Marker Derived Core Sets and Their Application to Allele Mining

The primary targets of allele mining efforts are loci of agronomic importance. Agronomic loci typically exhibit patterns of allelic diversity that are consistent with a history of natural or artificial selection. Natural or artificial selection causes the distribution of genetic diversity at such loci to deviate substantially from the pattern found at neutral loci. The germplasm utilized for allele mining should contain maximum allelic variation at loci of interest, in the smallest possible number of samples. While core collections have been used for decades, their utility as a general purpose set for starting a search for agronomically important variation has not been tested.  An extensive coalescent simulation was performed to demonstrate more generally the retention of neutral versus selected allelic variation in core subsets assembled. A negative correlation in level of allelic diversity between neutral and selected loci was observed in 42% of simulated data sets. When core collection assembly is guided by neutral marker loci, as is the current common practice, enhanced allelic variation at agronomically important loci should not necessarily be expected.