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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Publications at this Location » Publication #285891
Title: Identification, analysis and mapping of SNP markers in Theobroma cacao

Author
item LIVINGSTONE III, DONALD - Mars, Inc
item MOCKAITIS, KEITHANNE - Indiana University
item MAY, GREGORY - National Center For Genome Research
item FARMER, ANDREW - National Center For Genome Research
item SASKI, CHRISTOPHER - Clemson University
item SCHNELL, RAYMOND - Mars, Inc
item MOTAMAYOR, JUAN CARLOS - Mars, Inc
item Kuhn, David

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/15/2012
Publication Date: N/A
Citation: N/A

Interpretive Summary: Theobroma cacao, the source of cocoa beans for chocolate, is an important tropical agriculture commodity that is affected by a number of fungal pathogens and insect pests, as well as concerns about yield and quality. We are trying to find molecular genetic markers that are linked to disease resistance and other important economic traits to aid in a marker assisted selection (MAS) breeding program for cacao to ensure a reliable supply of cocoa for the US confectionary industry. The identification and analysis of genetic markers serves as the foundation for Marker Assisted Selection. To this end a Theobroma cacao single nucleotide polymorphism (SNP) discovery project was undertaken to create saturated genetic maps to guide genome assembly and to benefit cacao breeders worldwide. Over 48,000 high quality SNPs were identified from RNA of 15 individual cacao lines, representing the 10 genetically diverse groups of cacao. These SNPs have been filtered for various purposes including the creation of a 6k Illumina Infinium genotyping SNP chip. With this Infinium chip 1,152 individual cacao plants representing different mapping populations were genotyped. Genetic recombination maps were generated and compared to previously published microsatellite based genetic maps as well as the position of QTLs identified for both types of maps. Allele calls and Minor Allele Frequencies estimated from the short read sequencing used to identify SNPs are evaluated with regards to the observed SNP chip genotypic data. Furthermore, genotype data has been characterized to isolate different subsets of SNP markers (e.g. unique to a diversity group). SNP markers identified in this, and similar, SNP discovery projects can be directly converted into easily assayable markers for cacao breeders using a variety of assay platforms of low to high throughput. The ability to assay SNPs in cacao growing regions will positively impact cacao breeders throughout the world. 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 and more productive cultivars produced through our MAS breeding program.

Technical Abstract: The identification and analysis of genetic markers serves as the foundation for Marker Assisted Selection. To this end a Theobroma cacao single nucleotide polymorphism (SNP) discovery project was undertaken to create saturated genetic maps to guide genome assembly and to benefit cacao breeders worldwide. Over 48,000 high quality SNPs were identified from RNA of 15 individual cacao lines, representing the 10 genetically diverse groups of cacao. These SNPs have been filtered for various purposes including the creation of a 6k Illumina Infinium genotyping SNP chip. With this Infinium chip 1,152 individual cacao plants representing different mapping populations were genotyped. Genetic recombination maps were generated and compared to previously published microsatellite based genetic maps as well as the position of QTLs identified for both types of maps. Allele calls and Minor Allele Frequencies estimated from the short read sequencing used to identify SNPs are evaluated with regards to the observed SNP chip genotypic data. Furthermore, genotype data has been characterized to isolate different subsets of SNP markers (e.g. unique to a diversity group). SNP markers identified in this, and similar, SNP discovery projects can be directly converted into easily assayable markers for cacao breeders using a variety of assay platforms of low to high throughput. The ability to assay SNPs in cacao growing regions will positively impact cacao breeders throughout the world.