Circannual rhythms often rely on endogenous seasonal photoperiodic timers involving "clock" genes, and Clock gene polymorphism has been associated to variation in phenology in some bird species. In the long-distance migratory barn swallow Hirundo rustica, individuals bearing the rare Clock allele with the largest number of polyglutamine repeats found in this species show a delayed reproduction and moult later.

We are currently  investigating the role played by the genetic polymorphism at candidate phenological genes in shaping migration traits, and their role in controlling phenological variation in birds.

My most recent publications on the topic

• Le Clercq, L. et al. (2023) Time trees and clock genes: a systematic review and comparative analysis of contemporary avian migration genetics, Biological Reviews. doi: 10.1111/brv.12943. IF2021: 14.355
• Secomandi S, Gallo GR, Sozzoni M, Iannucci A, Galati E, et al. (2023) A chromosome-level reference genome and pangenome for barn swallow population genomics. Cell Reports 42 (1), 111992 doi: 10.1016/j.celrep.2023.111992 IF 2021: 9.995. 
  
• Lombardo G, et al. (2022) The Mitogenome Relationships and Phylogeography of Barn Swallows (Hirundo rustica). Molecular Biology and Evolution, doi:10.1093/molbev/msac113 IF 2020: 16.24
• Secomandi S. et al. (2022) Pangenomics Provides Insights into the Role of Synanthropy in Barn Swallow Evolution. BioRxiv, 2022.03.28.486082 doi: 10.1101/2022.03.28.486082
• Saino N., Albetti B., Ambrosini R., Caprioli M., Costanzo A., Mariani J., Parolini M., Romano A., Rubolini D., Formenti G., Gianfranceschi L. & Bollati V. (2019). Inter-generational resemblance of methylation levels at circadian genes and associations with phenology in the barn swallow. Scientific Reports, 9(1), 6505. doi:10.1038/s41598-019-42798-3
• Formenti, G., Chiara, M., Poveda, L., Francoijs, K., Bonisoli-Alquati, A., & Canova, L. et al. (2019). SMRT long-read sequencing and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica). GigaScience, 8(1) 1 January 2019, giy142. doi:10.1093/gigascience/giy142 IF 2017: 7.27 

Androsace brevis (Hegetschw.) is a narrow endemic cushion plant growing on rocky ridges of a restricted area of Southern Lombardy Alps and adjacent Switzerland. The species conservation status at global scale has been recently assessed as Endangered (EN) following the IUCN criteria. Due to its peculiar habitat, the species forms scattered populations of few individuals, often many km apart from each other. The occurrence on mountain tops and ridges makes upslope migration impossible for this species, and evidence of population decline due to competition from low altitude taxa has been observed. Little is known about A. brevis reproductive and pollination biology and subsequent possible long-distance pollen dispersal, as well as about the genetic and demographic structure of extant populations.

The research project aims at setting up a multidisciplinary study on A. brevis. The assessment of the genetic structure of the species through the development of highly informative molecular markers is of the utmost importance since it could allow gathering precious information about its reproductive strategies, the structure and variability existing in the natural populations and ultimately the formulation of appropriate conservation strategies. Together with the investigation of the genetic structure, we will also take into account the underlying aspects of reproductive biology, including pollen viability, flower-visiting insect assemblages and reproductive success. The integration of different topics and approaches will shed light on the factors underpinning the peculiar distribution pattern of A. brevis as a model species for threatened endemic taxa.

Title: "Apple fruit quality in the post-genomic era, from breeding new genotypes to post-harvest: nutrition and health"

Funding: AGER Filiera del Melo 2010-2015.

Website: http://www.agermelo.it/

The Italian apple chain, from production to consumers, operates in a context of international competition. Among the main pressing factors are the high cost of production (Italy cannot compete with the production costs of non-western countries) and the need of a more sustainable agriculture in terms of environmental impacts. Additionally, the consumers appear sensitive to a higher fruit quality not only in sensorial terms (which however must remain at the highest standard) but also regarding nutritional and health-related (functional) properties. To respond to these challenges, this project will address the study and the improvement of the apple fruit quality using a global perspective at three main levels:

1. KNOWLEDGE and TOOLS. By developing fundamental technological genetic/genomics tools for apple breeding and technologies and tools for non-invasive fruit quality assessment; by elucidating the main structure of the apple fruit metabolome and its relationship with standard fruit quality parameters to improve the knowledge about the molecular bases of fruit quality with emphasis on nutritional and health-related properties.
2. APPLICATIONS FOR GLOBAL IMPROVEMENT OF FRUIT QUALITY. By applying the above powerful molecular genetics tools and knowledge to molecular breeding and to the production chain in order to a) improve apple resistance to pathogens, b) enhance fruit quality (mainly in terms of nutritional aspects), c) reduce environmental impacts and increase sustainability, and d) optimize the production chain.
3. SCIENTIFIC AND TECHNOLOGICAL TRANSFER OF KNOWLEDGE. The transfer of the information to all the relevant apple chain stakeholders and to the scientific community will pursued by dedicated initiatives, events and publications.

Title: FRUIT BREEDOMICS (Integrated approach for increasing breeding efficiency in fruit tree crops)

Funding: European Union FP7-KBBE 

Website: http://fruitbreedomics.com/

The objective of FRUITBREEDOMICS is to improve the efficiency of fruit breeding (apple and peach but many tools will also benefit to other species of the Rosaceae family) by bridging the gap between scientific genetics research and application in breeding. FruitBreedomics will: - provide molecular and bioinformatics breeding tools to improve selection efficiency, - provide superior pre-breeding material to meet grower and consumer demands for healthy cultivars of high quality that can be used in future breeding programmes.

My most recent publications on the topic

• Di Pierro Erica et al. (2016) A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species. Horticulture Research (in press)
• Bink MCAM, Jansen J, Madduri M, Voorrips RE, Durel CE, Kouassi AB, Laurens F, Mathis F, Gessler C, Gobbin D, Rezzonico F, Patocchi A, Kellerhals M, Boudichevskaia A, Dunemann F, Peil A, Nowicka A, Lata B, Stankiewicz-Kosyl M, Jeziorek K, Pitera E, Soska A, Tomala K, Evans KM, Fernandez-Fernandez F, Guerra W, Korbin M, Keller S, Lewandowski M, Plocharski W, Rutkowski K, Zurawicz E, Costa F, Sansavini S, Tartarini S, Komjanc M, Mott D, Antofie A, Lateur M, Rondia A, Gianfranceschi L, van de Weg WE (2014) Bayesian QTL Analyses Using Pedigreed Families of an Outcrossing Species, with Application to Fruit Firmness in Apple. Theoretical and Applied Genetics 127(5): 1073-90. ISSN: 0040-5752 doi: 10.1007/s00122-014-2281-3, IF 2014: 3.790