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

Author
item STACK, J.CONARD - Mars, Inc
item ROYAERT, STEFAN - Mars, Inc
item Gutierrez, Osman
item NAGAI, CHIFUMI - Hawaii Agricultural Research Center
item SCHNELL, RAYMOND - Mars, Inc
item MOTAMAYOR, JUAN - Mars, Inc

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/15/2015
Publication Date: 2/7/2015
Citation: Stack, J., Royaert, S., Gutierrez, O.A., Nagai, C., Schnell, R.J., Motamayor, J.C. 2015. Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L and its impact on association mapping. Tree Genetics and Genomes. 11:19.

Interpretive Summary: Cacao wild accessions, cultivated varieties and a segregating population were fingerprinted with Simple Sequence Repeats (SSR) to study linkage disequilibrium (LD) breakdown in cacao. Results indicated that genome-wide LD decays more rapidly in wild compared to the more-cultivated diversity groups. Also association mapping outcome for pod color, a well-characterized phenotype, indicated that a more rapid LD decay in wild germplasm leads to higher-resolution mapping intervals when compared to results from cultivated germplasm. Since many desirable traits targeted by cacao breeders are found exclusively in wild populations, it is concluded that association mapping in wild cacao populations holds significant promise for cacao improvement through marker-assisted breeding.

Technical Abstract: Linkage disequilibrium (LD) is the nonrandom association of alleles and loci within sets of genetic data and when 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 L., where experimental crosses are inherently time-consuming and logistically expensive. While LD has been evaluated in Theobroma cacao L., previous work has been narrowly focused on a few specific populations comprising relatively narrow genetic bases. In this study, 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 such differences can have on association analyses are demonstrated through association mapping analyses using phenotypic data on pod color and genotypic data from two difference cacao populations with contrasting demographic histories and patterns of LD decay. Our results indicate that the more rapid LD decay in wild and primitive germplasm leads to higher-resolution mapping intervals when compared to results from cultivated germplasm. A more general corollary from these results is demonstrated through simulations: In planning future association mapping analyses, 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 desirable traits that are targeted by cacao breeders are found exclusively in wild and primitive germplasm, we conclude that association mapping in wild cacao populations holds significant promise for cacao improvement through marker-assisted breeding and emphasize the need to conserve and further explore the natural diversity of Amazonian cacao.