W120 Assessing the evolutionary history of Theobroma cacao from resequenced genomes

Date: Sunday, January 15, 2012
Time: 2:05 PM
Room: Royal Palm Salons 3-4
Omar Cornejo , Stanford University, Stanford, CA
Keithanne Mockaitis , Indiana University Center for Genomics and Bioinformatics, Bloomington, IN
Muh-Ching Yee , Stanford University, Stanford, CA
Stefan Royaert , USDA ARS SHRS, Miami, FL
Donald Livingstone III , MARS Inc., Miami, FL
Ram Podicheti , Indiana University, Bloomington, IN
David Kuhn , USDA, ARS SHRS, Miami, FL
Carlos Bustamante , Stanford University, stanford, CA
Juan Carlos Motamayor , MARS Inc., Miami, FL
The drastic reductions in cost and time associated with the collection of DNA sequence and genotype data have opened the possibility to examine in detail questions regarding the origin of domestication and demographic history of plant and animal species of interest (e.g. rice, dogs). In the case of cacao, recent work based on microsatellite markers has provided with insights into the geographic and genetic differentiation of cacao. Here, we report preliminary results from 12 fully re-sequenced genomes of Theobroma cacao L. Our analyses on ~ 4 Million bialellic SNPs across accessions allowed us to examine a variety of demographic models that include population bottlenecks and expansions.  We discuss the relevance of accounting for the demographic history of cacao while attempting to discover the genetic bases for adaptation during its domestication.  Specifically, we discuss how understanding the demographic history of cacao will let us to generate adequate null models to identify regions under putative selection, and potentially identify the bases for adaptation of cacao during domestication.  We discuss several of the challenges associated with the inference of demographic history of cacao based on full genome sequence in heterozygous systems (e.g. calling heterozygotes, phasing, imputation), that must first be overcome and included while performing these analyses.