Geographic Patterns of Genetic Variation among Cacao (Theobroma cacao L.) Populations Based on Chloroplast Markers

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 of natural cacao populations. We studied the geographic distribution of cpDNA variation in different populations representing natural cacao stands, cacao farms in Ecuador, and breeding populations. We used six earlier published cacao chloroplast microsatellite markers to genotype 233 cacao samples. In total, 23 chloroplast haplotypes were identified. The highest variation of haplotypes was observed in western Amazonia including geographically restricted haplotypes. Two observed haplotypes were widespread across the Amazon basin suggesting long distance seed dispersal from west to east in Amazonia. Most cacao genetic groups identified earlier using nuclear SSRs are associated with specific chloroplast haplotypes. A single haplotype was common in selections representing cacao plantations in west Ecuador and reference Trinitario accessions. Our results can be used to determine the chloroplast diversity of accessions and in combination with phenotypic assessments can help to select geographically distinctive varieties for cacao breeding programs.

Geographic distribution, conservation, and genomic resources of cacao Theobroma cacao L

“…Likewise, five forest refugia for cacao in Amazonia were proposed by modeling potential past geographic distributions to explain the putative origin of cacao clusters (Thomas et al, 2012). The rich chloroplast diversity observed in wild cacao com-pared to cultivated cacao supports the forest refugia theory in north western Amazonia (Nieves-Orduña et al, 2021). Furthermore, the distribution of cacao genetic diversity in Amazonia may have also been affected by ancient and modern human intervention (Levis et al, 2017;Peters, 2000;Somarriba & Lachenaud, 2013;Thomas et al, 2012), which may explain the convergence of five genetic clusters (Iquitos, Nanay, Marañon, Contamana, and Purús) in the Peruvian Amazon, and the patterns of diversity decline from west to east in Amazonia (Figure 1; Cornejo et al, 2018;Motamayor et al, 2008;Nieves-Orduña et al, 2021).…”

“…Conservation strategies for widespread tropical tree species, such as cedar or cedro amargo ( Cedrela odorata ), have been proposed based on the distribution of cpDNA variants (haplotypes) in its natural habitat (Cavers et al., 2004). In the case of cacao, a center of cpDNA diversity was observed in the northwestern Amazon, including the occurrence of seven geographically restricted chloroplast haplotypes in the Peruvian Amazon (Nieves‐Orduña et al., 2021). Because cacao is a non‐pioneer species, in situ conservation needs to consider ecological conditions provided by natural forests to favor seed germination and adaptive changes (Akinnagbe et al., 2019; Finkeldey & Hattemer, 2007).…”

Evaluation of Land Suitability for Cacao in Takapala Watershed Using Geographic Information System

“…Theobroma cacao L., a tree that is grown on plantations and has its origins in South America, is typically grown in diverse tropical climates. This plant's seeds are used to make processed food known as chocolate [14]. The natural habitat of the cocoa plant is in tropical forests.…”

“…The natural habitat of the cocoa plant is in tropical forests. Cocoa or cocoa is a shade-loving tropical plant with a yield potential of 50-120 fruits per year [14]. Cocoa frequently grows in clumps along riverbanks, where the roots may be submerged for significant stretches of the year.…”

Use of sensors for mathematical modeling during the roasting of cocoa beans (Theobroma cacao) of the Chuncho variety

“…La provincia La Convención, región Cusco, la provincia de Carabaya y Sandia en la región Puno son regiones montañosas que poseen valles interandinos donde se cultivan desde tiempos antiguos diversos genotipos del cacao fino de aroma o cacao Chuncho. Hay evidencias de la existencia de diversidad genética en la región sur del Perú (Nieves-Orduña et al, 2021). Además, el mucílago del cacao Chuncho tiene una diversidad de aromas (Eskes et al, 2018) que hacen que los chocolates elaborados con los granos de cacao sean muy reconocidos en el mundo.…”