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. 2019 Jan 10;20(1):29.
doi: 10.1186/s12864-018-5421-3.

The genome-wide transcriptional consequences of the nullisomic-tetrasomic stocks for homoeologous group 7 in bread wheat

Rongzhi Zhang  1 , Shuaifeng Geng  2 , Zhengrui Qin  2 , Zongxiang Tang  3 , Cheng Liu  4 , Dongfeng Liu  5 , Guoqi Song  4 , Yulian Li  4 , Shujuan Zhang  4 , Wei Li  4 , Jie Gao  4 , Xiaodong Han  4 , Genying Li  6
Affiliations

The genome-wide transcriptional consequences of the nullisomic-tetrasomic stocks for homoeologous group 7 in bread wheat

Rongzhi Zhang et al. BMC Genomics. .

Abstract

Background: Hexaploid bread wheat (Triticum aestivum L) arose by two polyploidisation events from three diploid species with homoeologous genomes. Nullisomic-tetrasomic (nulli-tetra or NT) lines are aneuploid wheat plants lacking two and adding two of six homoeologous chromosomes. These plants can grow normally, but with significantly morphological variations because the adding two chromosomes or the remaining four chromosomes compensate for those absent. Despite these interesting phenomena, detailed molecular mechanisms underlying dosage deletion and compensation in these useful genetic materials have not been determined.

Results: By sequencing the transcriptomes of leaves in two-week-old seedlings, we showed that the profiles of differentially expressed genes between NT stocks for homoeologous group 7 and the parent hexaploid Chinese Spring (CS) occurred throughout the whole genome with a subgenome and chromosome preference. The deletion effect of nulli-chromosomes was compensated partly by the tetra-chromosomes via the dose level of expressed genes, according to the types of homoeologous genes. The functions of differentially regulated genes primarily focused on carbon metabolic process, photosynthesis process, hormone metabolism, and responding to stimulus, and etc., which might be related to the defective phenotypes that included reductions in plant height, flag leaf length, spikelet number, and kernels per spike.

Conclusions: The perturbation of the expression levels of transcriptional genes among the NT stocks for homoeologous group 7 demonstrated the gene dosage effect of the subgenome at the genome-wide level. The gene dosage deletion and compensation can be used as a model to elucidate the functions of the subgenomes in modern polyploid plants.

Keywords: Dosage compensation; Dosage deletion; Gene expression; Nullisomic-tetrasomic stocks; Triticum aestivum L.

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Conflict of interest statement

Ethics approval and consent to participate

The original seeds of NT stocks used in this study were provided by the Wheat Genetics Resource Center (WGRC). The experimental research on wheat including NT stock and Chinese Spring, complied with the Crop Research Institute, Shandong Academy of Agricultural Sciences (SAAS), and followed the Material Transfer Agreement (MTA) and Code of Ethics of the WGRC guidelines. The field studies was conducted in accordance with the legislation of Crop Research Institute, SAAS.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Phenotypes of the NT stocks for group 7 and CS in Spike (a), plant height (b), flag leaf length (c), spikelet number (d), and kernels in per spike (e)
Fig. 2
Fig. 2
Gene expression profiles in the NT stocks for group 7. a The correlation of gene expression among the NT stocks for group 7. b The distribution of the lowly (RPKM < 10, black rectangles), mediumly (10 < = RPKM < 100, red rectangles), and highly (RPKM > = 100, blue rectangles) expressed genes. c The density distribution of fold change (log2(NT/CS)) of gene expression for the lowly (black lines), mediumly (red lines), and highly (blue lines) expressed genes in the NT stocks for group 7 compared with CS. The grey background represented the model normalisation distribution
Fig. 3
Fig. 3
The distribution of ratios of gene number (NT/CS; a) and gene expression level (log2(NT/CS); c) for the lowly, mediumly, and highly expressed genes in the NT stocks for group 7 compared with CS. The pink, light pink, and dark pink rectangles represented the subgenome A, subgenome B, and subgenome D, respectively. b Correlation between the expression level and the percentage of up-regulated genes. d The preference of proportion distribution of SDEGs on the tetra-chromosome 7A, 7B, and 7D. e-f The up- (e) and down- (f) regulated significantly differentially expressed genes
Fig. 4
Fig. 4
Fold changes (log2(NT/CS)) of gene expression were organized in chromosomal domains. The profile comparison of the differentially expressed genes between the NT stocks and CS along the wheat chromosomes
Fig. 5
Fig. 5
The categories of the SDEGs. a Distribution of the SDEGs for the three categories including triplet genes, duplet genes, and singleton genes. The light cadet blue, cadet blue, and dark cadet blue represented the triplet genes, duplet genes, and singleton genes, respectively; b Distribution of singleton genes for the lowly (black rectangle), mediumly (red rectangle), and highly expressed genes (dark rectangle); c-d Distribution of duplet genes with two (c) or one (d) homoeologous SDEGs for the low, medium and high expression level; e-g Distribution of triplet genes with three (e), or two (f) or one (g) homoeologous SDEGs for the low, medium and high expression level
Fig. 6
Fig. 6
The GO enrichment analysis in the down-regulated (a) and up-regulated (b) genes overlapped among N7A (N7AT7B∩N7AT7D), N7B (N7BT7A∩N7BT7D), and N7D (N7DT7A∩N7DT7B) referred to CS
Fig. 7
Fig. 7
The Module of gene partial dosage compensation due to the asymmetrical gene distribution (the top and middle panels) in the gene regulation network (the top and bottom panels) for the NT stocks of group 7. Red circles and rectangles represented the triplet and duplet genes; Purple, green and blue ones represented for the singleton gene on the chromosome 7A, 7B and 7D respectively; The grey ones represented the null-homoeologs; The black ones represented the genes on the non-chromosome 7
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