Haplotype allele assignment and imputation in pedigrees

Research output: Chapter in Book/Report/Conference proceedingAbstract


With current genotyping platforms it is affordable to generate high‐density
SNP data for large pedigrees. However, the use of SNP genotypes for QTL
mapping in pedigrees is limited, especially because multiple QTL alleles may
be segregating whereas individual SNP markers have only two alleles. Using
pedigree information, the FlexQTL software is able to phase the SNP
genotypes to a large extent. It also provides information that allows the
definition of “haploblocks”: groups of tightly linked SNPs without any
recombination events within the pedigree. Here we present complementary
software (FQ‐haplotyper) that uses the phased SNP genotypes and defined
haploblocks to (1) impute missing SNP data, (2) delete and where possible
correct erroneous SNP scores and (3) define and assign haploblock alleles.
Full information on the imputations is provided, which may be used as a tool
for curation of the data. The multi‐allelic nature of the haploblock genotypes
as assigned by FQ‐haplotyper makes them much more informative than
individual SNPs. Therefore they represent the information present in the SNP
genotypes in a compact form which allows efficient QTL mapping. Our FQhaplotyper software exports data in a form suitable for QTL mapping by
FlexQTL and also produces data files for Pedimap software to visualize the
flow of alleles through the pedigree. SNP data from an Illumina 20K array on
a large apple pedigree will be used for demonstration.
Original languageEnglish
Title of host publicationBook of abstracts EUCARPIA
Subtitle of host publication16th Meeting of EUCARPIA Section Biometrics for Plant Breeding
Place of PublicationWageningen
Publication statusPublished - 2015
EventXVIth meeting of the Eucarpia Section Biometrics in Plant Breeding - Hotel de Wageningsche Berg, Wageningen , Netherlands
Duration: 9 Sept 201511 Sept 2015


ConferenceXVIth meeting of the Eucarpia Section Biometrics in Plant Breeding
Internet address


Dive into the research topics of 'Haplotype allele assignment and imputation in pedigrees'. Together they form a unique fingerprint.

Cite this