Generation of an integrated Hieracium genomic and transcriptomic resource enables exploration of small RNA pathways during apomixis initiation

Abstract

BackgroundApplication of apomixis, or asexual seed formation, in crop breeding would allow rapid fixation of complex traits, economizing improved crop delivery. Identification of apomixis genes is confounded by the polyploid nature, high genome complexity and lack of genomic sequence integration with reproductive tissue transcriptomes in most apomicts.ResultsA genomic and transcriptomic resource was developed for Hieracium subgenus Pilosella (Asteraceae) which incorporates characterized sexual, apomictic and mutant apomict plants exhibiting reversion to sexual reproduction. Apomicts develop additional female gametogenic cells that suppress the sexual pathway in ovules. Disrupting small RNA pathways in sexual Arabidopsis also induces extra female gametogenic cells; therefore, the resource was used to examine if changes in small RNA pathways correlate with apomixis initiation. An initial characterization of small RNA pathway genes within Hieracium was undertaken, and ovary-expressed ARGONAUTE genes were identified and cloned. Comparisons of whole ovary transcriptomes from mutant apomicts, relative to the parental apomict, revealed that differentially expressed genes were enriched for processes involved in small RNA biogenesis and chromatin silencing. Small RNA profiles within mutant ovaries did not reveal large-scale alterations in composition or length distributions; however, a small number of differentially expressed, putative small RNA targets were identified.ConclusionsThe established Hieracium resource represents a substantial contribution towards the investigation of early sexual and apomictic female gamete development, and the generation of new candidate genes and markers. Observed changes in small RNA targets and biogenesis pathways within sexual and apomictic ovaries will underlie future functional research into apomixis initiation in Hieracium.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-016-0311-0) contains supplementary material, which is available to authorized users.

Controlling Apomixis: Shared Features and Distinct Characteristics of Gene Regulation

“…Differential representation of small RNA reads in Paspalum notatum points towards their involvement in regulation of meiosis, cell cycle control, transcriptional regulation and hormonal signaling [117]. In contrast, in Hieracium only small numbers small RNA targets were identified as differentially expressed [114]. From comparisons of sexual and apomictic Boechera ovules differential activity of the small RNAs miR156/157 has been identified which is relevant for the regulation of the transcription factor SQUAMOSA PROTEIN BINDING PROTIEN LIKE 11 (SPL11) [139].…”

Apomixis Technology: Separating the Wheat from the Chaff

“…Attempts to identify components of apomixis by transcriptional profiling of reproductive organs using Differential Display PCR (DD-PCR), SuperSAGE (serial analysis of gene expression), and high-throughput sequencing on microdissected ovules revealed 1) differentially expressed genes in reproductive tissues of apomictic and sexual relatives from different plant systems (e.g., Pennisetum, [69,70]; Brachiaria, [71,72]; Panicum, [73,74]; Poa, [75], Eragrostis, [76][77][78]; Paspalum, [42,64,[79][80][81]; Hieracium, [82,83]; Hypericum [84,85]) and 2) an overall shift in gene regulation at the MMC stage and a global heterochronic gene expression between the sexual and apomeiotic ovules (e.g., Boechera, [86][87][88][89]; Paspalum [79,90,91]; Pennisetum, [92]; Hieracium, [83,93,94]; Hypericum [85,95]; Ranunculus [96,97]). Such wide-ranging de-regulation on gene expression levels between sexual and apomictic ovules affect genes encoding varied biological functions (GO classes) and regulatory pathways, including key genes of the sexual pathway, RNA-directed DNA methylation and transcription regulation, hormonal signaling, and cell cycle control (see details in the next section).…”

“…Moreover, analyses of transcriptomes are complicated in most apomictic species by the high complexity, redundancy and polyploid nature of their genomes. The limitations of de novo transcriptomic assemblies in the absence of genomic information frequently lead to the compression of multiple gene copies into single transcriptome contigs, effectively reducing the gene space, but with potential loss of informative alleles [94,111].…”

“…In Hieracium, using dihaploid and tetraploid apomictic plants and deletion mutants for apomixis (LOA) and parthenogeneisis (LOP) loci, Rabiger et al [94] identified ovary-expressed ARGONAUTE genes and differentially expressed genes enriched for processes involved in small RNA biogenesis and chromatin silencing in apomicts, plus a small number of putative differentially targeted genes within the mutants and potential candidates in the specification and initiation of aposporous initial (AI) cells. Diverse Arabinogalactan-proteins (AGPs) were identified in AI and FM cells, expressed during early sexual and aposporous gametophyte development, which suggest a role in communication and signal transduction events leading to megaspore death and AI cell differentiation and progression toward gametogenesis [123].…”

“…Nees] (genome size~660 Mb; [209]), a diploid sexual forage grass having apomictic polyploid cytotypes, and the genomes of Boechera stricta (genome size 216 Mb) and B. retrofracta (genome size 200 Mb) [210][211][212], two sexual diploid herbs relative to apomictic B. holboellii and B. divaricarpa, represent an effort in that direction. Two recently-initiated projects aiming at sequencing the genome of several sexual and apomictic Boechera species in Canada [213] and Switzerland [214], and the generation of an apomictic Hieracium (predicted genome size 3.6 Gb) genomic and transcriptomic resource [94], may provide the first datasets for sexual-apomictic pair genomic comparisons.…”