The abundance of homoeologue transcripts is disrupted by hybridization and is partially restored by genome doubling in synthetic hexaploid wheat

Abstract

Background: The formation of an allopolyploid is a two step process, comprising an initial wide hybridization event, which is later followed by a whole genome doubling. Both processes can affect the transcription of homoeologues. Here, RNA-Seq was used to obtain the genome-wide leaf transcriptome of two independent Triticum turgidum × Aegilops tauschii allotriploids (F1), along with their spontaneous allohexaploids (S1) and their parental lines. The resulting sequence data were then used to characterize variation in homoeologue transcript abundance.

Results: The hybridization event strongly down-regulated D-subgenome homoeologues, but this effect was in many cases reversed by whole genome doubling. The suppression of D-subgenome homoeologue transcription resulted in a marked frequency of parental transcription level dominance, especially with respect to genes encoding proteins involved in photosynthesis. Singletons (genes where no homoeologues were present) were frequently transcribed at both the allotriploid and allohexaploid plants.

Conclusions: The implication is that whole genome doubling helps to overcome the phenotypic weakness of the allotriploid, restoring a more favourable gene dosage in genes experiencing transcription level dominance in hexaploid wheat.

Keywords: Genome duplication; Interspecific hybridization; Polyploidy; Synthetic wheat; Transcriptome evolution.

Fig. 1

The morphology and cytology of T. turgidum AS2255 (AABB), A. tauschii AS60 (DD), the allotriploid AS2255 × AS60 (ABD) and the derived allohexaploid (AABBDD). a Fluorescent in situ hybridization (FISH) analysis of the 21 univalents presents at meiosis metaphase I in the meiocyte of an allotriploid plant. The probe 6C6-3 hybridizing to the centromeres fluoresced green. Bar: 10 μm. b Allotriploid pollen mother cells comprise a mixture of dyads (green arrowheads) and tetrads (red arrowheads). c Multi-colour genomic in situ hybridization of a root tip mitotic cell from an allohexaploid plant, showing 2n = 6x = 42. d Sequential multi-colour FISH of a root tip mitotic cell from an allohexaploid plant, showing that chromosomes of the A, B and D genome were all represented on basis of probes pSc119.2 (green), pAs1 (red), and pTa71 (yellow). e Morphology of 120 day old plants of AS2255, AS60 and their derived allotriploid (F1) and allohexaploid (S1). f Leaf width and length of the first four leaves of the plants. Whiskers indicate SD (allotriploid: n = 7, AS2255, AS60 and allohexaploid: n = 12)

Fig. 2

Variation in the transcription of homoelogues as a result of allotriploidization and WGD in the AS2255 × AS60 lineage. a Differentially transcribed homoeologues. The number next to the symbol for the species represents the number of differentially up-regulated homoeologues vs. the neighboring species linked by a line. A consistent colour has been used to refer to each genome (A genome: blue, B genome: yellow, D genome: purple). Numbers in the middle of each line represent the total numbers of differentially transcribed homoeologues (black). b Boxplots illustrating the effect of allotriploidization and WGD on transcript abundance: homoeologues from (1) the A genome, (2) the B genome, (3) the D genome. Differentially transcribed D genome homoeologues between the allotriploid and parent that were transmitted into allohexaploid are used as controls (4). Boxes span the data range between the first and third quartiles, and the median is represented as a horizontal line. Whiskers extend to the most extreme data point, which is no more than 1.5 times the interquartile range away from the first and third quartiles. The widths of the boxes are proportional to the gene numbers

Fig. 3

Non-additive transcription of genes in the allotriploid and allohexaploid in the lineage AS2255 × AS60. a Numbers of non-additively transcribed genes in the progeny compared to mid-parent value (MPV). The red numbers shown refer to genes up-regulated (bottom) or down-regulated (top) in the allotriploid (F1) and allohexaploid (S1). b The number of non-additive genes common to the allotriploid and allohexaploid. GO enrichment terms for the genes non-additively down-regulated in the allotriploid are shown below the figure. c Homoeologue expression patterns of non-additively expressed genes. “Up” and “down” refer to homoeologues differentially transcribed between the progeny and the parents, whereas “no change” implies that the transcription levels were statistically unchanged by either the allotriploidization or the WGD

Fig. 4

Parental expression level dominance (ELD) genes in the allotriploid and allohexaploid. a The number of genes with a transcription level similar to that in T. turgidum (ELD-ab genes) or that in AS60 (ELD-d genes) in both the AS2255 × AS60 and LDN × AS60 lineages. b The number of ELD-ab genes common to the allotriploid and allohexaploidand the associated enriched GO terms. c Genes encoding major components of the RNA-dependent DNA methylation pathway (DMS3, AGO4, and IDN2) were classified as ELD-ab genes. The histograms show the FPKMs of the relevant homoeologues in AS2255 (A genome blue, B genome red), AS60 (green), allotriploid (ABD) and allohexaploid (AABBDD)

Fig. 5

The transcription of singletons in the AS2255 × AS60 lineage. a Singletons classified according to genome origin; enriched GO terms found in the shared singleton genes are shown below the Venn diagram. b The function of singletons derived from the MapMan program