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Identification of vernalization-related genes in Easter Lily
bulbs for molecular markers production, vernalization control and improved flower production

Final Report Summary - LILY VERNALIZATION (Identification of vernalization-related genes in Easter Lily <br/>bulbs for molecular markers production, vernalization control and improved flower production)

Background and objectives of the project
Lilium longiflorum (Easter lily) is a leading bulbous crop worldwide, produced as cut flower, potted plants, garden plants and as dry cell bulbs. L. longiflorum flowering requires cooling of the bulbs to meet the obligatory vernalization (extended exposure of the plant to cold as prerequisite for flowering) requirement of this plant species, which is also the main parameter regulating flowering time and of major importance for flower quality.
In this project, we aimed to shed light on the molecular mechanism of the vernalization response in lily and obtain fundamental scientific data and valuable molecular markers, that can be used in breeding programs and ultimately promote flower production of bulbous plants.
The realization of these aims relied on combining state-of-the-art, next generation sequencing (NSG) technologies and bio-informatics analyses developed at the Genetwister (GT) SME, with basic plant physiology and molecular biology theoretical and experimental resources from the Ben Gurion University (BGU) team.

Main results
A de-novo transcriptome from cooled and non-cooled bulbs was assembled, yielding 15,414 annotated genes, with up to 3,657 Gene Ontology (GO) terms, finally mapped to the more general GO slim plant with a total of 94 terms. The response to cold exposure was summarized in 6 expression clusters, providing useful patterns for dissecting the dynamics of vernalization in lily. Functional annotation was used to group transcripts in gene sets, whose analyses revealed that most of the enriched functions among genes up-regulated by cold exposure were related to epigenetic processes and chromatin remodeling. Integrating bioinformatics analyses and literature searches, we broadened the genes’ characterization and selected potential candidate genes regulating vernalization. Full cDNA coding sequences of several genes were cloned and expressed in lily and in the model plant Arabidopsis. These functional analyses in planta demonstrated that some of the lily genes, whose expression was upregulated by cold, induced early flowering when over-expressed both in lily and in Arabidopsis.
In addition, we tested the expression pattern of a large number of candidate genes in a series of lily tissues during plant development under different growing conditions to obtain correlations between gene expression and flowering parameters and select reliable markers. First results of these investigations (still ongoing) enabled rejection of several genes and selection of others as potential molecular markers.

The resulting collection of transcripts and novel isoforms from the transcriptome provided an effective resource for studying the changes occurring during vernalization at a fine level. Overall, the transcriptome analyses provided a strong and detailed platform for gene and marker selection. These analyses also provided an attracting source of information about additional important mechanisms regulated by cold in lily bulbs.
In planta functional analyses provided interesting information on the role and the conservation of several lily genes associated with flowering, which will be completed and deepen by the correlation experiments. Overall, this project yielded valuable progress towards the finding of
molecular markers that can further be used for the breeding flowering bulbs.

Socio-economic impact of the project
Data from this project, i.e. insights into the molecular regulation of vernalization and flowering in lily and potential development of molecular tools for breeding, are aimed to introduce a fundamental change into bulb-based flower production. Therefore, bulbs and flower production would be more attractive and beneficiary to growers and lead to developments in the agriculture sector.
The project has given young academic researchers the occasion to be acquainted with a SME environment and to SME researchers to be involved in an academic research group. During these training periods, the researchers were exposed to new techniques and management practices, which enriched and strengthened their CV for further employment in the academic or industry sector. For several teams’ members, the project had a direct impact on career development and employment finding.