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Title: Population Structure and History in Developing Core Sets in Wild Germplasm

item Richards, Christopher
item Volk, Gayle
item Reeves, Patrick

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 1/1/2009
Publication Date: 1/1/2009
Citation: Richards, C.M., Volk, G.M., Reeves, P.A. 2009. Population Structure and History in Developing Core Sets in Wild Germplasm. Plant and Animal Genome Conference Proceedings. Volume W008. January 10-14, 2009 San Diego California

Interpretive Summary: This talk was given in a symposium on Allele Mining and Genomic Diversity. The focus of the talk was to review some of the analytical approaches for finding specific functional variation within large germplasm collection. In particular we reviewed some of the ways the research community can use these methods to identify lineages within genetic resources in order to recover novel and potentially valuable genes for breeding. As a case study we reviewed our research into the wild relatives of apple.

Technical Abstract: Accurate inference of genetic discontinuities between populations is an essential component in studies of intraspecific biodiversity and evolution, as well as associative genetics. Multi-locus genotypes were amplified from 949 individuals representing seedling trees from 88 half-sib families from eight M. sieversii populations collected in Kazakhstan. Analyses using a hierarchical model to estimate Fst showed that differentiation among individual families is more than three times greater than differentiation among sites. In addition, average gene diversity and allelic richness varied significantly among sites. A rendering of a genetic network among all sites showed that differentiation is largely congruent with geographical location. In addition, non-hierarchical Bayesian assignment methods were used to infer genetic clusters across the collection area. We detected four genetic clusters in the data set. The spatial pattern of genetic assignments among the eight collection sites shows two broadly distributed and two narrowly distributed clusters. These data indicate that the southwestern collection sites are more admixed and more diverse than the northern sites. Estimates of structure and admixture can be exploited when developing representative core sets for allele mining.