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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Publications at this Location » Publication #319496

Research Project: Genetic Improvement of Cacao Through Genomics-Assisted Breeding

Location: Subtropical Horticulture Research

Title: Making a chocolate chip: development and evaluation of a 6K SNP array for Theobroma cacao.

item Livingstone Iii, Donald - Mars, Inc
item Royaert, Stefan - Mars, Inc
item Stack, Conrad - Mars, Inc
item Mockatis, Keithanne - Mars, Inc
item Greg, May - National Center For Genome Resources
item Farmer, Andrew - National Center For Genome Resources
item Saski, Christopher - Clemson University
item Schenll, Raymond - Mars, Inc
item Kuhn, David
item Motomayer, Juan - Mars, Inc

Submitted to: DNA Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/1/2014
Publication Date: 6/11/2015
Citation: Livingstone Iii, D., Royaert, S., Stack, C., Mockatis, K., Schenll, R., Kuhn, D.N., Motomayer, J. 2015. Making a chocolate chip: development and evaluation of a 6K SNP array for Theobroma cacao. 2015, 1-13.

Interpretive Summary: Theobroma cacao, whose seeds are the source of cocoa, the raw material for the multi-billion dollar US chocolate industry, is an important tropical agriculture commodity that is affected by a number of fungal diseases, including Black Pod disease caused by Phytophthora spp. We are trying to find molecular genetic markers that are linked to disease resistance in Theobroma cacao to aid in a marker assisted selection (MAS) breeding program to ensure a reliable supply of cocoa for the US confectionary industry. We developed a high throughput assay for single nucleotide polymorphism (SNP) molecular markers to identify candidate genes for traits such as pod color and disease resistance. Our results are important to scientists trying to understand the mechanism of disease resistance and, eventually, to cacao farmers who will benefit from superior disease resistant cultivars produced through our MAS breeding program.

Technical Abstract: Theobroma cacao, the key ingredient in chocolate production, is one of the world's most important tree fruit crops, with ~4,000,000 metric tons produced across 50 countries. To move towards gene discovery and marker-assisted breeding in cacao, a single-nucleotide polymorphism (SNP) identification project was undertaken using RNAseq data from 16 diverse cacao cultivars. RNA sequences were aligned to the assembled transcriptome of the cultivar Matina 1-6, and 330,000 SNPs within coding regions were identified. From these SNPs, a subset of 6,000 high-quality SNPs were selected for inclusion on an Illumina Infinium SNP array: the Cacao6kSNP array. Using Cacao6KSNP array data from over 1,000 cacao samples, we demonstrate that our custom array produces a saturated genetic map and can be used to distinguish among even closely related genotypes. Our study enhances and expands the genetic resources available to the cacao research community, and provides the genome-scale set of tools that are critical for advancing breeding with molecular markers in an agricultural species with high genetic diversity.