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Figure 1. Map showing sample collecting site of traditional farmer clones in the Sambirano valley, in northwest Madagascar.
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Figure 2. PCoA plot of 190 cacao accessions, including 40 farmer varieties from Madagascar and 150 reference clones from the International Genebanks. The plane of the first three main PCO axes accounted for 76.3% of total variation. First axis = 40.5% of total information, the second = 30.16% and the third = 5.72%. All accessions correspond to the sample list in Table 1.
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Figure 3. Inferred clusters in the 40 Madagascar farmer selections and 150 reference international clones using STRUCTURE (K = 7), where K is the potential number of genetic clusters that may exist in the overall sample of individuals. Clusters of individuals are represented by colors. Individuals with multiple colors have admixed genotypes from multiple clusters. Each color represents the most likely ancestry of the cluster from which the genotype or partial genotype was derived.
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# Accession Type of variety* 1 MA01 Criollo 2 MA02 Amelonado 3 MA03 Criollo 4 MA04 Amelonado 5 MA05 Amelonado 6 MA06 Criollo 7 MA07 Criollo 8 MA08 Amelonado 9 MA10 Amelonado 10 MA11 Criollo 11 MA12 Criollo 12 MA13 Amelonado 13 MA14 Trinitario 14 MA15 Criollo 15 MA16 Trinitario 16 MA17 Trinitario 17 MA18 Amelonado 18 MA19 Trinitario 19 MA20 Amelonado 20 Izaka1 Uknown 21 Izaka2 Uknown 22 Izaka3 Uknown 23 Izaka4 Uknown 24 Izaka5 Uknown 25 Izaka7 Uknown 26 Izaka8 Uknown 27 Izaka9 Uknown 28 Izaka10 Uknown 29 Somia11 Trinitario 30 Somia12 Amelonado 31 Somia13 Amelonado 32 Somia14 Trinitario 33 Somia15 Criollo 34 Somia16 Trinitario 35 Somia17 Criollo 36 Somia18 Trinitario 37 Somia19 Trinitario 38 Somia20 Amelonado 39 Somia21 Amelonado 40 Somia22 Trinitario Reference accessions Genetic group Sample size Country of origin Source IMC 20 Peru ICGT, Trinidad Nanay 20 Peru ICGT, Trinidad Parinari 20 Peru ICGT, Trinidad Nacional 20 Ecuador INIAP, Ecuador Scavina 20 Peru ICGT, Trinidad Amelonado 20 Puerto Rico,
Nicaragua,
Costa Rica,
TrinidadICGT, Trinidad;
CATIE, Costa Rica;
SPCL, USDACriollo 20 Puerto Rico,
Nicaragua,
Costa Rica,
TrinidadICGT, Trinidad;
CATIE, Costa Rica;
SPCL, USDATrinitario 10 Trinidad ICGT, Trinidad Total 190 * Perceived type of variety by local farmers based on morphological characteristics. Table 1. List of 190 cacao accessions, including 40 farmer clones from Madagascar and 150 reference accessions used in SNP genotyping.
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Name of accessions Assigned parentage (Q-value) based on seven reference populations Name Nacional IMC Nanay Parinari Scavina Criollo Amelonado Result of assignment MA01 0.000 0.001 0.000 0.000 0.000 0.997 0.000 Criollo MA02 0.001 0.001 0.001 0.001 0.001 0.001 0.995 Amelonado MA03 0.000 0.000 0.000 0.000 0.000 0.998 0.000 Criollo MA04 0.006 0.023 0.023 0.012 0.002 0.118 0.816 Amelonado MA05 0.001 0.001 0.001 0.001 0.001 0.047 0.948 Amelonado MA06 0.000 0.000 0.000 0.000 0.000 0.998 0.000 Criollo MA07 0.001 0.000 0.000 0.000 0.000 0.997 0.000 Criollo MA08 0.001 0.004 0.005 0.009 0.008 0.047 0.926 Amelonado MA10 0.000 0.001 0.001 0.002 0.001 0.001 0.995 Amelonado MA11 0.000 0.000 0.000 0.000 0.000 0.998 0.000 Criollo MA12 0.000 0.000 0.000 0.000 0.000 0.998 0.000 Criollo MA13 0.001 0.001 0.001 0.002 0.001 0.001 0.994 Amelonado MA14 0.001 0.001 0.001 0.001 0.001 0.291 0.705 Trinitario MA15 0.000 0.000 0.000 0.000 0.000 0.997 0.000 Criollo MA16 0.001 0.001 0.001 0.001 0.001 0.403 0.591 Trinitario MA17 0.001 0.002 0.002 0.002 0.001 0.569 0.424 Trinitario MA18 0.000 0.001 0.001 0.001 0.000 0.000 0.998 Amelonado MA19 0.001 0.001 0.001 0.001 0.001 0.289 0.707 Trinitario MA20 0.001 0.002 0.002 0.001 0.000 0.001 0.993 Amelonado Izaka1 0.016 0.010 0.003 0.001 0.014 0.083 0.875 Amelonado Izaka2 0.001 0.001 0.005 0.002 0.001 0.248 0.743 Trinitario Izaka3 0.001 0.001 0.001 0.001 0.002 0.110 0.885 Amelonado Izaka4 0.000 0.002 0.001 0.001 0.000 0.001 0.995 Amelonado Izaka5 0.002 0.002 0.003 0.001 0.001 0.387 0.604 Trinitario Izaka7 0.001 0.001 0.002 0.002 0.001 0.562 0.433 Trinitario Izaka8 0.004 0.003 0.003 0.002 0.001 0.186 0.802 Amelonado Izaka9 0.001 0.001 0.003 0.001 0.000 0.286 0.707 Trinitario Izaka10 0.001 0.001 0.001 0.002 0.001 0.290 0.705 Trinitario Somia11 0.001 0.001 0.001 0.002 0.001 0.488 0.507 Trinitario Somia12 0.001 0.001 0.001 0.001 0.001 0.010 0.985 Amelonado Somia13 0.000 0.002 0.007 0.002 0.001 0.001 0.986 Amelonado Somia14 0.001 0.001 0.001 0.001 0.001 0.260 0.736 Trinitario Somia15 0.000 0.000 0.000 0.000 0.000 0.998 0.000 Criollo Somia16 0.001 0.001 0.002 0.002 0.001 0.344 0.650 Trinitario Somia17 0.000 0.001 0.000 0.000 0.000 0.997 0.000 Criollo Somia18 0.001 0.002 0.003 0.002 0.001 0.445 0.547 Trinitario Somia19 0.001 0.001 0.001 0.001 0.001 0.487 0.507 Trinitario Somia20 0.000 0.001 0.001 0.001 0.000 0.000 0.997 Amelonado Somia21 0.001 0.005 0.005 0.002 0.001 0.002 0.982 Amelonado Somia22 0.001 0.001 0.002 0.007 0.001 0.366 0.622 Trinitario Table 2. Assigned parentage for 40 Madagascar cacao accessions based on seven reference germplasm groups, using Bayesian clustering analysis.
Figures
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Tables
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