Tree Genetics & Genomes

, Volume 8, Issue 1, pp 97–111 | Cite as

Identification and mapping of conserved ortholog set (COS) II sequences of cacao and their conversion to SNP markers for marker-assisted selection in Theobroma cacao and comparative genomics studies

  • David N. KuhnEmail author
  • Don LivingstoneIII
  • Dorrie Main
  • Ping Zheng
  • Chris Saski
  • F. Alex Feltus
  • Keithanne Mockaitis
  • Andrew D. Farmer
  • Gregory D. May
  • Raymond J. Schnell
  • Juan C. Motamayor
Original Paper


Theobroma cacao (cacao) is a tree cultivated in the tropics around the world for its seeds that are the source of both chocolate and cocoa butter. Genetic marker development for marker-assisted selection (MAS) is critical for the success of cacao breeding for disease resistance and yield. To develop conserved ortholog set II (COSII) single-nucleotide polymorphism (SNP) markers for MAS in cacao, we have used three strategies and three types of cacao genetic and sequence data to identify and map 98 cacao COSII genes. The resources available at the time these studies were first undertaken dictated the strategy utilized. For the first strategy, SNPs were identified using cacao expressed sequence tags homologous to COSII sequences. Strategy II utilized a leaf transcriptome of cacao genotype “Matina 1–6” and Strategy III the genomic sequence of a 3-Mb region of “Matina 1–6” linkage group 5 associated with an important quantitative trait locus (QTL) for resistance to black pod. We have identified SNP markers for 83 of the 98 mapped COSII genes, and 19 of these SNP markers co-locate with QTLs. These COSII SNP markers, the first identified for cacao, will be used for genotyping and off-typing in cacao breeding programs and employed for genetic mapping and syntenic studies to trace co-location of genes regulating traits of importance between cacao and other species.


Chocolate Genetic mapping Molecular markers Quantitative trait loci (QTL) co-localization 



We wish to acknowledge Mars, Inc. for partial funding of this project, Barbie Freeman for excellent technical support, Dr. Belinda Martineau for editing the manuscript, and Dr. J. Michael Moore for assistance with the statistical analysis of the synteny data.

Supplementary material

11295_2011_424_MOESM1_ESM.pdf (116 kb)
ESM 1 Table of all SNPs for the 83 COSII loci that contained SNPs. Table contains linkage group information for each COSII locus and minor allele frequency (MAF) for each SNP. (PDF 116 kb)
11295_2011_424_MOESM2_ESM.pdf (32 kb)
ESM 2 List of all flanking sequences for SNPs in ESM 1 in fasta format. (PDF 31 kb)


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Copyright information

© Springer-Verlag (outside the USA) 2011

Authors and Affiliations

  • David N. Kuhn
    • 1
    Email author
  • Don LivingstoneIII
    • 1
  • Dorrie Main
    • 2
  • Ping Zheng
    • 2
  • Chris Saski
    • 3
  • F. Alex Feltus
    • 4
  • Keithanne Mockaitis
    • 5
  • Andrew D. Farmer
    • 6
  • Gregory D. May
    • 6
  • Raymond J. Schnell
    • 1
  • Juan C. Motamayor
    • 1
    • 7
  2. 2.Department of Horticulture and Landscape ArchitectureWashington State UniversityPullmanUSA
  3. 3.Clemson University Genomics InstituteClemsonUSA
  4. 4.Department of Genetics and BiochemistryClemson UniversityClemsonUSA
  5. 5.Center for Genomics and BioinformaticsIndiana UniversityBloomingtonUSA
  6. 6.National Center for Genome ResourcesSanta FeUSA
  7. 7.Mars, Inc.HackettstownUSA

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