Periodic Reporting for period 1 - POLYPLOID (THE POLYPLOIDY PARADIGM AND ITS ROLE IN PLANT BREEDING)
Période du rapport: 2021-04-01 au 2023-09-30
Within WP2 we are sequencing diploid/natural polyploid/artificial polyploid genomes as well as polyploids from bilateral sexual polyploidization of several species (D2.1). The transcriptomes of all these populations are also being characterized (D2.2). We are also identifying candidate genes differentially expressed after polyploidization events (D2.3) and functionally characterizing some of them (D2.4). Moreover, we are characterizing the long-term effects of apomictic reproduction on polyploid genomes (D2.5).
Moreover, we are also characterizing the pan-genomes and/or pan-epigenomes of Eragrostis curvula, Paspalum spp. Solanum spp (D 2.5).
In Solanum commersonii, we induced genome doubling, and the new tetraploids, together with its diploid progenitor, are being maintained and propagated in vitro on MS medium.
The WP3 is dependent on the results of other WPs and so we are still working actively on it. Once the genomes originated from long-term and short term polyploidization events are ready, we will compare the structural variation. Moreover, once the pantranscriptomes and panepigenomes are characterized, we will search for stochastic and recurrent expression/epigenetic variation.
Within WP4, we identified a list of genes possibly related to desirable agronomic traits from the differentially expressed transcripts (DETs) data originating from previous studies of the POLYPLOID research groups (D4.1).
Moreover, the University of Galway (NUI) developed F1 triploid hybrid lines by performing crosses between a 4x Ler-0 maternal parent and 388 natural accessions of Arabidopsis thaliana as pollen donors and has generated homozygous mutant lines of candidate genes in tetraploid backgrounds to enable epigenetic modifier analyses in 3x and 4x backgrounds which is underway.
We, therefore, obtained mutant stocks for the aforementioned candidate genes (D4.2) and the Functional analysis in Arabidopsis of candidate genes for the emergence of desirable agronomic is ongoing (D4.3).
During the first part of the project, within WP5 we evaluated a field essay of several Paspalum species using three independent experimental blocks with and without nitrogen fertilization. Based on this phenotypic evaluation, we selected genotypes with contrasting profiles to carry on the genomic/epigenomic survey.
WP6 was dedicated to understanding the base of the triploid block.
At the beginning of the project, we charactered the developmental dynamics of triploid block (D6.1) and characterized different “natural tetraploid” Arabidopsis ecotypes. We are now performing allele-specific RNAseq analysis and qRT-PCR analysis of triploid block upon fertilization of sexual and apomictic plants (D6.2). We are also functionally characterizing candidate genes involved in the control of the triploid block process (D6.3). Moreover, we are looking for differentially methylated genes associated with dysregulation of the triploid block in sexual and apomictic plants (D6.4) and of new genes controlling the seed intercompartmental crosstalk in response to triploid block identified for both sexual and apomictic plants (D6.5)
There are major gaps in the polyploidy research field: 1) multidisciplinary, integrative approaches applied to multiple polyploid systems/ecological settings remain necessary to understand the genome response to polyploidization; 2) genes controlling the emergence of polyploidy-associated phenotypic characteristics need to be identified; 3) the ecological and physiological contexts of polyploidization need to be investigated; 4) the response to polyploidization in the seed, stemming from unbalanced paternal and maternal contribution is not known; 5) the response to increase of ploidy during sporogenesis in the context of apomixis is not known.
Through this project, we contribute to filling the above-mentioned gaps by providing a thorough characterization of chromosomal changes, gene loss, gene expression, DNA methylation, physiological changes, and ecological features of several autopolyploid and segmental allopolyploid crop species of the genera Paspalum, Eragrostis, Medicago, Solanum. Arabidopsis, Hieracium, and Taraxacum will be used as model species in the triploid block and apomixis-related investigations.