Microsatellite variation and population structure in the “Refractario” cacao of Ecuador

Abstract

Utilization of germplasm for crop improvement is often hampered by absence of information regarding origin, genetic identity and genealogical relationships of germplasm groups or populations. Molecular marker technology offers an efficient tool to verify or reconstruct passport data. Using a high-throughput genotyping system with 15 microsatellite loci, we fingerprinted 482 accessions in 48 putative half-sib families of Refractario cacao (a group of germplasm collected from nine farms in Ecuador). Based on the multilocus profiles, a Bayesian method for individual assignment was applied to verify membership in each half-sib family. Multivariate statistical analysis showed that the Refractario genetic profile was different from other groups tested, except for the ''Nacional'' cacao from the coastal valley of Ecuador. Hierarchical partitioning of genetic variance in the Refractario cacao showed that 76% of the variation was contributed by intra-family difference, whereas the inter-family and inter-farm difference accounted for 15 and 9% of total variance, respectively. All three sources of variation were highly significant (P < 0.01). Cluster and Principal Coordinates Analyses revealed a population sub-structure in Refractario, which was also highly heterozygous, suggesting hybridization derived from Nacional cacao and multiple other parental varieties, which all shared a similar genetic background. The improved understanding of identities and structure in Refractario cacao will contribute to more efficient conservation and use of this germplasm group in cacao breeding.

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

“…The genetic diversity observed for the present plot comprising a continuous stand of cacao trees under natural conditions in the lower Amazon region supports this hypothesis. The expected heterozygosity observed in the adults (H e ¼ 0.477) was less than that previously detected in other lower Amazon populations (for example, H e ¼ 0.553; Sereno et al, 2006), whereas both populations demonstrated lower values than that detected in populations in the upper Amazon region, such as the Huallaga (H e ¼ 0.610) and Ucayali (H e ¼ 0.740) valleys in the Peru or the coastal valley of Ecuador (H e ¼ 0.561, Zhang et al, 2008). In comparison, other studies investigated more diverse cacao germplasm from the upper Amazon region n is the sample size of each family and of the fruits within families; t m is the multilocus outcrossing rate; t m Àt s is the outcrossing rate among relatives; r p(m) is the multilocus outcrossing rate; N ep is the effective number of pollen donors; Y is the coancestry coefficient within a family; N e is the effective population size within a family.…”

“…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). However, the results obtained with less precise method of allele detection using silver-stained polyacrylamide gels cannot be discounted, as the other studies have utilised fluorescence capillary electrophoresis (Zhang et al, 2008;Efombagn et al, 2009b). Furthermore, the low level of genetic diversity in the present plot could also be explained by a small number of founder individuals followed by genetic drift.…”

“…Despite the importance of this plant, little is known about the natural genetic structure of the T. cacao population because most studies have utilised accessions that were originally collected in the wild, but maintained in ex situ germplasm repositories. The accessions have been analysed as a group according to the approximate collection location, the river basin (Sereno et al, 2006;Motamayor et al, 2008;Zhang et al, 2008). Moreover, to our knowledge, no report has estimated the clonality, intrapopulation spatial genetic structure (SGS), effective population size, mating system at the hierarchical level of fruits and individuals, and pollen flow in natural cacao populations, which are fundamental parameters that are required to establish long-term ex situ or in situ conservation strategies.…”

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

“…Other diverse populations of cacao exist, however, as part of germplasm collections, commercial operations, and wild populations (see Turnbull and Hadley 2014) for reference). Some of these populations and collections have been genotyped with both Simple Sequence Repeat (microsatellite) and Single Nucleotide Polymorphic (SNP) markers, but analyses have focused mainly on the conservation of genetic diversity (Boza et al 2013;Irish et al 2010;Motilal et al 2011;Zhang et al 2007Zhang et al , 2012. Characterizing the extent of LD in these various populations is an important step toward understanding how association mapping could be best employed in cacao.…”

Development and characterization of microsatellite markers in the fungus Antrodia cinnamomea from dbEST database

“…Recently, internal transcribed spacer (ITS) markers were developed to identify and distinguish the different Antrodia species (Chiu 2007). However, microsatellites or simple sequence repeats (SSRs) were commonly used for diversity analysis, quantitative trait loci (QTL) mapping and population genetic studies of many organisms (Thomson et al 2007;Selvaraju et al 2007;Zhang et al 2008) because of their abundance, multiallelic nature, co-dominance, easily detectable nature and reproducibility. As the development of genomic SSR markers are expensive, resource intensive and time consuming, highly transferable expressed sequence tag (EST)-derived SSR markers can be used to evaluate the genetic variation of transcribed genes in A. cinnamomea.…”