Phylogenetic relationships among the first and second introns of selectedPrunus S-RNase genes

Abstract

Phylogenetic relationships among the first and second introns of selected Prunus S-RNase genes. Can. J. Plant Sci. 95: 1145Á 1154. To identify and evaluate self-incompatible alleles in almonds and related germplasm, DNA from 15 Prunus species was amplified using two degenerate consensus primer pairs flanking first and second S-locus introns (PaConsI-FD'EMPc1ConsRD and EM-Pc2ConsFD'EM-Pc3ConsRD). Twenty-eight amplified PCR products were analyzed by automated sequencer capillary electrophoresis. Sequenced fragments were aligned against available Prunus S-locus sequences in the National Center for Biotechnology Information and S-alleles identities were determined. The phylogenetic relationships between S-alleles in the germplasm studied were determined by the homology between their sequences and dendrograms were obtained for each primer pair. The Maximum Likelihood (homology) ranged from 84 to 100%. Most sequences were similar to cultivated almond (Prunus dulcis) or to the European wild almond (P. webbii). Twenty-six alleles for the first and the second introns were registered in the database in the GenBank. Two sequences of the first and second introns, which were taken from Prunus nairica and had similarity in GenBank, were registered in the database under a common sequence of the first and second intron. Analysis of phylogenetic relationships (dendrograms) among S-alleles from wild almond species as well as S-alleles cluster relations showed most pairs of alleles well supported by bootstrap. Key words: Germplasm diversity, self-incompatibility, S-allele, PrunusRahemi, A., Gradziel T.M., Chaparro J.X., Folta, K.M., Taghavi, T., Fatahi, R., Ebadi, A. et Hassani, D. 2015. Liens phyloge´ne´tiques entre le premier et le deuxie`me intron des ge`nes de la S-RNase de certaines espe`ces du genre Prunus. Can. J. Plant Sci. 95: 1145Á1154. Les auteurs ont amplifie´l'ADN de 15 espe`ces du genre Prunus pour identifier puis e´valuer les alle`les auto-incompatibles dans l'amande et le mate´riel ge´ne´tique connexe. À cette fin, ils ont utilise´deux paires d'amorces consensuelles de´ge´ne´re´es, situe´es de part et d'autre du premier et du deuxie`me intron du locus-S (PaConsI-FD'EMPc1ConsRD et EM-Pc2ConsFD'EM-Pc3ConsRD). Vingt-huit produits amplifie´s de la PCR ont e´te´analyse´s par e´lectrophore`se capillaire a`se´quenc¸age automatique. Les fragments se´quence´s ont e´te´compare´s aux se´quences du locus-S du genre Prunus disponibles au National Center for Biotechnology Information et les alle`les ont e´te´identifie´s. Les liens phyloge´ne´tiques entre les alle`les-S du mate´riel ge´ne´tique a`l'e´tude ont e´te´e´tablis par homologie entre les se´quences, et les auteurs ont obtenu les dendrogrammes de chaque paire d'amorces. La fourchette de probabilite´maximale (homologie) varie de 84 a`100 pour cent. La plupart des se´quences ressemblent a`celles de l'amandier cultive´(Prunus dulcis) ou de l'amandier sauvage d'Europe (P. webbii). Vingt-six alle`les du premier et du deuxie`me intron ont e´te´enregistre´s dans la base de donne...