A new, highly assertive scar marker potentially useful to assist selection for seedlessness in table grape breeding

In grapevines, seedlessness or stenospermocarpy is produced due to the abortion of the embryo during the early steps of seeds development, leaving traces or rudiments almost non-detectable. At La Platina Resarch Centre (Chilean Agriculture Research Institute), a table grape breeding program using apirenic commercial varieties as progenitors and in vitro, pre-abortion embryo rescue, was established 10 to 15 years ago. Since the grapevine does not produce berries up to four or five years after the crossing, the identification of molecular markers related to seedlessness is of great interest, because they could be used to exclude seeded segregants in early stages of their development, reducing the cost of generation of new lines. For the search of this type of markers, a bulk segregant analysis (BSA) approach was choosed. In this scheme, pooled groups of plants that present or not the trait are compared, "neutralizing" the individual differences and enhancing the genetic difference(s) that could be related to the trait of interest. To build the groups, there were selected plants previously evaluated for the different stenospermocarpy sub-traits, of the crossing Ruby x Sultanina (crossing #33). Of 336 RAPD primers tested, six fragments were seedless-specific and one was related to the seeded phenotype. RAPD fragment named WF27-2000 was cloned and sequenced, and then converted into a SCAR marker (Sequence-Characterized Amplified Region). This SCAR, called SCF27, generated a specific amplicon of 2.0 kb present in all of the seedless segregants. On the other hand, the analysis of 127 plants of the crossing #33 with the SCF27 marker showed a 3:1 segregation, in agreement with both of their parents being heterozygous for this locus. When the marker was evaluated on the fruited segregants of crossing #33, an 81% correlation was observed. This SCAR produces an amplicon in a simple PCR reaction, their results being easily interpreted in agarose gels, which makes it usable in a marker assisted selection scheme. These results reinforce partially the theory proposed by Bouquet & Danglot (1996) about the existence of a major gene whose expression would be related to the seedlessness character. The use of the SCAR marker SCF27 in an early stage of the development of the segregants of the crossing #33 (in plantlets still maintained in vitro) would allow to reduce until one third the operational costs of the breeding program, because of the reduction in the number of plants handled in vitro, in greenhouse and in the field.