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United States Department of Agriculture

Agricultural Research Service

Research Project: IDENTIFICATION OF GENES REGULATING MAJOR AGRONOMIC TRAITS IN CACAO THROUGH ASSOCIATION AND LINKAGE MAPPING USING LARGE SEQUENCE DATA SETS

Location: Subtropical Horticulture Research

2012 Annual Report


1a.Objectives (from AD-416):
To provide analytical bioinformatic support to the MARS-USDA Theobroma cacao L. sequencing project in various research activities: a) SNP diversity and association mapping analyses of cacao populations, b) Gene expression analysis to study self incompatibility in cacao with special emphasis on the effect of micro RNAs, c) comparative genomics of Theobroma grandiflorum vs. Theobroma cacao, d) sequencing of Phytophthora megakarya, and (e) functional annotation of the T. cacao, T. grandiflorum, and P. megakarya genomes and polymorphisms based on bioinformatic approaches as well as integration of RNAseq data.


1b.Approach (from AD-416):
The research activities outlined in the objectives are not enunciated in order of priority and will be implemented according to the availability of the data.

The cacao genome sequencing project will generate a large amount of Single Nucleotide Polymorphism (SNP) data that will be selected to establish a high throughput SNP genotyping platform. The selection of the SNPs and their utilization for diversity and association mapping studies, requires bionformatic analytical support. A post doctoral fellow (or later research associate, depending on rank) will be hired to work in the laboratory and the Center for Genomics and Personalized Medicine at the Stanford University School of Medicine. The post-doctoral fellow will perform the required analyses for the SNPs studies. Other scientific activities, within the context of the cacao genome project, will also benefit from bioinformatics expertise in the lab and the CGPM. Specifically, the department and center’s expertise on the study of gene expression and the action of microRNAs will be of great value for the analysis of the gene expression data that have been generated to understand the genetic determinism of self incompatibility in cacao.

The genome of Theobroma grandiflorum, a related species showing significant traits of importance such as disease resistance, will be sequenced and compared to the cacao genome. This comparison will help identifying key genes involved in the domestication of cacao. The sequencing project also comprises the study of important diseases affecting cacao; The lab and specifically the post-doctoral fellow hired to support the activities outlined in this SCA will contribute to the assembly of the genome of main diseases affecting cacao. For example, P. megakarya has a detrimental impact in cacao production, causing hundreds of millions of dollars in damages to West African cacao producer countries.


3.Progress Report:

This research relates to inhouse project objective: The development and implementation of an international Marker Assisted Selection (MAS) program for cacao is the major objective of this project.

Stanford University has continued generating data and developing resources for the Cacao Genome Sequencing Project. Specifically for (a) the genotype-by-sequencing (GBS) technology development project with primary aim to test the efficacy of GBS for deployment in marker-assisted breeding programs, and (b) a genome assembly pilot with primary aim of improving the cacao reference assembly by addition of long sequencing reads based on the technology of Moleculo, a startup Company in the San Francisco Bay area, that has developed a novel DNA sequencing method that provides very long and accurate reads. Currently we are in the process of re-sequencing 150 genotypes from the 10 cacao genetic groups.


Last Modified: 8/1/2014
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