Genomic characterization of extant genetic diversity in grapevine
Context and purpose of the study – Dating back to the early domestication period of grapevine (Vitis vinifera L.), expansion of human activity led to the creation of thousands of modern day genotypes that serve multiple purposes such as table and wine consumption. They also encompass a strong phenotypic diversity. Presently, viticulture faces various challenges, which include threatening climatic change scenarios and an historical track record of genetic erosion. Paritularly with regards to wine varieties, there is a pressing need to characterize the extant genetic diversity of modern varieties, as a means to delvier knowledge-based solutions under a rapidly evolving scenario, that may enable improved yields and profiles, resistance to pathogens, and increased resilience to climate change. Here, we are using whole genome resequencing and Pool-Seq strategies to tackle multiple aspects associated with the extant genetic diversity present in grapevine germplasm, with an emphasis on the species’s domestication history and the rich Portuguese/Iberian genetic pool.
Material and methods – Work revolves around the use of genomics strategies for the genome-level analysis of genetic diversity. Specifically, strategies employed the use of the Illumina short-read next generation sequencing platform, to generate either whole genome resequencing data of individual genotypes, or PoolSeq data of multiple individuals of the same variety. Susbquent analysis envolved bioinformatics characterization of population structure, genetic variation and introgression.
Results – Our analysis incorporates, to the best of our knowledge, the first PoolSeq analysis of intra-varietel diversity associated with multiple grapevine varieties, which is being used to qualtify genetic variation and detect the presence of selection signatures. Meanwhile, individual genomes are being used to address important features of the domestication history of grapevine, namely the presence of adaptive introgression and a tentative significant role for the Iberian Peninsula in grapevine domestication.
Funding: Fundação para a Ciência e Tecnologia (FCT/MCTES) for project GrapeVision (PTDC/BIA-FBT/2389/2020) and support to H.A. (CEECIND/00399/2017/CP1423/CT0004); FCT/MCTES and POCH/NORTE2020/FSE for support to S.F. (SFRH/BD/120020/2016); FCT/MCTES and POPH-QREN/FSE for support to M.C. (CEECINST/00014/2018/CP1512/CT0002).
Issue: GiESCO 2023
1CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
2Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
3BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
4Departamento de Genética, Facultad de Ciencias, Universidad de Granada. Campus Fuentenueva, 18071, Granada, Spain
5MHNC-UP – Museum of Natural History and Science of the University of Porto – PO Herbarium, University of Porto, Praça Gomes Teixeira, 4099-002, Porto, Portugal
6Centre for Archaeology, UNIARQ, School of Arts and Humanities, University of Lisbon, Portugal
7LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
8Portuguese Association for Grapevine Diversity-PORVID, Tapada da Ajuda, 1349-017 Lisboa, Portugal