Transcriptome inheritance of a citrus somatic hybrid
Ontology highlight
ABSTRACT:
ORGANISM(S): Citrus Citrus x limon Citrus reticulata Citrus limon x Citrus reticulata
PROVIDER: GSE18386 | GEO | 2009/10/03
SECONDARY ACCESSION(S): PRJNA118067
REPOSITORIES: GEO
Similar Datasets
Project description:The main objective of the present study was to analyze whether the novel phenotype of this complex three-way tetraploid interspecific hybrid, displaying mixed dominant, codominant and transgressive traits is associated with non additive expression of the two diploid parental genomes. Keywords: Comparative transcriptomic hybridization Three replicates for each sample category (C. reticulata Blanco, C. limon (L.) Burm.) and a allotetraploid somatic hybrid between both) were generated and compared by a reference design.
2010-06-21 | E-GEOD-18386 | biostudies-arrayexpress
Project description:Speciation via interspecific or intergeneric hybridization and polyploidization triggers genomic responses Examination of small RNA of diploid Parent, Tetraploid parent, F1 hybrid and hexaploid amhiploid. Four pools of plants for each sample
2011-05-12 | E-GEOD-29243 | biostudies-arrayexpress
Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in two types of hybrid necrosis-showing plants; one was derived from interspecific crosses of two diploid wheat species Triticum monococcum ssp. aegilopoides and Triticum urartu, and another from intraspecific hybrids of common wheat. Of the up-regulated genes, defense-related and carbohyfrate metabosim-related genes were frequently found, whereas photosythesis-related genes down-regulated in the hybrid necrosis-showing plants. These observations strongly suggests that autoimmune responses might be triggered by Ne1-Ne2 interaction in common wheat and by Ned1-Ned2 interaction in the wild diploid wheat, and that genetically programmed cell death could be regarded as a hypersensitive response-like cell death similar to that observed in other wheat hybrid necrosis such as type III necrosis in the ABD wheat triploids crossed between tetraploid wheat and Aegilops tauschii.
2014-12-19 | GSE64342 | GEO
Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in two types of hybrid necrosis-showing plants; one was derived from interspecific crosses of two diploid wheat species Triticum monococcum ssp. aegilopoides and Triticum urartu, and another from intraspecific hybrids of common wheat. Of the up-regulated genes, defense-related and carbohyfrate metabosim-related genes were frequently found, whereas photosythesis-related genes down-regulated in the hybrid necrosis-showing plants. These observations strongly suggests that autoimmune responses might be triggered by Ne1-Ne2 interaction in common wheat and by Ned1-Ned2 interaction in the wild diploid wheat, and that genetically programmed cell death could be regarded as a hypersensitive response-like cell death similar to that observed in other wheat hybrid necrosis such as type III necrosis in the ABD wheat triploids crossed between tetraploid wheat and Aegilops tauschii. Expression patterns were compared between a wild-type wheat hybrid plant (as a reference) and a hybrid necrosis-showing hybrid plant in each of common and wild diploid wheat. Total RNA samples were isolated from leaf tissues. Two independent experiments were conducted in each expriment.
2014-12-19 | E-GEOD-64342 | biostudies-arrayexpress
Project description:The "triploid block" prevents interploidy hybridizations in flowering plants, and is characterized by failure in endosperm development and function, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed imprinted genes (PEGs) that are up-regulated in the tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed abortion is bypassed in plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early plant growth. We have identified strong suppressor lines showing transgenerational inheritance of hypomethylation in CG context, as well as normalized expression of PEGs. Importantly, differentially methylated loci segregate in the progeny of "epimutagenized" plants, which may allow the identification of epialleles involved in the triploid block response in future studies. Finally, we demonstrate that chemically-induced epimutagenesis allows bypassing interploidy hybridizations in Arabidopsis and interspecific hybridization barriers in crosses between Capsella species, thus potentially emerging as a novel strategy for seed-based breeding of triploids and interspecific hybrids with agronomical interest.
2021-11-23 | GSE179702 | GEO
Project description:The "triploid block" prevents interploidy hybridizations in flowering plants, and is characterized by failure in endosperm development and function, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed imprinted genes (PEGs) that are up-regulated in the tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed abortion is bypassed in plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early plant growth. We have identified strong suppressor lines showing transgenerational inheritance of hypomethylation in CG context, as well as normalized expression of PEGs. Importantly, differentially methylated loci segregate in the progeny of "epimutagenized" plants, which may allow the identification of epialleles involved in the triploid block response in future studies. Finally, we demonstrate that chemically-induced epimutagenesis allows bypassing interploidy hybridizations in Arabidopsis and interspecific hybridization barriers in crosses between Capsella species, thus potentially emerging as a novel strategy for seed-based breeding of triploids and interspecific hybrids with agronomical interest.
2021-11-23 | GSE179697 | GEO
Project description:Transcriptome inheritance of a citrus somatic hybrid
| PRJNA118067 | ENA
Project description:The creation of intergeneric somatic hybrids between Citrus and Poncirus is an efficient approach for citrus rootstock breeding, offering the possibility of combining beneficial traits from both genera into novel rootstock lineages. These somatic hybrids are also used as parents for further tetraploid sexual breeding. In order to optimize these latter breeding schemes, it is essential to develop knowledge on the mode of inheritance in the intergeneric tetraploid hybrids. We assessed the meiotic behavior of an intergeneric tetraploid somatic hybrid resulting from symmetric protoplast fusion of diploid Citrus reticulata and diploid Poncirus trifoliata. The analysis was based on the segregation patterns of 16 SSR markers and 9 newly developed centromeric/pericentromeric SNP markers, representing all nine linkage groups of the Citrus genetic map. We found strong but incomplete preferential pairing between homologues of the same ancestral genome. The proportion of gametes that can be explained by random meiotic chromosome associations (?) varied significantly between chromosomes, from 0.09 ± 0.02 to 0.47 ± 0.09, respectively, in chromosome 2 and 1. This intermediate inheritance between strict disomy and tetrasomy, with global preferential disomic tendency, resulted in a high level of intergeneric heterozygosity of the diploid gametes. Although limited, intergeneric recombinations occurred, whose observed rates, ranging from 0.09 to 0.29, respectively, in chromosome 2 and 1, were significantly correlated with ?. Such inheritance is of particular interest for rootstock breeding because a large part of the multi-trait value selected at the teraploid parent level is transmitted to the progeny, while the potential for some intergeneric recombination offers opportunities for generating plants with novel allelic combinations that can be targeted by selection.
| S-EPMC6224360 | biostudies-literature
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
Project description:In this study, 17 plants of tetraploid “Zhique” were firstly identified by screening 570 natural seedlings of Citrus wilsonii Tanaka. These tetraploid plants showed different morphology and exhibited significantly increased drought tolerance than the diploids via determination of leaf water potential, relative water content and electrolyte leakage. Large number of genes involved in photosynthesis-responsive were differentially expressed in tetraploids under drought stress by global transcriptome analysis, which was consistent with the detection of photosynthesis indicator including photosynthetic rate, stomatal conductance, chlorophyll and so on. Compared with diploids, phosphorylation modification also plays an important role in the tetraploids after drought stress through the transcriptional and protein level analysis. Additionally, the genes involved in the phenylpropanoid biosynthesis and starch and sucrose metabolism pathways were enriched in both tetraploids and diploids in response to water deficient. Importantly, tetraploids significantly take priority over the diploid via regulating plant hormone signal transduction, especially improving the levels of 3-indoleacetic acid, abscisic acid and salicylic acid and reducing gibberellic A3 and jasmonic acid contents. Collectively, our data reveals that synergistic regulation photosynthesis, phosphorylation modification and plant hormones accumulation contribute to drought tolerance of autotetraploid in Citrus wilsonii.
2022-06-09 | PXD031236 | Pride