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United States Department of Agriculture

Agricultural Research Service

Title: Genetic Divesity of Cultivated and Wild Type Peanuts Evaluated with M13-Tailed SSR Markers and Sequencing

Authors
item Barkley, Noelle
item Dean, Robin - UNIVERSITY OF GEORGIA
item Pittman, Roy
item Wang, Ming
item Holbrook, C
item Pederson, Gary

Submitted to: Genetical Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 4, 2007
Publication Date: May 1, 2007
Citation: Barkley, N.L., Dean, R.E., Pittman, R.N., Wang, M.L., Holbrook Jr, C.C., Pederson, G.A. 2007. Genetic Divesity of Cultivated and Wild Type Peanuts Evaluated with M13-Tailed SSR Markers and Sequencing. Genetical Research. 89:93-106.

Interpretive Summary: DNA marker technology is an important tool to fingerprint germplasm and evaluate genetic relationships between different plants classified in separate species or genera. Some cultivated peanuts are classified into subspecies and botanical varieties; however, many accessions examined in this study have not been classified past the species level. Using marker data and publicly available morphological data on the germplasm resources information network (GRIN) has allowed the tentative classification of accessions in the collection into subspecies and botanical varieties. Many accessions are currently being grown in the field to confirm these tentative classifications. In this study, simple sequence repeat (SSR) markers were used to evaluate the genetic diversity of a collection of cultivated peanuts and some wild relatives. These markers also allowed the assessment of the relationships between wild and cultivated species in the genus Arachis. The markers demonstrated that the wild peanut accessions were more genetically diverse than cultivated accessions. Clarifying the proper classification of these accessions and understanding the genetic diversity and relationships of cultivated peanut will help in the overall management of the peanut germplasm collection.

Technical Abstract: Thirty-one peanut genomic SSR markers with a M13-tail attached were used to assess the genetic diversity in the peanut mini core collection, which is maintained by the USDA, ARS, Plant Genetic Resources Conservation Unit (USDA, ARS, PGRCU). The M13-tailed method was effective in discriminating individuals and was cost effective. The data set consisted of all but one of the 112 accessions from the peanut (Arachis hypogaea L) mini core, 14 botanical varieties, and 14 wild relatives for a total of 139 accessions. A few alleles were sequenced from an SSR marker used in this study and demonstrated that the repeat motif is conserved when transferring the marker across species borders. A total of 477 alleles were detected in this data set with an average of 15.4 alleles per locus. The mean polymorphic information content (PIC) score was 0.687. The cultivated peanut (Arachis hypogaea L) mini core produced a total of 312 alleles with an average of 10.1 alleles per locus. A phylogenetic tree was constructed to determine the interspecific and intraspecific relationships in this data set. Most all of the peanut accessions in this data set classified as botanical varieties such as Arachis hypogaea hypogaea hypogaea, Arachis hypogaea fastigiata fastigiata and Arachis hypogaea fastigiata vulgaris clustered with other accessions with the same classification, lending further support to the current taxonomy. This study allowed the examination of the diversity present and the phylogenetic relationships in the peanut mini core which has not been previously reported.

Last Modified: 11/25/2014