Effect of aneuploidy of a non‐essential chromosome on gene expression in maize

Abstract

The non-essential supernumerary maize (Zea mays) B chromosome (B) has recently been shown to contain active genes and to be capable of impacting gene expression of the A chromosomes. However, the effect of the B chromosome on gene expression is still unclear. In addition, it is unknown whether the accumulation of the B chromosome has a cumulative effect on gene expression. To examine these questions, the global expression of genes, microRNAs (miRNAs), and transposable elements (TEs) of leaf tissue of maize W22 plants with 0-7 copies of the B chromosome was studied. All experimental genotypes with B chromosomes displayed a trend of upregulated gene expression for a subset of A-located genes compared to the control. Over 3000 A-located genes are significantly differentially expressed in all experimental genotypes with the B chromosome relative to the control. Modulations of these genes are largely determined by the presence rather than the copy number of the B chromosome. By contrast, the expression of most B-located genes is positively correlated with B copy number, showing a proportional gene dosage effect. The B chromosome also causes increased expression of A-located miRNAs. Differentially expressed miRNAs potentially regulate their targets in a cascade of effects. Furthermore, the varied copy number of the B chromosome leads to the differential expression of A-located and B-located TEs. The findings provide novel insights into the function and properties of the B chromosome.

Rye B chromosomes differently influence the expression of A chromosome–encoded genes depending on the host species

“…Among annotated transcripts common to + 2B and + 4B samples, in line with other studies showing that transposable elements are a major component of the B chromosome of rye and other species (Blavet et al 2021;Carchilan et al 2009;Coan and Martins 2018;Klemme et al 2013;Shi et al 2022), we found transcripts encoding transposable elements (MuDR transposase, MULE transposase, retrotransposon Gag protein). In addition, cell cycle-related B-specific transcripts were identified like encoding the kinetochore protein Nuf2, kinesins (KIN4C, KIN6, KIN 10B), a DEAD/DEAH box helicase, and the microtubule-associated protein (TPX2).…”

“…A comparable transcription effect of Bs was found in maize (Huang et al 2016 ; Shi et al 2022 ). Also, in Lilium amabile plants, recent RNA-seq analysis from leaf tissues of 0B and + 1B chromosomes revealed that 5.1% of the total transcripts were differentially expressed (threshold log 2 FC >|2|) (Park et al 2019 ).…”

“…A detailed analysis of selected B-encoded genic fragments revealed alternative splicing expression patterns and the ability to modulate the expression of their counterparts on A chromosomes in a tissue‐ and genotype‐dependent manner, suggesting that at least for some B-located genic sequences, the regulatory elements remained functional (Banaei-Moghaddam et al 2013 ). A similar transcription and regulatory behaviour have been demonstrated for the B chromosome of maize (Huang et al 2016 ; Shi et al 2022 ). However, the influence of the rye B on the rye host transcriptome and its impact on an alien host genome like wheat at the genome level has not been analysed yet.…”

Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize

“…sRNA libraries were generated directly from total RNA with TruSeq Small RNA Library Preparation Kit (Illumina, RS-200-0048) and were sequenced on the NextSeq500 platform at the University of Missouri Genomics Technology Core. sRNA-seq data of W22 maize plants with one B chromosome and W22 wild-type plants with no B chromosome were from a previous study 98 . The grouping information of the above materials was summarized in Supplementary Data 1 .…”

“…Targets of miRNAs were predicted using psRNATarget with an expected value of 3 or less 98 , 107 . miRNAs that function through translation repression were filtered out while those that function through target cleavage were retained.…”