Abstract
DNA sequence reads contain information about the genomic variants located on a single chromosome. By extracting and extending this information using the overlaps between the reads, the haplotypes of an individual can be obtained. Using parent-offspring relationships in a population can considerably improve the quality of the haplotypes obtained from short reads, as pedigree information can be used to correct for spurious overlaps (due to sequencing errors) and insufficient overlaps (due to short read lengths, low genomic variation and shallow coverage). We developed a novel method, PopPoly, to estimate polyploid haplotypes in an F1-population from short sequence data by taking into consideration the transmission of the haplotypes from the parents to the offspring. In addition, this information is employed to improve genotype dosage estimation and to call missing genotypes in the population. Through simulations, we compare PopPoly to other haplotyping methods and show its better performance. We evaluate PopPoly by applying it to a tetraploid potato cross at nine genomic regions involved in tuber formation.
Highlights
Genetic polymorphism is the key to understanding inheritance patterns of traits and to identifying genomic regions that affect a trait
The average haplotype reconstruction rate (RR), which is a measure of overall phasing accuracy, obtained by PopPoly for the offspring was 0.96 across different population sizes, which was higher than the other methods (Figure 2A)
We present a novel algorithm, PopPoly, to exploit parentoffspring relationships for the estimation of haplotypes in an outcrossing F1-population that consists of two heterozygous parents and their F1 offspring, using short DNA sequence reads and Single Nucleotide Polymorphism (SNP) genotypes called in the population
Summary
Genetic polymorphism is the key to understanding inheritance patterns of traits and to identifying genomic regions that affect a trait. While the traits of interest usually have medical importance in human genetics, in plant sciences these traits are often of importance for breeding and selection of the best varieties. Polymorphic genomic loci are used as genetic markers to investigate co-segregation of genetic variants (alleles) with qualitative traits, e.g., flower color, in populations from crosses or in natural populations. These markers can be used to investigate the genetic components of quantitative traits such as yield and the degree of tolerance to biotic or abiotic stresses. To phase markers means to determine these k haplotypes, which might be identical (harboring the same alleles) or different (having different alleles at some or all of the marker positions)
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