An SSR kit to study genetic diversity in Sorghum

The sorghum SSR kit has been elaborated in the frame of a large genotyping project (3400 sorghum accessions x 48 SSR loci) supported by the Generation Challenge Program, Sub-Programs 1 and 5 (grants dedicated to Daniel Fonceka and M'Baye N'Doye Sall, formerly working at the Ceraas, Senegal). It is composed of the allelic sizes of 3 controls for each of the 48 SSR locus.

Composition of the controls: includes the accession number (as provided by ICRISAT), in the genotyping order, and there belonging to the controls.
The 3 controls are composed of 10 DNA samples mixed in 2 pools of 3 and 1 pool of 4 individuals.  The 10 individuals were chosen from 48 Sorghum samples presenting a fair picture of the overall genetic diversity, in order to represent a large range of allelic diversity, both in term of allele number and allele sizes. Each control is amplified for each marker, and allelic sizes are used as control sizes.

Characteristics of the 48 markers: includes, for each locus, its name, the microsatellite motive, forward and reverse primer sequences, the number of alleles observed among the controls and their size range, and linkage group assignation (following Kim et al. (2005) nomenclature).

The 48 loci are located regularly throughout the genome, so that there are roughly 5 markers per chromosome. Most of the markers were previously published markers (Brown et al., 1996; Taramino et al., 1997; Battramakki et al., 2000; Kong et al., 2000; Schloss et al., 2002). Additional markers were developed from microsatellites enriched libraries using the SAT pipeline.

Allelic patterns of control samples : shows the Licor IR2 locus image, allelic content of each sample and of the controls. For each marker, the 10 individuals and the 3 mix controls were amplified and analyzed on Licor IR2 sequencer. A subset of the individual alleles detected for each marker were sequenced in order to determine their exact sizes. The size of the remaining alleles were determined relatively to the sequenced alleles based on stutter information.

All experiments related to this kit were performed on the Languedoc Roussillon Genotyping Platform, hosted by the CIRAD, under the supervision of Claire Billot and with the collaboration of Ronan Rivallan, Jean-François Rami and Monique Deu.