Haplotype assembly in polyploid genomes and identical by descent shared tracts

This paper reviews the causes of linkage disequilibrium and its use in mapping quantitative trait loci. The many causes of linkage disequilibrium can be understood as due to similarity in the coalescence tree of different loci. Consideration of the way this comes about allows us to divide linkage disequilibrium into 2 types: linkage disequilibrium between any 2 loci, even if they are unlinked, caused by variation in the relatedness of pairs of animals; and linkage disequilibrium due to the inheritance of chromosome segments that are identical by descent from a common ancestor. The extent of linkage disequilibrium due to the latter cause can be logically measured by the chromosome segment homozygosity which is the probability that chromosome segments taken at random from the population are identical by descent. This latter cause of linkage disequilibrium allows us to map quantitative trait loci to chromosome regions. The former cause of linkage disequilibrium can cause artefactual quantitative trait loci at any position in the genome. These artefacts can be avoided by fitting the relatedness of animals in the statistical model used to map quantitative trait loci. In the future it may be convenient to estimate this degree of relatedness between individuals from markers covering the whole genome. The statistical model for mapping quantitative trait loci also requires us to estimate the probability that 2 animals share quantitative trait loci alleles at a particular position because they have inherited a chromosome segment containing the quantitative trait loci identical by descent. Current methods to do this all involve approximations. Methods based on concepts of coalescence and chromosome segment homozygosity are useful, but improvements are needed for practical analysis of large datasets. Once these probabilities are estimated they can be used in flexible linear models that conveniently combine linkage and linkage disequilibrium information.

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Identical By Descent

Encyclopedia of Genetics, Genomics, Proteomics and Informatics ◽

10.1007/978-1-4020-6754-9_8192 ◽

2008 ◽

pp. 954-954

Keyword(s):

Identical By Descent

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A Hopfield neural network based algorithm for haplotype assembly from low-quality data

2014 International Joint Conference on Neural Networks (IJCNN) ◽

10.1109/ijcnn.2014.6889588 ◽

2014 ◽

Author(s):

Xiao Chen ◽

Qinke Peng ◽

Libin Han ◽

Xiao Wang

Keyword(s):

Neural Network ◽

Hopfield Neural Network ◽

Quality Data ◽

Haplotype Assembly

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Blocks of chromosomes identical by descent in a population: Models and predictions

PLoS ONE ◽

10.1371/journal.pone.0187416 ◽

2017 ◽

Vol 12 (11) ◽

pp. e0187416 ◽

Cited By ~ 1

Author(s):

Mathieu Tiret ◽

Frédéric Hospital

Keyword(s):

Population Models ◽

Identical By Descent

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HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

Genome Research ◽

10.1101/gr.213462.116 ◽

2016 ◽

Vol 27 (5) ◽

pp. 801-812 ◽

Cited By ~ 121

Author(s):

Peter Edge ◽

Vineet Bafna ◽

Vikas Bansal

Keyword(s):

Haplotype Assembly ◽

Sequencing Technologies

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Haplotype assembly of autotetraploid potato using integer linear programing

Bioinformatics ◽

10.1093/bioinformatics/btz060 ◽

2019 ◽

Vol 35 (18) ◽

pp. 3279-3286 ◽

Cited By ~ 4

Author(s):

Enrico Siragusa ◽

Niina Haiminen ◽

Richard Finkers ◽

Richard Visser ◽

Laxmi Parida

Keyword(s):

Experimental Data ◽

Experimental Studies ◽

Simulated Data ◽

Supplementary Information ◽

Linear Programs ◽

Plant Genomics ◽

Optimal Method ◽

Haplotype Assembly ◽

Open Issue ◽

Removal Model

Abstract Summary Haplotype assembly of polyploids is an open issue in plant genomics. Recent experimental studies on highly heterozygous autotetraploid potato have shown that available methods do not deliver satisfying results in practice. We propose an optimal method to assemble haplotypes of highly heterozygous polyploids from Illumina short-sequencing reads. Our method is based on a generalization of the existing minimum fragment removal model to the polyploid case and on new integer linear programs to reconstruct optimal haplotypes. We validate our methods experimentally by means of a combined evaluation on simulated and experimental data based on 83 previously sequenced autotetraploid potato cultivars. Results on simulated data show that our methods produce highly accurate haplotype assemblies, while results on experimental data confirm a sensible improvement over the state of the art. Availability and implementation Executables for Linux at http://github.com/Computational Genomics/HaplotypeAssembler. Supplementary information Supplementary data are available at Bioinformatics online.

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