diversity Article Geographic Patterns of Genetic Variation among Cacao (Theobroma cacao L.) Populations Based on Chloroplast Markers Helmuth Edisson Nieves-Orduña 1,2, Markus Müller 1 , Konstantin V. Krutovsky 1,2,3,4 and Oliver Gailing 1,2,* 1 Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077 Göttingen, Germany;
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[email protected] (K.V.K.) 2 Center for Integrated Breeding Research, Georg-August University of Göttingen, 37075 Göttingen, Germany 3 Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia 4 Laboratory of Population Genetics, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia * Correspondence:
[email protected] Abstract: The cacao tree (Theobroma cacao L.) is native to the Amazon basin and widely cultivated in the tropics to produce seeds, the valuable raw material for the chocolate industry. Conservation of cacao genetic resources and their availability for breeding and production programs are vital for securing cacao supply. However, relatively little is still known about the phylogeographic structure Citation: Nieves-Orduña, H.E.; of natural cacao populations. We studied the geographic distribution of cpDNA variation in different Müller, M.; Krutovsky, K.V.; Gailing, populations representing natural cacao stands, cacao farms in Ecuador, and breeding populations. O. Geographic Patterns of Genetic Variation among Cacao (Theobroma We used six earlier published cacao chloroplast microsatellite markers to genotype 233 cacao samples. cacao L.) Populations Based on In total, 23 chloroplast haplotypes were identified.