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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT OF AN INTERNATIONAL MARKER ASSISTED SELECTION PROGRAM FOR CACAO

Location: Subtropical Horticulture Research

Title: Comparison of SNPs and microsatellites in identifying offtypes of cacao clones from Cameroon

Authors
item Livingstone, Donald
item Motamayor, Juan-Carlos - MARS, INC.
item Schnell Ii, Raymond
item Kuhn, David

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 12, 2009
Publication Date: January 12, 2009
Citation: Livingstone, D., Motamayor, J., Schnell Ii, R.J., Kuhn, D.N. 2009. Comparison of SNPs and microsatellites in identifying offtypes of cacao clones from Cameroon. Plant and Animal Genome Conference.

Technical Abstract: Single Nucleotide Polymorphism (SNP) markers are increasingly being used in crop breeding programs, slowly replacing microsatellites and other markers. SNPs provide many benefits over microsatellites, including ease of analysis and unambiguous results across various platforms. We compare SNPs to microsatellites for the purpose of determining offtypes in clonal collections. Clones are used as parents in a breeding population and the presence of misidentified clones (offtypes) can lead to the propagation of undesired traits. Screening was performed on 186 trees representing 21 clones of Theobroma cacao from Cameroon to determine the correct clone genotypes and offtypes. DNA extracts from this population were first quantified and normalized using a dual curve Sybr Green I based protocol to improve efficiency of both microsatellite and SNP analysis. Microsatellites representing 12 distinct highly polymorphic loci from seven different linkage groups and 11 different SNP markers representing seven distinct loci from seven linkage groups were used to determine how the genotype results of the two different marker types compared. We show that the SNP assay identified 88% of the offtypes found via microsatellite screening, and determined additional offtype individuals not identified by microsatellite analysis. SNP markers spread across multiple linkage groups may serve as a more efficient method for offtyping, especially in cacao producer countries where the equipment necessary for microsatellite analysis may not be available.

Last Modified: 7/25/2014