Genetic diversity and structure of farm and GenBank accessions of cacao (Theobroma cacao L.) in Cameroon revealed by microsatellite markers

Abstract

The genetic diversity of 400 accessions collected in cacao farms, 95 GenBank, and 31 reference accessions was analyzed using the 12 microsatellite markers. The GenBank and reference accessions were subdivided into 12 accession groups (AG) that belong to the traditional cacao genetic groups (GG) Lower Amazon Forastero (LA), Upper Amazon Forastero (UA), Trinitario, and Criollo (Cr). The 12-microsatellite loci revealed a total of 125 alleles, 113 of which were present in the farm accession group (FA). The within and between group variation for all AGs accounted respectively for 81% and 19% of the total molecular variation. The average F is for the FA was 0.15 suggesting a moderate level of inbreeding. Significant differences for the level of gene diversity were found between the farm (0.50), GenBank (0.42 to 0.62), and reference (0.10 to 0.60) AGs. Genetic differentiation among AGs was variable with F st values varying between 0.14 and 0.57 for the different AGs. Analysis using a Bayesian model-based method showed the existence of a high level of admixture for the farm accessions group. The LA genes were most represented in the FA (54%), followed by UA (33%) and Cr (7%). The genes of LA were also the most represented in the GenBank (48%), followed by UA (24%) and Cr (14%). Only 14% and 6% of the genes of the GenBank and farm accessions, respectively, could not be attributed to any of the reference GGs. The results suggest the predominating presence of LA genes in the Cameroon farm accessions and a high level of admixture, with apparent presence of genes of more than three GGs in most accessions. The traditional Trinitario types appear to have almost disappeared from farmers fields. The admixture must be the result of hybridization and recombination of these genes from the different GGs in seed gardens and in farmers' fields. The use of selected farm accessions will depend on the GG that it belongs to and also on their level of heterozygosity. Further implications of the results for breeding and for introduction of new germplasm into the Cameroon GenBank are discussed.

Understanding the genetic diversity, spatial genetic structure and mating system at the hierarchical levels of fruits and individuals of a continuous Theobroma cacao population from the Brazilian Amazon

“…or from the hybrid Trinitario genetic group and detected greater genetic diversity (H e ¼ 0.620, Efombagn et al, 2009a) than that determined herein. One possible explanation for the lower expected heterozygosity observed herein could be related to the origin of the population, which was typically the lower Amazon Amelonado (Motamayor et al, 2008).…”

“…This diploid species (2n ¼ 20) is monoecious with bisexual flowers, but it demonstrates high outcrossing rates that range from 30 to 100% (Voelcker, 1938;Benton, 1986;Efombagn et al, 2009a). Cacao is typically pollinated by midges, mainly Forcipomyia species, or by other small insects, such as ants and aphids.…”

Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L. and its impact on association mapping

“…The physical location of each marker loci was determined by comparing microsatellite flanking sequences and their primers against a recently published, high-resolution cacao genome (Motamayor et al 2013) using both BLAST and e-PCR (Altschul et al 1990;Schuler 1997). All base-pair positions reported in this study indicate a physical location on this reference genome, which was built from the Matina 1-6 cultivar, the most common cultivated type of cacao and belonging to the Amelonado diversity group (Aikpokpodion et al 2009;Efombagn et al 2008;Motamayor et al 2013Motamayor et al , 2003. These physical locations are consistent with their locations on a previously published composite genetic map .…”

“…While Motamayor et al (2008;Efombagn et al 2008) was able to distinguish between wild and primitive diversity groups using a genome-wide set of microsatellite genotypes, they are historically difficult to segregate based on phenotypic and passport data (as noted in Bartley 2005). Without extensive genetic pre-screening of candidate populations therefore, samples chosen to represent either wild or primitive diversity groups for the purpose of association mapping are likely to represent a mix of both.…”

Comparative Study Of DNA Preservation Under Various Conditions On Local Egyptian Cowpea Germplasm

“…The genomic DNA extraction is a primordial stage in several practices and genetic analyses such as those that involves the use of molecular markers, which has had a growing application in the plant systematics and in the population analysis. Studies based in molecular markers can be used successfully in phylogenetic analyses, serving as a great help in matters unresolved by traditional methods of analysis (Salamin et al, 2005;Chapman et al, 2007); the characterization of genetic diversity of germplasm banks, discrimination among germplasm, detecting duplications, mixed seeds, drift and uncontrolled intersections (Efombagn et al, 2008 andXie et al, 2010); in determining the degree of relatedness between individuals; the study of population's genetic structure, genetic effects of fragmentation and gene flow (Takayama et al, 2008;Bittencourt and Sebbenn, 2009); construction of genetic maps (Song et al, 2004;Moretzsohn et al, 2005); in studies of polyploidy (Doyle et al, 2002 andJoly andBruneau, 2004) and speciation (Barraclough and Vogler, 2000). All molecular analyses, to be successful, depend on obtaining DNA samples of quality.…”