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United States Department of Agriculture

Agricultural Research Service

Research Project: Conservation, Genetic Analyses, and Utilization of Subtropical/Tropical Fruit Crops, Sugarcane, and Miscanthus Genetic Resources

Location: Subtropical Horticulture Research

Title: The Role Of Haplotyping In Mapping The Pod Color Trait

Authors
item Haiminen, Niina -
item Livingstone Iii, Donald -
item Cornejo, Omar -
item Utro, Filippo -
item Royaert, Stefan -
item Mockaitis, Keithanne -
item Motamayor Arias, Juan Carlos -
item Parida, Laxmi -
item Kuhn, David

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: January 13, 2013
Publication Date: January 13, 2013
Citation: Haiminen, N., Livingstone Iii, D.S., Cornejo, O., Utro, F., Royaert, S., Mockaitis, K., Motamayor Arias, J., Parida, L., Kuhn, D.N. 2013. The Role Of Haplotyping In Mapping The Pod Color Trait. Meeting Abstract. Plant and Animal Genome Meeting XXI, January 12-16, 2013 San Diego, CA.

Technical Abstract: 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. T. cacao pod color is an oligogenic trait that can not be predicted in the progeny purely based on parental phenotypes (due to allelic dominance). To improve the quality of cultivated cacao, it is of interest to be able to distinguish between clones bearing red pods (such as CCN 51, linked to undesirable flavor profile) and green pods associated with desirable flavor profiles. Previous linkage studies have mapped the pod color trait onto linkage group 4, between a pair of microsatellite markers 30 cM apart. Utilizing the Matina 1-6 genome sequence and a novel haplotyping algorithm, we have identified the parental origin of pod color in three T. cacao mapping populations with high resolution. The iXora haplotyping framework was applied to phase genotypes from these populations, with up to hundreds of progeny and several hundred markers per chromosome. The results support the hypothesis of a single allele responsible for the pod color trait, and identifying this allele allows for molecular testing for the pod color phenotype. The iXora analysis framework is available for non-commercial use from http://researcher.ibm.com/project/3430 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.

Last Modified: 12/22/2014
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