Genetic analysis of traits of interest in Vitis vinifera using a progeny of wine grapes: Monastrell x Syrah

Summary: The wine industry has a high value throughout the world, and the vine breeders are working to obtain new varieties well adapted to the new climatic conditions and with better genetic composition. In wine grapes there are some traits that are important for viticulture and the winery, such as phenological period, productivity, and the quality of the berries. Most of these traits are controlled by a large number of genes of minor effect, together with influences of the environment. Early identification of individuals carrying the desired allele combinations allows breeders to grow larger effective populations. One approach to the improvement of conventional breeding is the identification of chromosomal regions or QTL (Quantitative Trait Loci) involved in the genetic control of quality traits, based on genetic maps and phenotypic evaluation of a segregating progeny. The purpose of QTL mapping is to identify the number and location of the genetic determinants responsible for the variation of the quantitative traits under study and their stability among different years. The identification of genes and molecular markers underlying quality traits will accelerate the breeding process, creating new opportunities for crop improvement. The goal of this work is the identification of the major genetic determinants for a given phenotypic trait in genetic maps and their co-localization with the position of candidate gene sequences related to the relevant phenotype. For this purpose, three specific objectives were considered: (1) The phenotypic evaluation of a progeny of 229 hybrids derived from a controlled cross between the wine grape cultivars Monastrell and Syrah; (2) The construction of grapevine genetic maps, using this progeny and molecular markers; (3) The use of these maps and the phenotypic data for QTL analyses, in order to develop helpful markers for breeding programs. Crossing Monastrell and Syrah generated a large phenotypic variability that may be useful in the development of new cultivars with improved attributes. Twenty-two segregating agronomic traits, related to phenology, productivity, morphology and enological quality, were evaluated for each genotype in three or six seasons (2008-2013). Continuous variation and transgressive segregation were observed for most of the evaluated characters, suggesting a polygenic inheritance. Genetic maps were developed with JoinMap 3.0 software, applying the Kosambi mapping function to convert recombination rates into genetic distances. Parental and consensus genetic maps were established using 251 informative markers: 104 SSRs (Simple Sequence Repeat), 146 SNPs (Single Nucleotide Polymorphism), and 1 CAPS (Cleaved Amplified Polymorphic Sequence). The joint analysis of the phenotypic data and of genetic variations at SSR and SNP loci allowed us to identify several QTLs for most of the traits evaluated, using the MapQTL 4.0 software. Several QTLs confirm the results reported by other authors and additional QTLs are new findings. Candidate genes have been proposed, which represent a valuable resource for further validation. These results contribute to our knowledge of the genetic determinants that control these traits of interest in grapevine.