Periodic Reporting for period 1 - MAD (Mechanisms of Apomictic Developments)
Berichtszeitraum: 2020-12-01 bis 2023-11-30
Numerous plants evolved the ability to form viable seeds harbouring maternal embryos, an intriguing phenomenon, known as apomixis. By allowing the development of true-breeding crops, harnessing apomixis would revolutionize agriculture. In particular, faster and cheaper plant breeding could yield locally adapted varieties and, therefore, help mitigate climate changes by making agrifood systems more efficient for food security and nutrition.
Despite decades of research using both sexual plant models and apomictic species, apomixis remains an enigma for plant biologists and a long-awaited tool by breeders and farmers. However, the recent advances in plant biotechnologies have provided valuable information to understand sexual reproduction in plants and, occasionally, to redirect the sexual development program toward apomixis-like reproductive modes. They also have opened the route for investigating apomictic species at unprecedented, cellular and molecular levels.
The MAD (Mechanisms of Apomictic Developments) project will establish an international, research and training network aiming at contributing significantly to our understanding of key mechanisms involved in redirecting sexuality towards apomixis. It bridges knowledge and biological resources recently generated by collaborative efforts in the field of apomixis biology, and novel expertise in biotechnology and breeding by aggregating new partners. Through research, training and dissemination actions, the project will clarify the genetic architecture of apomixis and support the deployment of innovative strategies in crop improvement. This knowledge will contribute to overcome the barriers that prevent plant breeders and farmers from reaping the benefits of apomixis.
Despite decades of research using both sexual plant models and apomictic species, apomixis remains an enigma for plant biologists and a long-awaited tool by breeders and farmers. However, the recent advances in plant biotechnologies have provided valuable information to understand sexual reproduction in plants and, occasionally, to redirect the sexual development program toward apomixis-like reproductive modes. They also have opened the route for investigating apomictic species at unprecedented, cellular and molecular levels.
The MAD (Mechanisms of Apomictic Developments) project will establish an international, research and training network aiming at contributing significantly to our understanding of key mechanisms involved in redirecting sexuality towards apomixis. It bridges knowledge and biological resources recently generated by collaborative efforts in the field of apomixis biology, and novel expertise in biotechnology and breeding by aggregating new partners. Through research, training and dissemination actions, the project will clarify the genetic architecture of apomixis and support the deployment of innovative strategies in crop improvement. This knowledge will contribute to overcome the barriers that prevent plant breeders and farmers from reaping the benefits of apomixis.
WP1 ensured transparent and effective governance and compliance with scientific and education objectives through regular coordination meetings and the organisation of two general meetings and through the set up and collect of documents for material and data transfer (WP1) and ethical rules (WP7).
WP2 ensured wide visibility of the project and of its objectives and achievements by : producing a logo and a short video for presenting the project to a broad audience; setting up and maintaining a website presenting the project and its progress; publishing a on-line course on Plant Reproductive Biology; organizing two workshops in relation with WP3 and WP6 activities, and; contributing to the organization of the IV international conference on apomixis in Rosario, Argentina (Dec 3-7, 2023). Finally, participants contributed to 13 scientific publications and 15 presentations at international congresses.
WP3 - What is the functional role of the genomic regions specific of apomicts genomes? Since genetic analyses in grasses have long revealed that apomixis is controlled by a single chromosomic region, so-called the ACL (Apomixis Controlling Locus), the MAD partners assembled the genome sequence of several apomictic grasses, ie Eragrostis curvula at a chromosome-scale resolution and, to lower resolutions, that of Paspalum simplex and P. notatum. This led, first, to the identification of candidate genes in the ACL of Paspalum and E. curvula, some of them currently under investigation in plant model species. Finally, owing to the newly assembled genome and of transcriptomic resources in P. notatum, we set up a bioinformatic pipeline for comparing genic expression in sexual and apomictic ovules. First results identified a set of ~1700 genes showing significant differences in isoform variants.
WP4 - Are the transcriptional patterns promoting apomixis shaped transcriptionally or post-transcriptionally? First, the partners initited the characterization of candidate genes obtained from previous comparative analyses in Paspalum, Eragrostis and Hypericum. For two of them, Tgs1 and ARF10, our observations indicate that altered expression results in apomixis-like reproduction. Similarly, several short non-coding RNAs, post-transcriptional regulators of the expression of key genes such as ARF10, are also under investigation. Finally, two other regulatory processes of gene expression, alternative splicing and epigenetic chromatin modifications, are being studied in conjunction with WP3 to identify candidate genes for the emergence of apomixis in sexual plants.
WP5 - How do phytohormones interact to establish and control reproductive cell fate during plant reproduction? MAD partners first generated biosensors for analysing two key hormones, auxin and cytokinin, during ovule development in Paspalum notatum. Another approach consists in the characterization of auxin response factors (ARF) that contribute to auxin signal transduction in plants. Previous results in Paspalum have suggested a possible role for ARFs in the establishment of apomixis leading MAD partners to functionally characterize several ARF genes in sexual model species. As a first result, they showed that overexpression of ARF10 in Arabidopsis thaliana leads to phenotypes reminiscent of apomixis.
WP6: does ovule architecture exert control over female germ line fate? Progress was achieved mainly through 3D imaging and quantitative analysis of early ovule architecture, cell divisions and shapes in a sexual model crop, maize, and in an apomictic Paspalum rufum. Through the assembly and analysis of a collection of >1000 images from maize and P.rufum ovules, the first 3D atlas of maize ovule primordium was published, and for P.rufum a pilot for quantitative analysis using MorphographXs and R softwares was developped.
WP2 ensured wide visibility of the project and of its objectives and achievements by : producing a logo and a short video for presenting the project to a broad audience; setting up and maintaining a website presenting the project and its progress; publishing a on-line course on Plant Reproductive Biology; organizing two workshops in relation with WP3 and WP6 activities, and; contributing to the organization of the IV international conference on apomixis in Rosario, Argentina (Dec 3-7, 2023). Finally, participants contributed to 13 scientific publications and 15 presentations at international congresses.
WP3 - What is the functional role of the genomic regions specific of apomicts genomes? Since genetic analyses in grasses have long revealed that apomixis is controlled by a single chromosomic region, so-called the ACL (Apomixis Controlling Locus), the MAD partners assembled the genome sequence of several apomictic grasses, ie Eragrostis curvula at a chromosome-scale resolution and, to lower resolutions, that of Paspalum simplex and P. notatum. This led, first, to the identification of candidate genes in the ACL of Paspalum and E. curvula, some of them currently under investigation in plant model species. Finally, owing to the newly assembled genome and of transcriptomic resources in P. notatum, we set up a bioinformatic pipeline for comparing genic expression in sexual and apomictic ovules. First results identified a set of ~1700 genes showing significant differences in isoform variants.
WP4 - Are the transcriptional patterns promoting apomixis shaped transcriptionally or post-transcriptionally? First, the partners initited the characterization of candidate genes obtained from previous comparative analyses in Paspalum, Eragrostis and Hypericum. For two of them, Tgs1 and ARF10, our observations indicate that altered expression results in apomixis-like reproduction. Similarly, several short non-coding RNAs, post-transcriptional regulators of the expression of key genes such as ARF10, are also under investigation. Finally, two other regulatory processes of gene expression, alternative splicing and epigenetic chromatin modifications, are being studied in conjunction with WP3 to identify candidate genes for the emergence of apomixis in sexual plants.
WP5 - How do phytohormones interact to establish and control reproductive cell fate during plant reproduction? MAD partners first generated biosensors for analysing two key hormones, auxin and cytokinin, during ovule development in Paspalum notatum. Another approach consists in the characterization of auxin response factors (ARF) that contribute to auxin signal transduction in plants. Previous results in Paspalum have suggested a possible role for ARFs in the establishment of apomixis leading MAD partners to functionally characterize several ARF genes in sexual model species. As a first result, they showed that overexpression of ARF10 in Arabidopsis thaliana leads to phenotypes reminiscent of apomixis.
WP6: does ovule architecture exert control over female germ line fate? Progress was achieved mainly through 3D imaging and quantitative analysis of early ovule architecture, cell divisions and shapes in a sexual model crop, maize, and in an apomictic Paspalum rufum. Through the assembly and analysis of a collection of >1000 images from maize and P.rufum ovules, the first 3D atlas of maize ovule primordium was published, and for P.rufum a pilot for quantitative analysis using MorphographXs and R softwares was developped.
The MAD project have generated key biological resources such as plants carrying biosensors and/or mutations of interest; vast amounts of data in several area including genome sequencing, DNA methylation and gene expression analyses, imaging, and; protocols and analytical tools in cellular biology, bioinformatics and 3D confocal image analysis. Overall, we expect that the data collected by MADS scientists will generate new knowledge in the field of plant reproductive biology and, in particular, in explaining the molecular and cellular mechanisms capable of mediating the emergence of novel reproductive pathways in sexual plants. In regards, the publications generated during the period establish several landmarks in the field of apomixis research, including: apomicts grass genomes characterization; candidate genes for apomixis (e.g. ARF10, TGS1), and; 3D imaging and analysis of plant ovules.
In addition to advancing our understanding of female reproductivon in plants, we expect that the delivery to plant breeders and farmers of the results presented here, and expected in the two next years, will have an impact by providing genomic resources for molecular breeding in sub-tropical forages and, more globally, by developing new tools for engineering apomixis in crops. In the context of global climate change, these outcomes will likely contribute to food security worldwide.
In addition to advancing our understanding of female reproductivon in plants, we expect that the delivery to plant breeders and farmers of the results presented here, and expected in the two next years, will have an impact by providing genomic resources for molecular breeding in sub-tropical forages and, more globally, by developing new tools for engineering apomixis in crops. In the context of global climate change, these outcomes will likely contribute to food security worldwide.