De novo transcriptome sequencing and assembly from apomictic and sexual Eragrostis curvula genotypes

In higher plants, sexual and asexual reproduction through seeds (apomixis) have evolved as alternative strategies. As apomixis leads to the formation of clonal offspring, its great potential for agricultural applications has long been recognized. However, the genetic basis and the molecular control underlying apomixis and its evolutionary origin are to date not fully understood. Both in sexual and apomictic plants, reproduction is tightly controlled by versatile mechanisms regulating gene expression, translation, and protein abundance and activity. Increasing evidence suggests that interrelated pathways including epigenetic regulation, cell-cycle control, hormonal pathways, and signal transduction processes are relevant for apomixis. Additional molecular mechanisms are being identified that involve the activity of DNA- and RNA-binding proteins, such as RNA helicases which are increasingly recognized as important regulators of reproduction. Together with other factors including non-coding RNAs, their association with ribosomes is likely to be relevant for the formation and specification of the apomictic reproductive lineage. Subsequent seed formation appears to involve an interplay of transcriptional activation and repression of developmental programs by epigenetic regulatory mechanisms. In this review, insights into the genetic basis and molecular control of apomixis are presented, also taking into account potential relations to environmental stress, and considering aspects of evolution.

Section: Transcriptional Analysis Identifies Genes Differentially Regmentioning

confidence: 99%

Controlling Apomixis: Shared Features and Distinct Characteristics of Gene Regulation

Schmidt

2020

“…Eragrostis curvula (weeping lovegrass), an African grass with cytotypes of different ploidy levels (e.g., 2x–8x) and displaying obligate and facultative apomixis and sexual reproduction [ 46 ], has become a model for the analysis of apomixis mechanisms, due to its particular diplosporous development (meiotic diplospory maintaining the same embryo: endosperm ploidy ratio as in sexual seeds). In recent years, the reproductive mode of this grass was studied extensively, providing information about the cytoembryological aspects of its apomictic–sexual development [ 47 ], differentially expressed (DE) transcripts [ 48 , 49 , 50 , 51 ], epigenetic aspects of apomictic regulation [ 52 , 53 ], mapping of the apomixis locus [ 54 ] and a high quality genome assembly [ 55 ]. Our group also demonstrated that under different internal and external stressful situations, including a change in ploidy, water stress, in vitro culture and intraspecific hybridization, the number of sexual embryo sacs increased in facultative apomictic plants of this grass [ 40 , 56 ].…”

Section: Introductionmentioning

confidence: 99%

“…The aim of the present study was to identify genes that are differentially expressed in weeping lovegrass inflorescences of control and water-stressed facultative apomictic plants and to compare them with the differentially expressed genes between apomictic and sexual plants previously reported by our group [ 51 ]. This approach was taken based on previous findings about increases of sexual processes under stress conditions [ 40 ], in order to look for common pathways between stress and apomixis.…”

Section: Introductionmentioning

confidence: 99%

Genes Modulating the Increase in Sexuality in the Facultative Diplosporous Grass Eragrostis curvula under Water Stress Conditions

Selva

Zappacosta

Carballo

et al. 2020

Self Cite

Eragrostis curvula presents mainly facultative genotypes that reproduce by diplosporous apomixis, retaining a percentage of sexual pistils that increase under drought and other stressful situations, indicating that some regulators activated by stress could be affecting the apomixis/sexual switch. Water stress experiments were performed in order to associate the increase in sexual embryo sacs with the differential expression of genes in a facultative apomictic cultivar using cytoembryology and RNA sequencing. The percentage of sexual embryo sacs increased from 4 to 24% and 501 out of the 201,011 transcripts were differentially expressed (DE) between control and stressed plants. DE transcripts were compared with previous transcriptomes where apomictic and sexual genotypes were contrasted. The results point as candidates to transcripts related to methylation, ubiquitination, hormone and signal transduction pathways, transcription regulation and cell wall biosynthesis, some acting as a general response to stress and some that are specific to the reproductive mode. We suggest that a DNA glycosylase EcROS1-like could be demethylating, thus de-repressing a gene or genes involved in the sexuality pathways. Many of the other DE transcripts could be part of a complex mechanism that regulates apomixis and sexuality in this grass, the ones in the intersection between control/stress and apo/sex being the strongest candidates.

“…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).…”

Section: Genetic and Genomic Features Of Apomixismentioning

confidence: 99%

Apomixis Technology: Separating the Wheat from the Chaff

Hojsgaard

2020

Projections indicate that current plant breeding approaches will be unable to incorporate the global crop yields needed to deliver global food security. Apomixis is a disruptive innovation by which a plant produces clonal seeds capturing heterosis and gene combinations of elite phenotypes. Introducing apomixis into hybrid cultivars is a game-changing development in the current plant breeding paradigm that will accelerate the generation of high-yield cultivars. However, apomixis is a developmentally complex and genetically multifaceted trait. The central problem behind current constraints to apomixis breeding is that the genomic configuration and molecular mechanism that initiate apomixis and guide the formation of a clonal seed are still unknown. Today, not a single explanation about the origin of apomixis offer full empirical coverage, and synthesizing apomixis by manipulating individual genes has failed or produced little success. Overall evidence suggests apomixis arise from a still unknown single event molecular mechanism with multigenic effects. Disentangling the genomic basis and complex genetics behind the emergence of apomixis in plants will require the use of novel experimental approaches benefiting from Next Generation Sequencing technologies and targeting not only reproductive genes, but also the epigenetic and genomic configurations associated with reproductive phenotypes in homoploid sexual and apomictic carriers. A comprehensive picture of most regulatory changes guiding apomixis emergence will be central for successfully installing apomixis into the target species by exploiting genetic modification techniques.