Title: Diversity captured in the USDA-ARS National Plant Germplasm System apple core collection Authors
|Gross, Briana -|
|Forsline, Philip -|
|Chao, C Thomas|
Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 10, 2013
Publication Date: September 30, 2013
Citation: Gross, B., Volk, G.M., Richards, C.M., Henk, A.D., Forsline, P., Szewc-Mcfadden, A.K., Fazio, G., Chao, C.T. 2013. Diversity captured in the USDA-ARS National Plant Germplasm System apple core collection. Journal of the American Society for Horticultural Science. 138(5):375-381. Interpretive Summary: Core collections have been used widely in genetic resources to provide a representative and compact sample to use in breeding evaluation. In the 1990’s, a core subset of accessions was selected to represent the entire grafted apple collection maintained by the USDA-ARS Plant Genetic Resources Unit (PGRU) in Geneva, NY. We used nine microsatellite markers and 13 phenotypic traits to provide a quantitative assessment of the genetic diversity captured in the diploid portion of the core subset to the entire diploid portion of the grafted apple collection. Specifically we compared the fraction of microsatellite alleles and phenotypic trait categories in the 2114 diploid trees in the grafted collection that were present in the established core. Our results show that the 198 diploid members of the core subset capture 82% of total collection allelic diversity and phenotypic character states. We used maximization algorithms to identify an additional 67 individuals that could complement the established core by increasing the coverage of the allelic and phenotypic character states to 100%. We also provided several de novo core sets that capture all the allelic and phenotypic character states in 100 individuals. Use of these proposed sets of individuals will help ensure that a broad range of apple diversity is included in evaluations that use the core subset of trees.
Technical Abstract: Core collections have been used widely in genetic resources to provide a representative and compact sample to use in breeding evaluation. In the 1990s a core set was developed by the USDA-ARS Plant Genetic Resources Unit (PGRU) in Geneva, NY. Using data available at the time, a core set was developed using geographical information, pedigree and phenotypic information. This paper set out to quantitatively assess the genetic diversity of this core and see how well it captured variation at a set of genetic markers and a set of phenotypic characters that were binned into discrete character states. By comparing variation in the core to variation observed in the larger collection, we found that the core collection captured about 82% of the variation. We used maximization algorithms that generate sub sets maximized for variation at these traits (alleles in the case of the genetic markers and trait states in the case of phenotypic traits) and were able to identify a set of 67 individuals that could compliment the core and capture all the scored variation. In addition we proposed a new smaller core of 100 accessions sets that include all the observable traits states for the markers and phenotypes. Use of these proposed sets of individuals will help ensure that a broad range of Malus diversity is included in evaluations that use the core subset of trees.