In silico mining of microsatellites in coding sequences of the date palm (arecaceae) genome, characterization and transferability

Frédérique Aberlenc-Bertossi (1) , Karina Castillo (1) , Christine Tranchant-Dubreuil (1) , Emira Cherif (1, 2) , Marco Ballardini (3) , Sabira Abdoulkder (1, 4) , Muriel Gros-Balthazard (5, 1) , Nathalie Chabrillange (1) , Sylvain Santoni (5) , Antonio Mercuri (6) , Jean Christophe Pintaud (1)

1 UMR DIADE - Diversité, adaptation, développement des plantes
2 Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie
3 Unità di Ricerca per la Floricoltura e le Specie Ornamentali
4 CERD - Centre d’Etudes et de Recherche de Djibouti
5 UMR AGAP - Amélioration génétique et adaptation des plantes méditerranéennes et tropicales
6 Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO)

Premise of the study: To complement existing sets of primarily &nucleotide microsatellite loci from noncoding sequences of date palm, we developed primers for tri- and hexanueleotide microsatellite loci identified within genes. Due to their conserved genomic locations, the primers should be useful in other palm taxa, and their utility was tested in seven other Phoenix species and in Chamaerops, Liyistona, and Hyphaene. Methods and Results: Tandem repeat motifs of 3-6 bp were searched using a simple sequence repeat (SSR)-pipeline package in coding portions of the date palm draft genome sequence. Fifteen loci produced highly consistent amplification, intraspecitic polymorphisms, and stepwise mutation patterns. Conclusions: These microsatellite loci showed sufficient levels of variability and transferability to make them useful for population genetic, selection signature, and iinterspecific gene flow studies in Phoenix and other Coryphoideae genera.

Mots clés: Arecaceae; Coryphoideae; microsatellite/SSR mining; Phoenix dactylifera; transferability; phoenix-dactylifera l.; markers; genus

Domaines: Sciences du Vivant [q-bio]

Frédérique Aberlenc-Bertossi, Karina Castillo, Christine Tranchant-Dubreuil, Emira Cherif, Marco Ballardini, et al.. In silico mining of microsatellites in coding sequences of the date palm (arecaceae) genome, characterization and transferability. Applications in Plant Sciences, 2014, 2 (1), ⟨10.3732/apps.1300058⟩. ⟨hal-01268884⟩