Comparative transcriptome analysis of the wild-type model apomict Hieracium praealtum and its loss of parthenogenesis (lop) mutant

Abstract

Background: Asexual seed formation (apomixis) has been observed in diverse plant families but is rare in crop plants. The generation of apomictic crops would revolutionize agriculture, as clonal seed production provides a low cost and efficient way to produce hybrid seed. Hieracium (Asteraceae) is a model system for studying the molecular components of gametophytic apomixis (asexual seed reproduction).

Results: In this study, a reference transcriptome was produced from apomictic Hieracium undergoing the key apomictic events of apomeiosis, parthenogenesis and autonomous endosperm development. In addition, transcriptome sequences from pre-pollination and post-pollination stages were generated from a loss of parthenogenesis (lop) mutant accession that exhibits loss of parthenogenesis and autonomous endosperm development. The transcriptome is composed of 147,632 contigs, 50% of which were annotated with orthologous genes and their probable function. The transcriptome was used to identify transcripts differentially expressed during apomictic and pollination dependent (lop) seed development. Gene Ontology enrichment analysis of differentially expressed transcripts showed that an important difference between apomictic and pollination dependent seed development was the expression of genes relating to epigenetic gene regulation. Genes that mark key developmental stages, i.e. aposporous embryo sac development and seed development, were also identified through their enhanced expression at those stages.

Conclusion: The production of a comprehensive floral reference transcriptome for Hieracium provides a valuable resource for research into the molecular basis of apomixis and the identification of the genes underlying the LOP locus.

Keywords: Apomixis; Asexual; Hieracium; Parthenogenesis; RNA sequencing; Transcriptome.

Fig. 1

Similarity search result. Putative Hieracium genes were searched against NCBI-NR and Swiss-Prot databases. a E-value distribution of best BLASTX result of genes (E-value of 1e-4). b Similarity distribution of the top BLASTX hit for each gene. c Proportion of genes with BLASTX results in relation of the length of genes

Fig. 2

Expression patterns of DE transcripts associated with epigenetic regulation. Hierarchically clustered expression heatmap with rows represent each transcript and relative expression (low in green and high in red) in the samples as indicated. Pre-embryo stages are indicated in light blue and post-embryo stages in dark blue text; the lop mutant pre-pollination (lop E1, E2) and post pollination (lop L1 and L2) are also highlighted)

Fig. 3

Expression pattern of DE transcripts (lop138 pre- vs post-pollination) associated with the GO category ‘reproduction’. Hierarchically clustered expression heatmap with rows represent each transcript (labeled by the putative protein and the transcript ID) and relative expression (low in green and high in red) in the samples as indicated. Pre-embryo stages are indicated in light blue and post-embryo stages in dark blue text; the lop mutant pre-pollination (lop E1, E2) and post pollination (lop L1 and L2) are also highlighted)

Fig. 4

Expression patterns of DE transcripts (lop138 vs WT) associated with the GO category ‘reproduction’. Hierarchically clustered expression heatmap with rows represent each transcript (labeled by the putative protein and the transcript ID) and relative expression (low in green and high in red) in the samples as indicated. Pre-embryo stages are indicated in light blue and post-embryo stages in dark blue text; the lop mutant pre-pollination (lop E1, E2) and post pollination (lop L1 and L2) are also highlighted)

Fig. 5

Expression patterns of DE transcripts associated with auxin transport and embryo development. Hierarchically clustered expression heatmap with rows represent each transcript (labeled by the putative protein and the transcript ID) and relative expression (low in green and high in red) in the samples as indicated. Pre-embryo stages are indicated in light blue and post-embryo stages in dark blue text; the lop mutant pre-pollination (lop E1, E2) and post pollination (lop L1 and L2) are also highlighted)

Fig. 6

Expression patterns of DE transcripts homologous to AGL61, AGL62 and AGL80. Hierarchically clustered expression heatmap with rows represent each transcript (labeled by the putative protein and the transcript ID) and relative expression (low in green and high in red) in the samples as indicated. Pre-embryo stages are indicated in light blue and post-embryo stages in dark blue text; the lop mutant pre-pollination (lop E1, E2) and post pollination (lop L1 and L2) are also highlighted)

Fig. 7

Capitulum stage-enhanced gene expression. Vertical axis is the UPC value and the horizontal axis shows the R35 ovary sample codes, the numbers in the sample code represent the capitulum stage sampled. The UPC values were plotted across the capitulum stages in order to select those that showed expression peaks in a capitulum stage (> 0.5 UPC)