Identification of key regulators for grapevine ripening by integrated genetic approaches

Grapevine is one of the most economically relevant fruit crops in the world. In the past few years climate change and in particular global warming have started to significantly impact agriculture and viticulture as well. Indeed, higher temperatures occurring early during the growing season may advance the date of the phenological stages like bud burst, flowering and veraison. As a consequence, the shift in veraison to earlier dates causes ripening to occur under higher temperatures which impairs wine quality. It is of great interest for viticulture to investigate the timing of veraison and disentangle its genetic control. Genetic variation between cultivars leads to differences in the expression of phenotypic traits such as veraison time. A deeper knowledge of the genes involved in the phenology processes is critical to select varieties that are well adapted for current and future climatic conditions. The aim of this thesis was to identify the most promising candidate genes for the regulation of the transition to grapevine berry ripening through complementary genetic study. The thesis is divided in two chapters: in the first chapter an approach based on the integration of data from QTL studies has been developed, in order to narrow down the number of candidate genes that may be related with berry ripening. Meta-QTL analysis integrated with transcriptomic data led to the identification of 61 candidate genes related to veraison, including well known transcription factors and genes related to carbohydrate metabolism. In the second part, we have characterized a wide germplasm collection of different grapevine accessions (from CREA-VIT Conegliano collection) with the aim to identify the best panels of grapevine varieties, representing the most diverse genotypes and phenotypes for the traits of interest, to be exploited to test the genotype-phenotype association. The Conegliano collection has been previously phenotyped for flowering time and veraison time in the last 50 years; our work focused on the phenotypic data of the last 13 years (data kindly made available by our partners). These phenotypic data have been firstly used to assist the construction of a core collection, including the most genetic diverse accessions and individuals with contrasting phenotypes. Approximately 600 CREA-VIT accessions were previously genotyped (Cipriani et al., 2010) using 45 microsatellite markers. The 6 genotypic data have been used to assess the genetic diversity and population structure of the Conegliano collection. The end of the second part was dedicated to performing the association analysis itself with two different approaches, firstly using the GrapeReSeq 18K Vitis genotyping chip, then with an innovative approach called XP-GWAS (Yang et al., 2015) where pool of individuals displaying extreme phenotypes are whole-genome resequenced and allele frequencies compared to a random pool are screened for enrichment. The findings of this study provide indications of the genetic factors controlling or influencing veraison time in grapevine. The elucidation of the genetic network underlying the beginning of the berry ripening phase is of fundamental importance for the need to breed new grapevine varieties adapted to changing climatic conditions.