â4xâ=â48, genome, BBCC), and conducted RNA-seq transcriptome profiling of the hybrids and their exact parental plants. We analyzed both homeolog expression bias and overall gene expression level difference in the hybrids relative to the in silico âhybridsâ (parental mixtures). We found that approximately 16% (2,541) of the 16,112 expressed genes in leaf tissue of the F1 hybrids showed nonadditive expression, which were specifically enriched in photosynthesis-related pathways. Interestingly, changes in the maternal homeolog expression, including non-stochastic silencing, were the major causes for altered homeolog expression partitioning in the F1 hybrids. Our findings have provided further insights into the transcriptome response to interspecific hybridization and heterosis.

2015-05-02 | E-MTAB-4225 | biostudies-arrayexpress

caArray_lavar-00109: Differential expression of genes characterize neuroblastic tumours with distinct ploidy status

Project description:Neuroblastic tumours (NBTs) represent a heterogeneous spectrum of neoplastic diseases associated with multiple genetic alterations. Structural and numerical chromosomal changes are frequent and are predictive parameters of NBTs outcome. We performed a comparative analysis of the biological entities constituted by NBTs with different ploidy status. Gene expression profiling of 49 diagnostic primary near-triploid (n= 22) and near-diploid/tetraploid (n=27) NBTs performed using Affymetrix U95Av2 arrays, revealed distinct expression profiles associated with each NBT subgroup. A statistically significant portion of genes mapped to 1p36 (P=0.01) and 17p13-q21 (P<0.0001). Specific chromosomal abnormalities observed in NBTs, 1p loss, 17q and whole chromosome 17 gains, were reflected in the gene expression profiles. This study demonstrates that NBTs with different cellular DNA content display distinct transcriptional profiles with a significant portion of differentially expressed genes mapping to specific chromosomal regions known to be associated with outcome. Furthermore, our results suggest that NBTs with different ploidy status may result from different mechanisms of aneuploidy driving tumourigenesis.

2016-05-26 | GSE81895 | GEO

Dysfunction of mitotic cell division at shoot apices triggered severe growth abortion in interspecific hybrids between tetraploid wheat and Aegilops tauschii Coss.

Project description:Common wheat is an allohexaploid species, derived through endoreduplication of an inter-specific triploid hybrid produced from a cross between cultivated tetraploid wheat and the wild diploid relative Aegilops tauschii Coss. Hybrid incompatibilities, including hybrid necrosis, have been observed in triploid wheat hybrids. A limited number of Ae. tauschii accessions show hybrid lethality in triploid hybrids crossed with tetraploid wheat due to developmental arrest at the early seedling stage, which is termed severe growth abortion (SGA). Despite the potential severity of this condition, the genetic mechanisms underlying SGA are not well understood. We conducted comparative analyses of gene expression profiles in crown tissues to characterize developmental arrest in triploid hybrids displaying SGA. A number of defense-related genes were highly up-regulated, whereas many transcription factor genes, such as the KNOTTED1-type homeobox gene, which function in shoot apical meristem (SAM) and leaf primordia, were down-regulated in the crown tissues of SGA plants. Transcript accumulation levels of cell cycle-related genes were also markedly reduced in SGA plants, and no histone H4-expressing cells were observed in the SAM of SGA hybrid plants. Our findings demonstrate that SGA shows unique features among other types of abnormal growth phenotypes, such as type II and III necrosis.

2011-11-01 | GSE33357 | GEO

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