iXora: Exact Haplotype Inferencing
and Trait Association


Niina Haiminen photo Laxmi Parida photoFILIPPO UTRO photo

iXora: Exact Haplotype Inferencing
and Trait Association - overview

iXora is a framework for inferring haplotypes from genotyped population data, and for associating observed phenotypes with the inferred haplotypes [1].

Given a set of genotypes for progeny of at most two heterozygous parents, iXora efficiently and accurately extracts all the equally-likely haplotypes of the progenies to produce an agglomerate structure. The results of the phasing can then be applied as input to statistical tests and visualization methods. iXora can phase the progeny even in the complete absence of parental genotype data. iXora performs the following three main steps:

  1. Exact haplotype inference: this is done via a rigorous mathematical analysis that examines the space of all the ``best'' possible haplotype solutions, as described in detail in [1].

  2. Statistical analysis of association, per genotyped marker, between the haplotypes and phenotypes.

  3. Visualization of the phasing and statistical association analysis.

Exact haplotype inference

Given n genotypes of F1 progenies on m loci, iXora produces all the equally-likely haplotypes of the progeny in three phases:

  1. Estimate the genotypes (if they are not available) of the parents from the progeny genotypes.
  2. Use the so called polarization property to phase the progeny.
  3. Agglomerate multiple equally-likely configurations into a single structure.

The interested reader is referred to [1] for more details about the method.

Statistical analysis

iXora outputs the resulting p-values for marker-phenotype association (via Fisher’s exact test) as a text file and visualizes the results.
An added value of iXora is the built-in feature to perform randomization tests on the phenotypes, to establish significance thresholds on the p-values.
iXora reports these limits and visualizes them along with the p-values on the real data. In addition, iXora outputs error measures on the phasing step, summarizing the ambiguity in the data regarding haplotype inference.


The output files from phasing and phenotype association can be visualized via a user-friendly graphical interface. A screenshot of the user interfout_enr_1, 56Bace main dialog, showing example visualizations, is given on the right. This visualization can help to study the parental haplotype distributions, and to spot unexpected distortions.


Related Publications

  1. Filippo Utro, Niina Haiminen, Donald Livingstone, Omar E Cornejo, Stefan Royaert, Raymond J Schnell, Juan Carlos Motamayor, David N Kuhn and Laxmi Parida:

    iXora: Exact Haplotype Inferencing and Trait Association

    BMC Genetics 14:48, 2013.

  2. Juan C Motamayor+*, Keithanne Mockaitis+, Jeremy Schmutz+, Niina Haiminen+, Donald Livingstone, Omar Cornejo, Seth D Findley, Ping Zheng, Filippo Utro, Stefan Royaert, Christopher Saski, Jerry Jenkins, Ram Podicheti, Meixia Zhao, Brian E Scheffler, Joseph C Stack, Frank A Feltus, Guiliana M Mustiga, Freddy Amores, Wilbert Phillips, Jean Philippe Marelli, Gregory D May, Howard Shapiro, Jianxin Ma, Carlos D Bustamante, Raymond J Schnell, Dorrie Main, Don Gilbert, Laxmi Parida* and David N Kuhn*:

    The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color

    Genome Biology 14:6 R53, 2013.

    + These authors contributed equally to this work. * Corresponding author.