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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

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Abstract

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.

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Acknowledgments

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.

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Authors and Affiliations

  1. USDA-ARS SHRS, Miami, FL, 33158, USA

    David N. Kuhn, Don Livingstone III, Raymond J. Schnell & Juan C. Motamayor

  2. Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, 99164-6414, USA

    Dorrie Main & Ping Zheng

  3. Clemson University Genomics Institute, Clemson, SC, 29634, USA

    Chris Saski

  4. Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634-0318, USA

    F. Alex Feltus

  5. Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA

    Keithanne Mockaitis

  6. National Center for Genome Resources, Santa Fe, NM, 87505, USA

    Andrew D. Farmer & Gregory D. May

  7. Mars, Inc., 800 High St., Hackettstown, NJ, 07840, USA

    Juan C. Motamayor

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  1. David N. Kuhn
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  2. Don Livingstone III
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Correspondence to David N. Kuhn.

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Communicated by A. Dandekar

Electronic supplementary material

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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)

ESM 2

List of all flanking sequences for SNPs in ESM 1 in fasta format. (PDF 31 kb)

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Kuhn, D.N., Livingstone, D., Main, D. et al. 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. Tree Genetics & Genomes 8, 97–111 (2012). https://doi.org/10.1007/s11295-011-0424-0

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