Periodic Reporting for period 1 - POLYPLOID (THE POLYPLOIDY PARADIGM AND ITS ROLE IN PLANT BREEDING)
Okres sprawozdawczy: 2021-04-01 do 2023-09-30
Plants can undergo spontaneous chromosome number duplication, or polyploidization, which is a major evolutionary trigger. While all seed plants have experienced at least one round of whole genome duplication in their history, it tends to be an isolated event within diploids. Plant breeders are aware of the potential of polyploidization for crop improvement. The present project focused on filling the knowledge gaps about non-model species regarding chromosomal changes, gene loss, gene expression, methylation and physiological changes, and ecological features. The project will encourage synergy between European and international expertise, aiming to facilitate plant breeding. The POLYPLOID Consortium involves nine partner institutions, six from 4 MS (Italy, Ireland, Spain, Netherlands) and three from TD (New Zealand, Argentina, and USA). It will have a sizable impact above and beyond those involved in the exchanges at different levels related to career prospects and the establishment of lasting research collaboration. This proposal aimed at strengthening and/or initiating partnerships between these groups, all focused on either model plants or crops, therefore facilitating interactions between fundamental and applied aspects of plant research. Therefore, POLYPLOID represents an attractive staff exchange platform for sharing knowledge and technical expertise and familiarizing with multicultural working environments. Enhancing the career prospects embraces the technical aspects of the research conducted and the capacity to design creative experiments, manage an interdisciplinary project in a multicultural environment, and acquire communication tools. This consolidates previous collaborations and generates opportunities for new ones within the Consortium. The action has succeeded in meeting the objectives posed for the second term of the project. Completed secondments allowed the follow-up of established research and the achievement of the common goals of participants. Some articles derived from the joint work were published or submitted to scientific journals.
During the first two years of WP1, we created a project logo and the project website (https://polyploid.eu).
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)
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)
The results presented in this project involve an unprecedented development of molecular data and tools to understand the basis and the role of polyploidization. In fact, polyploidy is a major force in the evolution of plants, and it is a currently accepted concept that all seed plants have experienced at least one round of whole genome duplication (WGD) in their evolutionary history. Frequent consequences of polyploidy are the increased size of plant organs (gigas effects), the increased tolerance to biotic and abiotic stresses, as well as the emergence of sterility and novel asexual reproductive modes (apomixis). This has attracted the attention of plant breeders who use polyploidy as a tool for crop improvement.
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.
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.