Robust and Inexpensive SSR Markers Analyses Using LI-COR DNA Analyzer

Abstract

Plant genotyping is performed for different purposes which dictate to a large extent the type of molecular makers and platform to be used. The level of throughput, the technical capacity of the genotyping facility, and the availability of reagents are also part of the decision towards a particular genotyping system. SSR markers are quite popular markers because they are easily implementable in standard laboratories, can be used on manual gel electrophoresis, require inexpensive reagents, are mostly randomly distributed in the genome, can be located within genes, have a good discriminatory power, and are codominant with Mendelian inheritance. These features have made SSR the marker of choice for low-resolution genetic mapping and genetic diversity studies including genetic identity verification. The LI-COR platform offers both qualitative and quantitative improvements over the conventional assays based on agarose and polyacrylamide (PAGE) gels with DNA stained with ethidium bromide and silver or radiolabeled. A fast run coupled with an automated detection system using fluorophores makes possible to achieve routinely in our genotyping facility five runs per day using the same gel up to four times which results in 48 genotypes genotyped with ten SSR markers (two per gel electrophoresis using low-cost M13-tailed primers). This gel-base, low cost per sample and equipment, and medium throughput makes the LI-COR platform ­particularly useful for laboratories with intermediate skills and expectations in molecular genetics.