Periodic Reporting for period 2 - PROCROP (Harnessing Plant Reproduction for Crop Improvement)
Reporting period: 2017-02-01 to 2019-01-31
The present project focused on exploring Plant Reproductive Biology in grasses using biological systems including sexual plant models (rice and maize) and sub-tropical and tropical apomictic species (Poa pratensis, Paspalum notatum, and Eragrostis curvula). The overarching objective of this proposal, “Plant Reproduction for Crop Improvement (PROCROP)” aimed therefore at strengthening research partnership through short period staff exchange and networking activities between European Research organizations and organizations from countries with which the Community shares an S&T agreement. This proposal aimed at strengthening, and/or initiating, partnerships between European and Latin-American research groups focusing on either model plants or crops, therefore facilitating interactions between fundamental and applied aspects of plant reproduction research. The research topic of this exchange program addressed plant reproduction and how its manipulation could contribute to increase crop productivity and quality. Increased productivity through genetic improvement has significantly impacted world agriculture and the world’s population food security. Crop plants have followed the general pattern of introduction, selection, and hybridization. Therefore, the main goal of this proposal was to investigate the mechanisms reshaping transcriptomic landscapes for installing apomixis in sexual grasses. PROCROP was very successful and in accordance with the original research plan. The action has succeeded meeting the objectives posed for the second term of the project. Completed secondments allowed the follow up of established researches and the achievement of common goals of participants. Several articles derived from the joint work were published or submitted to scientific journals.
The objective of this action was to extend our knowledge on the molecular basis of apomixis in the Gramineae and generate tools for harnessing this trait for the benefit of agriculture. The role of putative master genes in determining the switch between sexuality and apomixis is being validated in the species available from the PROCROP partners. A website (www.procropproject.eu) meant to contain all the information about the project was created and all the papers produced within the project are published there. Several meetings were carried out, in order to establish and to monitor PROCROP activities and secondments. A kick off conference was conducted in Milan. Then, most project participants met again in Montpellier during the EU mid-term evaluation meeting. Two meetings were organized in Argentina involving some of the beneficiaries (IRD, UMIL and UNIPG) participating together with the CONICET scientists. The meeting included also a 3-day workshops and also a final meeting to take stock of the situation and to define the last deliverables. The group was very satisfied by the number of manuscripts published or under preparation and scientific outcomes reached in the 4 years.
The work conducted in the first term of the project was aimed at: completing the sequencing and bioinformatics analysis of the sexual and apomictic floral transcriptomes from Poa pratensis (Illumina), Paspalum notatum (454) and Eragrostis curvula (454); elaborating a list of candidate genes differentially represented or displaying splice variants in the sexual and apomictic floral transcriptomes of P. pratensis, P. notatum and E. curvula; identifying miRNAs presenting differential activity in flowers of sexual and apomictic plants of P. notatum and E. curvula; detecting mRNAs controlled by silencing mechanisms in sexual and apomictic plants of P. notatum and E. curvula; identifying novel predicted miRNAs in sexual and apomictic P. notatum and E. curvula genotypes; identifying transcripts and miRNAs differentially expressed in flowers of apomictic and sexual E. curvula genotypes under control and water stress conditions; carrying out an MSAP wide genome methylation analysis in apomictic and sexual P. notatum genotypes, which led to the identification of one candidate gene (Pn-SCD1) epigenetically regulated in the nucellus of apomictic plants just before the onset of aposporous initials; conducting an analysis of the RdDM pathway activity in ovules of Eragrostis curvul; performing wide genome sequencing of Paspalum notatum by using Illumina (the raw data generated will be used in the next term to assemble the Paspalum notatum genome sequence); analyzing genes located within the ASR and expressed in the P. notatum libraries; obtaining a mapping population of E. curvula segregrating for the reproductive mode; identifying several developmental routes with different activity in apomictic and sexual plants; starting functional analysis of selected candidate genes.
In the second part of the project we established the list of selected candidate genes to be further examined through functional analysis; selection was based on positional linkage, expression association and relevant reproductive functional annotation criteria; completed a list of candidates showing te same expression pattern alterations in aposporous and diplosporous plants; completed an incomplete assembly of the P. notatum genome and the ASR structural analysis; mapped the sRNA databases onto the ASR and the DSR sequences; hypothesized on the ASR and the DSR functional role; carried out deep P. notatum Illumina floral transcriptome sequencing at specific developmental stages, and assembled it on the 454 reference transcriptome previously constructed, in order to detect additional candidate genes; completed functional analysis of selected candidate genes; and finally, organized a closing meeting
The work conducted in the first term of the project was aimed at: completing the sequencing and bioinformatics analysis of the sexual and apomictic floral transcriptomes from Poa pratensis (Illumina), Paspalum notatum (454) and Eragrostis curvula (454); elaborating a list of candidate genes differentially represented or displaying splice variants in the sexual and apomictic floral transcriptomes of P. pratensis, P. notatum and E. curvula; identifying miRNAs presenting differential activity in flowers of sexual and apomictic plants of P. notatum and E. curvula; detecting mRNAs controlled by silencing mechanisms in sexual and apomictic plants of P. notatum and E. curvula; identifying novel predicted miRNAs in sexual and apomictic P. notatum and E. curvula genotypes; identifying transcripts and miRNAs differentially expressed in flowers of apomictic and sexual E. curvula genotypes under control and water stress conditions; carrying out an MSAP wide genome methylation analysis in apomictic and sexual P. notatum genotypes, which led to the identification of one candidate gene (Pn-SCD1) epigenetically regulated in the nucellus of apomictic plants just before the onset of aposporous initials; conducting an analysis of the RdDM pathway activity in ovules of Eragrostis curvul; performing wide genome sequencing of Paspalum notatum by using Illumina (the raw data generated will be used in the next term to assemble the Paspalum notatum genome sequence); analyzing genes located within the ASR and expressed in the P. notatum libraries; obtaining a mapping population of E. curvula segregrating for the reproductive mode; identifying several developmental routes with different activity in apomictic and sexual plants; starting functional analysis of selected candidate genes.
In the second part of the project we established the list of selected candidate genes to be further examined through functional analysis; selection was based on positional linkage, expression association and relevant reproductive functional annotation criteria; completed a list of candidates showing te same expression pattern alterations in aposporous and diplosporous plants; completed an incomplete assembly of the P. notatum genome and the ASR structural analysis; mapped the sRNA databases onto the ASR and the DSR sequences; hypothesized on the ASR and the DSR functional role; carried out deep P. notatum Illumina floral transcriptome sequencing at specific developmental stages, and assembled it on the 454 reference transcriptome previously constructed, in order to detect additional candidate genes; completed functional analysis of selected candidate genes; and finally, organized a closing meeting
The results presented in this project involve an unprecedented development of molecular data and tools aimed at the harnessing of apomixis for the benefit of agriculture. The ability to produce genetically uniform progeny via seeds is of significant value for its potential in agriculture to fix complex favorable genotypes, particularly hybrids expressing heterosis or obtained from wide crosses. It can be harnessed to improve breeding programs efficiency in the context of rapidly evolving environmental and social constraints, consequently promoting seed marketing. In fact, the use of apomixis is currently having direct consequences on the breeding of natural apomictic forage grasses of the Brachiaria and Paspalum genera, allowing a significant increase in cattle production in tropical and sub-tropical areas of the Americas. However, major food crops such as maize, rice and wheat are not naturally apomictic and attempts to introduce the trait from wild relatives have failed.
The genomic and transcriptomic databases generated here can be readily exploited to achieve a better understanding of the switch from sexuality to apomixis in the gramineae and also to facilitate the breeding of naturally apomictic species and major crops. Currently, there is no genome sequence publicly available for any apomictic grass species. We achieved the assembly of the first complete grass genome, which will provide unevaluable information on the structure of the chromosomic region controlling the switch to asexuality in plants. The combination of genomic, 454 and miRNA data is allowing the detection of a number of candidate genes involved in particular molecular routes promoting in apomixis.
The genomic and transcriptomic databases generated here can be readily exploited to achieve a better understanding of the switch from sexuality to apomixis in the gramineae and also to facilitate the breeding of naturally apomictic species and major crops. Currently, there is no genome sequence publicly available for any apomictic grass species. We achieved the assembly of the first complete grass genome, which will provide unevaluable information on the structure of the chromosomic region controlling the switch to asexuality in plants. The combination of genomic, 454 and miRNA data is allowing the detection of a number of candidate genes involved in particular molecular routes promoting in apomixis.