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

Abstract

Linkage disequilibrium (LD) measured over the genomes of a species can provide important indications for how future association analyses should proceed. This information can be advantageous especially for slow-growing, perennial crops such as Theobroma cacao, where experimental crosses are inherently time-consuming and logistically expensive. While LD has been evaluated in cacao, previous work has been focused on relatively narrow genetic bases. We use microsatellite marker data collected from a uniquely diverse sample of individuals broadly covering both wild and cultivated varieties to gauge the LD present in the different cacao diversity groups and populations. We find that genome-wide LD decays far more rapidly in the wild and primitive diversity groups of cacao as compared to those representing cultivated varieties. The impact that such differences can have on association analyses is demonstrated using phenotypic data on pod color and genotypic data from two cacao populations with contrasting patterns of LD decay. Our results indicate that the more rapid LD decay in wild and primitive germplasm can lead to higher-resolution mapping intervals when compared to results from cultivated germplasm. Through simulations, we demonstrate how future association mapping analyses, comprising of cacao samples with a wild or primitive background, will likely exhibit lower LD and would be more suitable for fine-scale association mapping analyses. As many traits targeted by cacao breeders are found exclusively in wild and primitive germplasm, association mapping in wild cacao populations holds significant promise for cacao improvement through marker-assisted breeding and emphasize the need to further explore the natural diversity of Amazonian cacao.

Prediction of Cacao (Theobroma cacao) Resistance to Moniliophthora spp. Diseases via Genome-Wide Association Analysis and Genomic Selection

“…This was most apparent when observing the breakdown of LD ( Figure 4 ), which remained much higher in one population than the other two. Part of this finding may be explained by ancestry: both Ganaderia and Las Tecas are dominated by ‘Wild’ and ‘Nacional’ types, respectively, while Malvinas is composed mostly of crosses among “known accessions.” Malvinas is more diverse in terms of ancestry distribution ( Figure 2 , Table 1 , and Supplementary Table S1 ), but it is derived from long-cultivated varieties which likely have a higher degree of LD than their wilder counterparts, as has been described in cacao previously ( Stack et al, 2015 ).…”

Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases

“…This effect is probably due to the high LD in the samples due to limited recombination and admixture during recent breeding efforts. LD has been explored in other cacao populations, and although diversity panels with higher ancestral recombination may be better suited for GWAS (Stack et al, 2015 ), recently admixed populations may be better suited for genomic prediction, with much more effective selection for quantitative traits. In our analyses, the trait with the highest observed prediction accuracy was the proportion of frosty pod infection, a quantitative trait in our population, reaching prediction accuracies of 0.60 with 90 markers and 0.67 with all markers.…”

Identification of Climate and Genetic Factors That Control Fat Content and Fatty Acid Composition of Theobroma cacao L. Beans

“…The creation of the MP01 mapping population, including the genotyping procedure and its genetic map, was described in Motamayor et al (2013), Barreto et al (2015), Royaert et al (2016), and Stack et al (2015). Briefly, this study involves 420 of the total 459 offspring from a cross between “TSH 1188” and “CCN 51.” The MP01 mapping population was planted at Mars Center for Cocoa Science in Barro Preto, Bahia, Brazil (14°42′45 N, 39°22′13 E) in the year 2000 in a 3 × 3 m grid in a hydromorphic and typical tropudalf (Itabuna modal) mixed soil type.…”