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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: iXora: Haplotype Inferencing and Trait Association

item Utro, Filippo
item Haiminen, Niina
item Livingstone Iii, Donald
item Cornejo, Omar
item Royaert, Stefan
item Schnell, Raymond
item Motamayor, Juan Carlos
item Kuhn, David
item Parida, Laxmi

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/13/2013
Publication Date: 1/13/2013
Citation: Utro, F., Haiminen, N., Livingstone Iii, D.S., Cornejo, O., Royaert, S., Schnell, R.J., Motamayor, J., Kuhn, D.N., Parida, L. 2013. iXora: Haplotype Inferencing and Trait Association . Meeting Abstract. Plant and Animal Genome Meeting XXI, January 12-16, 2013 San Diego, CA.

Interpretive Summary:

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. iXora is a framework for inferring haplotypes from genomic marker data, on a population arising from a cross between two heterozygous parents; and subsequently utilizing the haplotypes to map genomic regions associated with observed phenotypes. Each allele in the progeny is assigned not just to a parent, but more precisely to a haplotype of the parent. This finer resolution in inheritance from the parents allows for more accurate association studies, hypothesis checking, as well as randomization tests. At the core of iXora is a novel exact haplotype inference algorithm that scales to large datasets. The algorithm provides a framework for examining the space of all equally-likely "best" solutions, and computes measures of preciseness regarding the stability of the solutions. The iXora framework also includes built-in statistical tests, randomization procedures, and visualization tools. The framework is especially well suited to plant breeding, where mapping populations of individuals of inbred (or non-inbred) parents are utilized; iXora has been successfully applied to localize the pod color phenotype in T. cacao. iXora is available for non-commercial use from 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: 06/22/2017
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