Haplotype inference in crossbred populations without pedigree information
<p>Abstract</p> <p>Background</p> <p>Current methods for haplotype inference without pedigree information assume random mating populations. In animal and plant breeding, however, mating is often not random. A particular form of nonrandom mating occurs when parental indi...
Main Authors: | , , , |
---|---|
Format: | Article |
Language: | deu |
Published: |
BMC
2009-08-01
|
Series: | Genetics Selection Evolution |
Online Access: | http://www.gsejournal.org/content/41/1/40 |
id |
doaj-6966b0331b5e4038bc2a4e3f216547bb |
---|---|
record_format |
Article |
spelling |
doaj-6966b0331b5e4038bc2a4e3f216547bb2020-11-24T23:22:44ZdeuBMCGenetics Selection Evolution0999-193X1297-96862009-08-014114010.1186/1297-9686-41-40Haplotype inference in crossbred populations without pedigree informationFernando Rohan LHeuven Henri CMCoster AlbartDekkers Jack CM<p>Abstract</p> <p>Background</p> <p>Current methods for haplotype inference without pedigree information assume random mating populations. In animal and plant breeding, however, mating is often not random. A particular form of nonrandom mating occurs when parental individuals of opposite sex originate from distinct populations. In animal breeding this is called <it>crossbreeding </it>and <it>hybridization </it>in plant breeding. In these situations, association between marker and putative gene alleles might differ between the founding populations and origin of alleles should be accounted for in studies which estimate breeding values with marker data. The sequence of alleles from one parent constitutes one haplotype of an individual. Haplotypes thus reveal allele origin in data of crossbred individuals.</p> <p>Results</p> <p>We introduce a new method for haplotype inference without pedigree that allows nonrandom mating and that can use genotype data of the parental populations and of a crossbred population. The aim of the method is to estimate line origin of alleles. The method has a Bayesian set up with a Dirichlet Process as prior for the haplotypes in the two parental populations. The basic idea is that only a subset of the complete set of possible haplotypes is present in the population.</p> <p>Conclusion</p> <p>Line origin of approximately 95% of the alleles at heterozygous sites was assessed correctly in both simulated and real data. Comparing accuracy of haplotype frequencies inferred with the new algorithm to the accuracy of haplotype frequencies inferred with PHASE, an existing algorithm for haplotype inference, showed that the DP algorithm outperformed PHASE in situations of crossbreeding and that PHASE performed better in situations of random mating.</p> http://www.gsejournal.org/content/41/1/40 |
collection |
DOAJ |
language |
deu |
format |
Article |
sources |
DOAJ |
author |
Fernando Rohan L Heuven Henri CM Coster Albart Dekkers Jack CM |
spellingShingle |
Fernando Rohan L Heuven Henri CM Coster Albart Dekkers Jack CM Haplotype inference in crossbred populations without pedigree information Genetics Selection Evolution |
author_facet |
Fernando Rohan L Heuven Henri CM Coster Albart Dekkers Jack CM |
author_sort |
Fernando Rohan L |
title |
Haplotype inference in crossbred populations without pedigree information |
title_short |
Haplotype inference in crossbred populations without pedigree information |
title_full |
Haplotype inference in crossbred populations without pedigree information |
title_fullStr |
Haplotype inference in crossbred populations without pedigree information |
title_full_unstemmed |
Haplotype inference in crossbred populations without pedigree information |
title_sort |
haplotype inference in crossbred populations without pedigree information |
publisher |
BMC |
series |
Genetics Selection Evolution |
issn |
0999-193X 1297-9686 |
publishDate |
2009-08-01 |
description |
<p>Abstract</p> <p>Background</p> <p>Current methods for haplotype inference without pedigree information assume random mating populations. In animal and plant breeding, however, mating is often not random. A particular form of nonrandom mating occurs when parental individuals of opposite sex originate from distinct populations. In animal breeding this is called <it>crossbreeding </it>and <it>hybridization </it>in plant breeding. In these situations, association between marker and putative gene alleles might differ between the founding populations and origin of alleles should be accounted for in studies which estimate breeding values with marker data. The sequence of alleles from one parent constitutes one haplotype of an individual. Haplotypes thus reveal allele origin in data of crossbred individuals.</p> <p>Results</p> <p>We introduce a new method for haplotype inference without pedigree that allows nonrandom mating and that can use genotype data of the parental populations and of a crossbred population. The aim of the method is to estimate line origin of alleles. The method has a Bayesian set up with a Dirichlet Process as prior for the haplotypes in the two parental populations. The basic idea is that only a subset of the complete set of possible haplotypes is present in the population.</p> <p>Conclusion</p> <p>Line origin of approximately 95% of the alleles at heterozygous sites was assessed correctly in both simulated and real data. Comparing accuracy of haplotype frequencies inferred with the new algorithm to the accuracy of haplotype frequencies inferred with PHASE, an existing algorithm for haplotype inference, showed that the DP algorithm outperformed PHASE in situations of crossbreeding and that PHASE performed better in situations of random mating.</p> |
url |
http://www.gsejournal.org/content/41/1/40 |
work_keys_str_mv |
AT fernandorohanl haplotypeinferenceincrossbredpopulationswithoutpedigreeinformation AT heuvenhenricm haplotypeinferenceincrossbredpopulationswithoutpedigreeinformation AT costeralbart haplotypeinferenceincrossbredpopulationswithoutpedigreeinformation AT dekkersjackcm haplotypeinferenceincrossbredpopulationswithoutpedigreeinformation |
_version_ |
1725566670463827968 |