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Exploring the molecular control of seed yield in crops

Periodic Reporting for period 2 - ExpoSEED (Exploring the molecular control of seed yield in crops)

Reporting period: 2018-01-01 to 2019-12-31

ExpoSEED represents an international and inter-sectoral consortium composed of nine partners spread all over the word: Mexico, Argentina, Colombia, Italy, Spain, Holland, Germany, Japan and Australia. These partners share the scientific interest of addressing food security with scientific basis; research activities, secondments of staff members and dissemination events are planned within the Action.
ExpoSEED aims to integrate forward and reverse genetic approaches to dissect the molecular mechanisms that control yield in model species and to transfer the acquired knowledge to selected cereals as wheat and barley. Furthermore, the evolutionary conservation of molecular mechanisms controlling reproductive organs is studied from an evo-devo point of view.
The identification of “molecular hubs” that determine seed number and size put the basis for the development of breeding tools to improve seed production at the beginning of the seed market. Research on model species has recently allowed to identify key factors that regulate plant reproduction together with exploring the conservation of the molecular mechanisms that finally control the plant fitness in distantly related species. The next challenge is now to deeper dissect the molecular networks controlled by these key factors to finally manipulate agronomic traits. The partners of ExpoSEED identified some of the targets of key factors controlling yield.
Candidate genes have been further characterized using genetic and cell-biology tools together with searching new alleles in large panel of wild and cultivated germplasm. As a parallel approach, germplasm collections and segregating populations have been used for mapping studies to identify novel factors controlling seed yield in cereals. ExpoSEED successfully created synergies to efficiently address scientific and societal issues. From the scientific perspective, now is the right moment: many completed crop genome sequences and novel genetic and cell biology tools supported the comparative biology approaches aimed in this project. Considering the societal issue, food security is a worldwide priority: in the context of population growth and less arable land, increasing food production is one of the challenges for this century.
ExpoSEED is composed of six work packages, WP2, WP3, WP4 and WP5 are focused on scientific aspects, WP1 is entirely dedicated to the coordination and management of the Action while WP6 develops training and dissemination activities. The scientific activities all converge on WP4, as represented in the attached images.

WP2 exploited a reverse genetics approach (from the candidate gene to phenotype) to identify key factors that control yield, in terms of seed number and size, in model species as Arabidopsis and rice. The information gained on model species have been tested and transferred to cereals as wheat and barley and to other distantly related species belonging to the poppy, tomato and coffee families. During the project the partners identified key factors acting as master regulators in controlling branching, carpel and seed differentiation. The functional characterization (WP4) of a subset of selected factors led to a more detailed description of the molecular pathways that control specific developmental stages with determinant effects on yield. Interestingly, strong interconnections with auxin and cytokinin metabolism have been described. Part of the information gained on model species, together with the identification of novel pathways controlling kernel formation, have been transferred to crop species in order to identify key genes that can be manipulated to increase yield in the very next future.

WP3 is strongly interconnected with WP2 and it is based on the observation that genetic variability can be exploited to search for novel functional alleles in the selected candidate genes. This approach has been mainly exploited in cereals, wheat and barley leading to the identification of promising novel alleles.

WP5 uses a complementary approach, named forward genetics (from the phenotype to the causal genes), that is expected to lead to the identification of novel factors that will be characterized within WP4. This strategy is only performed on crops as wheat and barley and it is based on the observation of specific phenotypes. Once a phenotype, for instance high yield, is detected in germplasm collections or in populations, statistical analysis is performed to identify the genetic locus correlated with the selected phenotype. Barley, durum wheat and bread wheat collections have been analyzed in different growing conditions to identify genotypes specifically adapted to the selected environment. QTL analysis or GWAS approaches have been performed to identify the combination of genetic loci conferring the better plant performance (novel loci influencing yield and gluten content have been identified).

Finally, WP4 collected the information from the other WPs, promising candidate genes (WP2), alleles (WP3) and genetic loci (WP5) to further proceed with the functional characterization. To do this, the partners used a wide variety of techniques (detailed expression profile studies, protein-protein and protein-DNA interaction experiments, development of mutant lines, microscopy analysis) to finally describe the precise function of selected genes.
Altogether, the ExpoSEED’s WPs and the collaboration between the partners expanded the knowledge on the mechanisms that control different aspects, all related to yield determination in model and crop species. Specific value has been added to the Action through the secondments between staff members, this indeed expanded the knowledge and techniques exploited in each laboratory to reach specific aims.
The main progresses beyond the state of the art are i) the scientific knowledge that the partners produced, ii) the development of novel pipelines to analyse genotypic data searching for novel alleles and iii) molecular markers to be exploited as pre-breeding tools.
During the reporting period, the cooperation between the partners produced more detailed information (i.e identification of genes and description of networks) that are permitting to select critical factors controlling i) branching in rice, ii) carpel differentiation and ovule formation in Arabidopsis iii) hormones crosstalk in Arabidopsis and wheat and iv) sugar metabolism in barley and wheat.
Expanding the look beyond the scientific results; the keyword within the Action is food security. The obtained results are adding novel information to be exploited to finally reach food security. Both novel data for basic research and pre-breeding tools have been produced.
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