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Schematic presentation of the chromosomes 5 and 6 in DpDf plants. (A) The chromosome 5 and 6 constitution for wild-type, T5-6b heterozygous, and DpDf plants is indicated. The gray shading is used to indicate chromosome 6 while the black shading indicates chromosome 5. The white box indicates the approximate position of the centromere while the gray oval indicates the position of the NOR. The lines indicate the position of the chromosomal breaks involved in the translocation and the cM indicates the approximate genetic position of the normal chromosome that is involved in the translocation. (B) Chromosome 5 and 6 constitution in gametes produced by alternate or adjacent I disjunction in a T5-6b heterozygote. The viability of gametes containing these chromosomal constitutions is indicated to the right of the chromosomes.
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While changes in chromosome number that result in aneuploidy are associated with phenotypic consequences such as Down syndrome and cancer, the molecular causes of specific phenotypes and genome-wide expression changes that occur in aneuploids are still being elucidated.
We employed a segmental aneuploid condition in maize to study phenotypic and ge...
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The fall armyworm (FAW) Spodoptera frugiperda, which originated in the Americas, is advancing across China and threatening the nation's maize crops. Currently, one widely used tool for its control is genetically modified (GM) Bacillus thuringiensis (Bt) maize. Sufficient content of Bt protein in appropriate plant parts is crucial for enhancing resi...
The fall armyworm (FAW) Spodoptera frugiperda, which originated in the Americas, is advancing across China and threatening the nation's maize crops. Currently, one widely used tool for its control is genetically modified (GM) Bacillus thuringiensis (Bt) maize. Sufficient content of Bt protein in appropriate plant parts is crucial for enhancing resi...
Citations
... The latter usually manifests as the addition or loss of individual chromosomes or chromosome segments from a diploid [1]. Both variations have clear impacts on the survival and development of different organisms [3][4][5], such as yeast [6], maize [7] and Arabidopsis [8]. However, the impact of aneuploidy, caused by a phenomenon referred to as "genomic imbalance", on an individual is usually more severe than that of altered ploidy of a whole set of chromosomes [9]. ...
Aneuploidy is usually more detrimental than altered ploidy of the entire set of chromosomes. To explore the regulatory mechanism of gene expression in aneuploidy, we analyzed the transcriptome sequencing data of metafemale Drosophila. The results showed that most genes on the X chromosome undergo dosage compensation, while the genes on the autosomal chromosomes mainly present inverse dosage effects. Furthermore, long noncoding RNAs (lncRNAs) have been identified as key regulators of gene expression, and they are more sensitive to dosage changes than mRNAs. We analyzed differentially expressed mRNAs (DEGs) and differentially expressed lncRNAs (DELs) in metafemale Drosophila and performed functional enrichment analyses of DEGs and the target genes of DELs, and we found that they are involved in several important biological processes. By constructing lncRNA-mRNA interaction networks and calculating the maximal clique centrality (MCC) value of each node in the network, we also identified two key candidate lncRNAs (CR43940 and CR42765), and two of their target genes, Sin3A and MED1, were identified as inverse dosage modulators. These results suggest that lncRNAs play an important role in the regulation of genomic imbalances. This study may deepen the understanding of the gene expression regulatory mechanisms in aneuploidy from the perspective of lncRNAs.
... The impact of gene dosage effects appears to be attenuated during transmission from parental to its offspring and the phenotypes of filial seems to be recovered. For trans genes, their prevalence has been reported in aneuploid of many species (Makarevitch et al 2008;Guo and Birchler 1994;Huettel et al 2008), the changes in trans genes in expression ratios appear to be cis-related. When the cis gene expression ratio approaches 1.00, the Fig. 6 Ratio distributions of gene expression of for the functional class of ribosomal structural genes in T11 and T12. ...
Aneuploid refers to the gene dosage imbalance due to copy number alterations. Aneuploidy is generally harmful to the growth, development and reproduction of organisms according to the numerous research. However, it has rarely been reported on whether aneuploid have a relevant pattern of genome expression between the parental and its offspring generations. In this study, mRNA sequencing analysis was performed on rice (Oryza sativa L.) primary trisomes 11 and 12, same primary trisomes and normal individuals in their filial generation. We systematically summarized the changes in gene expression patterns that occur on cis genes and on trans genes between parental and filial generations. In T11 and T12, the ratio of cis-gene expression showed intermediate type in parents and dosage compensation in filial generations, which maybe due to more genes being downregulated. The trans genes were also affected by aneuploidy and manifested as cis-related. The strains with normal chromosomes in filial generations, there are still aneuploid-sensitive genes differentially expressed in their genomes, indicating that the effect of aneuploidy is far-reaching and could not be easily eliminated. Meanwhile, among these differentially expressed genes, genes with low-expression level were more likely to be upregulated, while genes with medium- and high-expression level were easy to be downregulated. For the different types of rice aneuploid, upregulated genes were mainly associated with genomic imbalance while downregulated genes were mainly influenced by the specific added chromosome. In conclusion, our results provide new insights into the genetic characterization and evolution of biological aneuploidy genomes.
... Aneuploidy is a type of chromosomal anomaly that involves an increase or decrease in the number of chromosomes [33] and is caused by the non-separation of chromosomes during meiosis and mitosis [34][35][36]. While aneuploidy causes serious disorders in animals [35,37], in plants, the known consequences include myriad phenotypic and structural changes, such as growth retardation [38][39][40][41]. Although aneuploidy occurs spontaneously in some plants [42], it has also been reported to occur through crossbreeding in many crops, such as tobacco, corn, guava, pear, apple, and citrus [43][44][45][46]. ...
Citrus plants are important fruit tree species; however, the breeding of high-quality varieties of citrus species is a time-consuming process. Using haploid-derived plants from anther culture may reduce the time required for obtaining purebred lines. This study aimed to genetically verify whether anther culture-derived sour orange (Citrus aurantium L.) plants developed from somatic embryos or haploid tissues. Sour orange anthers were cultured in N6 and MS media to induce calli and somatic embryos. N6 liquid medium supplemented with 1 mg·L−1 gibberellic acid and 200 µM spermidine resulted in a 10% increase in callus and embryo induction rates. Regenerated plants were validated using simple sequence repeat markers. Out of the 109 regenerated plants, ploidy analysis identified 99 diploids, two haploids, and eight putative aneuploids; out of the 99 diploid plants, 33 were haploid-derived homozygous diploids. The chromosomal analysis confirmed most plants as diploids, whereas some were identified as aneuploids (19–21 chromosomes). Furthermore, phylogenetic analysis confirmed that the resultant homozygous or heterozygous plants were haploid-derived. This is the first report of haploid-derived homozygous diploid and aneuploid sour orange plants obtained through anther culture. Moreover, the anther cultivation technique described herein can be applied to other citrus varieties.
... It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in Eukaryotes. High abundances of trans-transcripts have been reported in several other aneuploidy studies on cells from humans, yeast, maize, and Arabidopsis [47][48][49][50] . These trans-transcriptomes were typically enriched for transcription factors, genes related to metabolic processes, protein metabolism, or cellular stress responses. ...
Aneuploidy causes system-wide disruptions in the stochiometric balances of transcripts, proteins, and metabolites, often resulting in detrimental effects for the organism. The protozoan parasite Leishmania has an unusually high tolerance for aneuploidy, but its molecular consequences remain poorly understood. Here, we present the first integrated analysis of the genome, transcriptome, proteome, and metabolome of highly aneuploid Leishmania donovani strains. Our analysis unambiguously establishes that, despite this tolerance, aneuploidy in Leishmania globally and proportionally impacts the transcriptome and proteome of affected chromosomes, ultimately explaining the degree of metabolic differences between strains. This impact was present in both proliferative and infectious life stages. Protein complex subunits, secreted proteins, and non-cytoplasmic proteins, responded less or even not at all to aneuploidy-induced dosage changes. In contrast to other Eukaryotes, widespread transcript regulation modulating aneuploidy-related stress was absent. Further, the majority of regulated proteins was encoded by non-aneuploid chromosomes and had no underlying transcript change, suggesting that aneuploidy induces extensive post-transcriptional protein-level modulation. This makes Leishmania a unique Eukaryotic model for elucidating post-transcriptional protein-abundance modulation in the context of aneuploidy.
... Indeed, aneuploidy results in dosage imbalance at the chromosome level which is often associated with changes in expression of genes that could have an effect on phenotype (Henry et al. 2007(Henry et al. , 2010. In maize, variation in phenotypes such as stature, tassel and formation of knots on leaves were found to be linked to changes in the expression of genes within and/or outside of the aneuploidy regions (Makarevitch et al. 2008;Makarevitch and Harris 2010;Johnson et al. 2020). In hexaploid bread wheat, collections of various types of aneuploid lines have been used for decades to assist in determining gene function (McIntosh 2016). ...
Main conclusion
Karyotyping using high-density genome-wide SNP markers identified various chromosomal aberrations in oil palm (Elaeis guineensis Jacq.) with supporting evidence from the 2C DNA content measurements (determined using FCM) and chromosome counts.
Abstract
Oil palm produces a quarter of the world’s total vegetable oil. In line with its global importance, an initiative to sequence the oil palm genome was carried out successfully, producing huge amounts of sequence information, allowing SNP discovery. High-capacity SNP genotyping platforms have been widely used for marker–trait association studies in oil palm. Besides genotyping, a SNP array is also an attractive tool for understanding aberrations in chromosome inheritance. Exploiting this, the present study utilized chromosome-wide SNP allelic distributions to determine the ploidy composition of over 1,000 oil palms from a commercial F1 family, including 197 derived from twin-embryo seeds. Our method consisted of an inspection of the allelic intensity ratio using SNP markers. For palms with a shifted or abnormal distribution ratio, the SNP allelic frequencies were plotted along the pseudo-chromosomes. This method proved to be efficient in identifying whole genome duplication (triploids) and aneuploidy. We also detected several loss of heterozygosity regions which may indicate small chromosomal deletions and/or inheritance of identical by descent regions from both parents. The SNP analysis was validated by flow cytometry and chromosome counts. The triploids were all derived from twin-embryo seeds. This is the first report on the efficiency and reliability of SNP array data for karyotyping oil palm chromosomes, as an alternative to the conventional cytogenetic technique. Information on the ploidy composition and chromosomal structural variation can help to better understand the genetic makeup of samples and lead to a more robust interpretation of the genomic data in marker–trait association analyses.
... These aneuploids exhibit few or subtle phenotypic abnormalities and can often compete with their euploid progenitors [8]. Plants therefore provide an excellent opportunity for genome-wide investigations of aneuploid syndromes [9][10][11][12]. ...
Aneuploids of a single species that have lost or gained different chromosomes are useful for genomic analysis. The polyploid nature of many crops including oilseed rape (Brassica napus) allows these plants to tolerate the loss of individual chromosomes from homologous pairs, thus facilitating the development of aneuploid lines. Here, we selected 39 lines from advanced generations of an intergeneric hybridization between Brassica rapa and Orychophragmus violaceus with accidental pollination by B. napus. The lines showed a wide spectrum of phenotypic variations, with some traits specific to O. violaceus. Most lines had the same chromosome number (2n = 38) as B. napus. However, we also identified B. napus nulli-tetrasomics with 22 A-genome and 16 C-genome chromosomes and lines with the typical B. napus complement of 20 A-genome and 18 C-genome chromosomes, as revealed by FISH analysis using a C-genome specific probe. Other lines had 2n = 37 or 39 chromosomes, with variable numbers of A- or C-genome chromosomes. The formation of quadrivalents by four A-genome chromosomes with similar shapes suggests that they were derived from the same chromosome. The frequent homoeologous pairing between chromosomes of the A and C genomes points to their non-diploidized meiotic behavior. Sequence-related amplified polymorphism (SRAP) analysis revealed substantial genomic changes of the lines compared to B. rapa associated with O. violaceus specific DNA bands, but only a few genes were identified in these bands by DNA sequencing. These novel B. napus aneuploids and introgressants represent unique tools for studies of Brassica genetics and for Brassica breeding projects.
... A recent study in Drosophila S2 cells, which contain segmental aneuploidy, found that dosage compensation not only occurs for the X chromosomes but also for aneuploid autosomes, although this compensation was imperfect and resulted in a sublinear relationship between copy number and gene expression . Autosomal dosage compensation was also noted in maize and the common wheat Triticum aestivum L. (Makarevitch et al., 2008;Zhang et al., 2017). In the ten studied aneuploid wheat strains, 50-90% of the expressed genes on a given aneuploid chromosome were found be subjected to dosage compensation. ...
Aneuploidy, chromosome stoichiometry that deviates from exact multiples of the haploid compliment of an organism, exists in eukaryotic microbes, several normal human tissues, and the majority of solid tumors. Here, we review the current understanding about the cellular stress states that may result from aneuploidy. The topics of aneuploidy-induced proteotoxic, metabolic, replication, and mitotic stress are assessed in the context of the gene dosage imbalance observed in aneuploid cells. We also highlight emerging findings related to the downstream effects of aneuploidy-induced cellular stress on the immune surveillance against aneuploid cells.
... Although many types of aneuploidy in plants are viable and fertile, they manifest pleiotropic developmental defects and generally impaired fitness. For example, in maize and Arabidopsis, the abnormal phenotypes caused by aneuploidy include developmental defects, partial sterility, alterations in plant architecture, and so forth (Birchler et al., 2001;Birchler and Veitia, 2007;Makarevitch et al., 2008;Henry et al., 2010). Qualitatively, hexaploid common wheat is no exception to this general rule. ...
Aneuploidy, a condition of unbalanced chromosome content, represents a large-effect mutation that bears significant relevancy to human health and microbe adaptation. As such, extensive studies of aneuploidy have been conducted in unicellular model organisms and cancer cells. Aneuploidy also frequently is associated with plant polyploidization, but its impact on gene expression and relevance to polyploid genome evolution/functional innovation remain largely unknown. Here, we used a panel of diverse types of whole-chromosome aneuploidy of hexaploid wheat, all under the common genetic background of cv. Chinese Spring, to systemically investigate the impact of aneuploidy on genome-, subgenome- and chromosome-wide gene expression. Compared with prior findings in haploid or diploid aneuploid systems, we unravel additional and novel features of alteration in global gene expression resulting from the two major impacts of aneuploidy, cis- and trans-regulation, as well as dosage compensation. We show that the expression-altered genes map evenly along each chromosome with no evidence for co-regulating aggregated expression domains. However, chromosomes and subgenomes in hexaploid wheat are unequal in their responses to aneuploidy with respect to the number of genes being dysregulated. Strikingly, homeologous chromosomes do not differ from non-homologous chromosomes in terms of aneuploidy-induced trans-acting effects, suggesting the three constituent subgenomes of hexaploid wheat are largely uncoupled at the transcriptional level of gene regulation. Together, our findings shed new insights into the functional interplay between homeologous chromosomes and interactions between subgenomes in hexaploid wheat, which bear implications to further our understanding of allopolyploid genome evolution and efforts in breeding new allopolyploid crops.
... Dosage effect is also 547 reported for relatively small duplications in plants (Xiao et al. 2008;Cook et al. 2012;548 Wang et al. 2015). However, studies of large segmental duplications in maize suggest that 549 dosage compensation is a commonly found response of many genes (Birchler and 550 Newton 1981; Guo and Birchler 1994;Makarevitch et al. 2008). ...
Copy-number alterations are widespread in animal and plant genomes, but their immediate impact on gene expression is still unclear. In animals, copy-number alterations usually exhibit dosage effects, except for sex chromosomes that tend to be dosage compensated. In plants, genes within small duplications (<100 kb) often exhibit dosage-dependent expression, whereas large duplications (>50 Mb) are more often dosage compensated. However, little or nothing is known about expression in moderately-sized (1--50 Mb) segmental duplications, and about the response of small RNAs to dosage change. Here, we compared maize (Zea mays) plants with two, three and four doses of a 14.6 Mb segment of chromosome 1 that contains ~300 genes. Plants containing the duplicated segment exhibit dosage-dependent effects on ear length and flowering time. Transcriptome analyses using GeneChip and RNA sequencing methods indicate that most expressed genes and unique small RNAs within the duplicated segments exhibit dosage-dependent transcript levels. We conclude that dosage effect is the predominant regulatory response for both genes and unique small RNA transcripts in the segmental dosage series we tested. To our knowledge this is the first analysis of small RNA expression in plant gene dosage variants. Because segmental duplications comprise a significant proportion of eukaryotic genomes, these findings provide important new insight into the regulation of genes and small RNAs in response to dosage changes.
... A typical example of aneuploidy is Down syndrome in humans attributed to maternal gametes containing an extra copy of chromosome 21. Although plants are more tolerant to aneuploidization, aneuploid plants exhibit developmental delay and reduced fertility [47,68,69]. ...
Aurora kinases are evolutionarily conserved key mitotic determinants in all eukaryotes. Yeasts contain a single Aurora kinase, whereas multicellular eukaryotes have at least two functionally diverged members. The involvement of Aurora kinases in human cancers has provided an in-depth mechanistic understanding of their roles throughout cell division in animal and yeast models. By contrast, understanding Aurora kinase function in plants is only starting to emerge. Nevertheless, genetic, cell biological, and biochemical approaches have revealed functional diversification between the plant Aurora kinases and suggest a role in formative (asymmetric) divisions, chromatin modification, and genome stability. This review provides an overview of the accumulated knowledge on the function of plant Aurora kinases as well as some major challenges for the future.
