Optimization of the Analysis of Almond DNA Simple Sequence Repeats (SSRs)Through Submarine Electrophoresis Using Different Agaroses and Staining Protocols

Simple sequence repeat (ssr markers or microsatellites), based on the specific pcr amplification ofdna sequences, are becoming the markers of choice for molecular characterization of a wide range of plantsbecause of their high polymorphism, abundance, and codominant inheritance. different methods have been usedfor the analysis of the ssr amplified fragments being submarine agarose electrophoresis the more suitablemethod for the routine application. in this work we have performed a comparative study of the utilization of fourdifferent types of low melting (metaphor®, sea kem®, and ms-8®) and regular (ld-2®) agaroses and twodifferent staining protocols using ethidium bromide and gel red nucleic acid gel sating®. almond cultivarsassayed included the spanish cultivars ‘anto?eta’, ‘marta’, ‘penta’, ‘tardona’ ‘desmayo’ and ‘guara’, thefrench cultivars ‘ferragnés’ and ‘r1000’, the usa cultivar ‘mission’, the tunisian cultivar ‘achaak’, the italiancultivar ‘tuono’ and the australian cultivar ‘chellaston’. ssr detection using metaphor® agarose gelelectrophoresis was the most efficient with higher resolution and would be able to resolve most of allelicvariation in comparison with the other three agaroses assayed. in addition, gel staining using ethidium bromideshowed similar results than the gelredtm nucleic acid gel stain® although it is much more toxic. the use ofmetaphor® agarose and gelredtm nucleic acid gel stain® appears good indicated for molecularcharacterization of mapping of population due to its good resolution in comparison with the rest of agaroses, lesstoxicity in comparison with the use of ethidium bromide, and lower cost and easier routine application incomparison with the automatic capillary sequencing.