Retention of agronomically important variation in germplasm core collections: implications for 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. We show that the popular core collection assembly procedure "M" (marker allele richness), which leverages variation at neutral loci, performs worse than random assembly for retaining variation at a locus of agronomic importance in sugar beet (Beta                         vulgaris L. subsp. vulgaris) that is under selection. We present a corrected procedure ("M+") that outperforms M. An extensive coalescent simulation was performed to demonstrate more generally the retention of neutral versus selected allelic variation in core subsets assembled with M+. 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.
National Center for Genetic Resources Preservation, United States Department of Agriculture, Agricultural Research Service, 1111 South Mason Street, Fort Collins, CO 80521, USA. pat.reeves@ars.usda.gov
Patrick A
PA
Reeves
Lee W
LW
Panella
Christopher M
CM
Richards
D000483:Alleles; D027461:Beta vulgaris / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D005787:Gene Frequency; D056426:Genetic Loci; D005819:Genetic Markers; D014644:Genetic Variation; D015810:Linkage Disequilibrium; D058974:Phylogeography; D017422:Sequence Analysis, DNA
D018744:DNA, Plant; D005819:Genetic Markers