Using High-Throughput Genotyping Information to Aid in Managing a Large Maize Collection.

The National Plant Germplasm System’s collection of maize inbred lines is curated by the USDA-ARS North Central Regional Plant Introduction Station (NCRPIS) personnel in Ames, Iowa.  The collection offers a rich set of genetic resources including key historical inbreds relevant to maize breeding history and breeding programs from all over the world.

In 2010 or 2011, nearly 3000 lines were phenotypically characterized in Ames, IA, Columbia, MO, Ithaca, NY, and Raleigh, NC.  These lines and additional lines from other sources were genotyped using Genotyping-By-Sequencing (GBS), a low cost, high-throughput sequencing technology. The method produced more than 1.3 million SNP markers distributed across the entire genome, with ability to call rare alleles at high confidence levels. Data analysis confirms high levels of genetic diversity among the lines, with extent of variation dependent on the different subpopulations, and clustering of very similar inbred lines.   The power of this resource will be examined with respect to both the responsibilities and issues associated with managing a large collection of diverse genetic resources, and a researcher’s ability to select germplasm with traits or alleles of interest.