Preliminary Assessment of the Efficacy of a Core Marker Set In Revealing Genetic Diversity In the U.S. Germplasm Collection

A comprehensive knowledge of the genetic diversity within the U.S. Gossypium Germplasm Collection is necessary to achieve its most effective utilization and the greatest efficiency in its maintenance.  To improve our knowledge of the collection’s diversity, a project was initiated in 2009 to characterize between 20 and 25 percent of the collection using a candidate core marker set of 105 SSRs.  Labeled primers for the SSRs were created using FAM, HEX, or NED labels, creating 35 primer sets for multiplex PCR amplification.  A pilot project using a 96 accession subset of the collection representing the tetraploid species and the A and D genome diploid progenitor species was conducted to verify the efficacy of the multiplex primer sets, develop protocols for amplification, develop data collecting bins for a data file, and assess the ability of the markers to reveal genetic diversity within the collection.  On average, 9.5 variants or alleles per marker were observed.  Within G. hirsutum, an average of 6.3 alleles per marker was observed in race stock accessions, whereas cultivars accessions only produced an average of 2.9 alleles per marker.  Lower levels of variation were observed within G. barbadense.  Overall, the candidate core marker set appears sufficient for the task of characterizing diversity the larger collection.