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Wageningen University (2014)

Identification of alleles involved in Solanum tuberosum plant maturity and quantification of alleles effects on phenotypic trait values

Mar Pérez Nicolás, M. del

Titre : Identification of alleles involved in Solanum tuberosum plant maturity and quantification of alleles effects on phenotypic trait values

Auteur : Mar Pérez Nicolás, M. del

Université de soutenance : Wageningen University

Grade : Master of Science (MS) 2014

Résumé
In potato (Solanum tuberosum) it is known that the main factor controlling plant maturity is the StCDF1 gene, a member of the DOF (DNA-binding with one finger) family. Two truncated alleles of this gene, StCDF1.2 and StCDF1.3, which contain a 7bp footprint insertion and a 865bp transposon insertion respectively, have been recognized as responsible for early phenotypes regarding plant maturity. A set of 470 potato cultivars, most of them with known phenotype, was screened for the presence or absence of these two alleles, and subsequently, a correlation between our results and phenotype was made. Although our approach was not able to detect StCDF1.2 allele, a significant difference on phenotype was found between cultivars containing the StCDF1.3 allele and the cultivars without it. Moreover, in order to know if plant maturity is a trait determined by the combination of different haplotypes and not only by the presence of the previously mentioned truncated alleles, a subset of 190 cultivars was selected and their PCR products from the first half on the intron were sequenced. Since the intron is a highly polymorphic region, the sequence chromatograms were not clear enough to extract haplotype information from them ; thus, PCR products of 15 cultivars were cloned. From the cloned product, 45 haplotypes could be identified, some of which contained haplotype specific DNA sequence variants which allowed us to recognise those haplotypes in 9 of the non-cloned cultivars. A nucleotide diversity value of π=0.115 was found, which correspond to 1 SNP every 8,7bp. The average number of alleles per individual (Ai) was 3.4 and three cultivars presented five different haplotypes, a fact that could be due to chimerism. Since only four of the 45 haplotypes were shared by more than one cultivar, association analysis was not successful ; hence, further studies are recommended in order to elucidate the role of StCDF1 alleles on plant maturity.

Mots clés : solanum tuberosum / potatoes / cultivars / plant development / growth stages / genes / alleles / haplotypes / dna sequencing / plant breeding

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Page publiée le 17 janvier 2015, mise à jour le 17 octobre 2018