Effectiveness of AFLPs and retrotransposon-based markers for the identification of portuguese grapevine cultivars and clones

Grapevine germplasm, including 38 of the main Portuguese cultivars and three foreign cultivars, Pinot Noir, Pinot Blanc and Chasselas, used as a reference, and 37 true-to-type clones from the Alvarinho, Arinto, Loureiro, Moscatel Galego Branco, Trajadura and Vinhão cultivars were studied using AFLP and three retrotransposon-based molecular techniques, IRAP, REMAP and SSAP. To study the retrotransposon-based polymorphisms, 18 primers based on the LTR sequences of Tvv1, Gret1 and Vine-1 were used. In the analysis of 41 cultivars, 517 IRAP, REMAP, AFLP and SSAP fragments were obtained, 83% of which were polymorphic. For IRAP, only the Tvv1Fa primer amplified DNA fragments. In the REMAP analysis, the Tvv1Fa-Ms14 primer combination only produced polymorphic bands, and the Vine-1 primers produced mainly ISSR fragments. The highest number of polymorphic fragments was found for AFLP. Both AFLP and SSAP showed a greater capacity for identifying clones, resulting in 15 and 9 clones identified, respectively. Together, all of the techniques allowed for the identification of 54% of the studied clones, which is an important step in solving one of the challenges that viticulture currently faces

Molecular mapping of grapevine genes

In this chapter, we review the history of grapevine genetics and gene mapping. Genetic markers are introduced considering both sequence-based and sequence-independent approaches used for variant discovery. We provide a survey of genotyping tools, from low- to high-throughput platforms. We describe general principles of map building and implementation, highlighting specificities for outbred species such as the grapevine. Then, we review the different approaches applied for QTL identification according to the genetic material, from bi-parental progenies, pedigree-supported segregating populations, to germplasm collection. In particular, our emphasis is on the relevance of such studies for the dissection of a complex trait. We describe the difficult process of identifying genes responsible for QTLs and the few cases of QTL cloning. Many years have passed from the first grapevine marker isolation, the development of genetic and physical maps, until the deciphering of the genome sequence. With such a wealth of detailed information on wild and cultivated grapevines, we discuss how data sharing and multidisciplinary data integration are the current challenges that the scientific community faces to effectively translate knowledge into practic