Development and use of Single Nucleotide Polymorphism markers for genetic fingerprinting of cocoa genotypes in Ghana
Abu M. Dadzie1, Jemmy Takrama1, Stephen Y. Opoku1, Francis K. Padi1, Samuel K. Offei 4, Eric Y. Dankwa4, Donald S. Livingstone2, Juan Carlos Motamayor3, Raymond Schnell3, David N. Kuhn2
1Cocoa Research Institute of Ghana (CRIG), P. O. Box 8 Tafo-Akim, Ghana
2USDA-ARS, SHRS, 13601 Old Cutler Road, Miami, FL 33158
3Mars, Inc., Hackettstown, NJ 07840
4Department of Crop Science, College of Agriculture
and Consumer Sciences, University of Ghana
Corresponding Author: Dr David N. Kuhn
Address : USDA-ARS, SHRS, 13601 Old Cutler Road, Miami, FL 33158
ABSTRACT
Lack of genetic markers in cocoa has limited progress in cocoa breeding in Ghana. In this study, two cocoa populations, ‘Pound 7’ x ‘P 30’ and ‘PA 7’ x ‘P 30’, together with their parental clones were initially fingerprinted using six simple sequence repeat (SSR) and five single nucleotide polymorphism (SNP) markers. ‘Pound 7’ x ‘P30’ was made up of 85 individual trees while ‘PA 7’ x ‘P 30’ consisted of 105 trees. The allelic configuration of the progeny with their parents’ alleles revealed that 5.6% of ‘Pound 7’ x ‘P 30’ were off-types while 7.6% off-types were observed in the ‘PA 7’ x ‘P 30’ population. The confirmed progeny were further screened with 10 additional SSR markers. Nine of the markers flanked multiple blackpod resistance quantitative trait loci (QTLs) and the other flanked a witches' broom resistance QTL on the composite map of cocoa. Genetic sequence of the flanking SSR markers were retrieved from the NCBI data base to design primers which were used in genome walking to identify further sequence in the QTL flanking regions. Thirteen SNPs were discovered in the additional sequence from genome walking. The SNPs were developed into markers and probes which will have wide application in the genetic fingerprinting of cocoa.
Keywords: Cocoa, Black pod, Primer, Probe, Polymorphism.