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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: iXora1: exact haplotype inferencing and trait association

Authors
item Utro, Filippo -
item Haiminen, Niina -
item Livingstone Iii, Donald -
item Cornejo, Omar -
item Royaert, Stefan -
item Schnell, Raymond -
item Motamayor, Juan -
item KUHN, DAVID
item Parida, Laxmi -

Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 14, 2013
Publication Date: June 6, 2013
Citation: Utro, F., Haiminen, N., Livingstone Iii, D., Cornejo, O.E., Royaert, S., Schnell, R.J., Motamayor, J.C., Kuhn, D.N., Parida, L. 2013. iXora1: exact haplotype inferencing and trait association. BioMed Central (BMC) Genetics. 14:48.

Interpretive Summary: The majority of computer programs that attempt to infer the haplotype of a parent using genotyping data from the progeny have been developed for human populations. These programs in general have a limitation to family size of about 10 progeny (children). When crosses are made between clones of agriculturally important plants (avocado, cacao), there can be hundreds of progeny. iXora was developed to infer the exact haplotype of both progeny and parents and use these haplotypes for trait association. Use of a haplotype for trait association is much more powerful than attempting to associate single markers, especially in F1 populations, which are the norm for tree crops such as avocado and cacao. iXora is compared to other haplotyping programs and its strengths especially for use in tree crops is demonstrated. Our findings will be of great interest to breeders and, eventually farmers, as marker assisted selection based on haplotypes will give stronger association of traits to markers for breeding improved tree crops.

Technical Abstract: Background: We address the task of extracting accurate haplotypes from genotype data of individuals of large F1 populations for mapping studies. While methods for inferring parental haplotype assignments on large F1 populations exist in theory, these approaches do not work in practice at high levels of accuracy. Results: We have designed iXora, a robust method for extracting reliable haplotypes of a mapping population, as well as parental haplotypes, that runs in linear time. Each allele in the progeny is assigned not just to a parent, but more precisely to a haplotype inherited from the parent. iXora shows an improvement of at least 15% in accuracy over similar systems in literature. Furthermore, iXora provides an easy-to-use, comprehensive environment for association studies and hypothesis checking in populations of related individuals. Conclusions: iXora provides detailed resolution in parental inheritance, along with the capability of handling very large populations, which allows for accurate haplotype extraction and trait association. iXora is available for non-commercial use from http://researcher.ibm.com/project/3430 Keywords: Haplotype, Phasing, Phenotype association, Trait association, QTL, Randomization

Last Modified: 8/19/2014
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