Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping
populations of Theobroma cacao L and its impact on association mapping.
Tree Genetics and Genomes
J. Conrad Stack1, Stefan Royaert2, Osman Gutiérrez3, Chifumi Nagai4, Ioná Santos Araújo Holanda5, Raymond Schnell1, Juan-Carlos Motamayor1*
1
Mars, Incorporated, McLean, VA, USA
Mars Center for Cocoa Science, CP55 Itajuípe, Bahia, Brazil, 45625-000
3
USDA-ARS, Subtropical Horticulture Research Station, Miami, FL, USA
4
Hawaii Agriculture Research Center, Kunia, HI, USA
5
Universidade Federal Rural do Semi-Arido, Departamento de Ciências Vegetais, BR 110 - Km 47, Bairro Pres. Costa e Silva, Mossoró-RN, Brazil
CEP 59.625-900
2
*corresponding author (juan.motamayor@effem.com)
Allele counts in different diversity groups
At mTcCIR18, haplotypes containing the alleles 331 and 335 (only present in Hawaii population) were strong associated with the red phenotype
and allele 333 with green in MP01. Allele 331 at this locus is only found at this locus in Criollo, allele 335 is most frequent in Nacional, Guiana,
and Iquitos. Allele 333 is most frequently found in Nanay and is observed to a less extent in the Iquitos and Guiana groups.
At the mTcCIR17 locus, alleles 271 and 281 were both associated with red pod color in the Hawaii population, however, in MP01 population 271
was associated with green pods and 281 with red pods. Allele 271 at this locus is observed in all diversity groups except Criollo, while allele 281
is observed almost exclusively in Criollo.
At mTcCIR12, alleles 187 and 211 were associated with red pods in both populations while alleles 199 and 203 were associated with green pods
in the MP01 population. Alleles 187 and 211 are overrepresented in the Criollo and Amelonado diversity groups, respectively. Alleles 199 and
203 are present throughout most diversity groups except Criollo and Amelonado.