The authors are interested in SNP development and haplotype assessment in grapevine, since these are valuable
tools in marker-assisted selection, especially useful for woody species due to its long reproductive cycle and the drawbacks this causes for the conventional development of varieties.
This research team assessed the degree of polymorphisms between Vitis riparia, Vitis vinifera and an intraspecific hybrid. They have also compared the efficiency of SSCP (Single Sequence Conformational Polymorphism) with re-sequencing genotyping.
Nine parental genotypes of inter- and intra-specific hybrids were used. SNPs were analysed on 50 fragments of genes involved in metabolic pathways of interest in terms of grapevine quality and resistance to disease.
Among 11629bp scanned, when comparing 9 genotypes, 247 polymorphic sites have been found, with an average of one SNP per 47 bases. When comparing the two species, a lower SNP frequency was found than when comparing two V. vinifera cultivars.
The nucleotide diversity found in coding regions was higher than in non-coding, which may suggest that the non-coding perigenic sequences have regulatory or splicing functions.
One hundred out of 177 polymorphic sites code for aminoacid changes, what may contribute to explain the high phenotypic variability among V. vinifera cultivars.
An average of 6.04 different haplotypes was found per gene.
SCCP detection has been confirmed by re-sequencing, which considering its much lower economical cost would justify a wider use of SCCP.
The data obtained support that
haplotype definition is a good alternative to traditional traditional mapping and that SSCP is useful and satisfyingly efficient for SNP detection.