Motazedi Ehsan, Maliepaard Chris, Finkers Richard, Visser Richard, de Ridder Dick
Bioinformatics Group, Wageningen University & Research, Wageningen, Netherlands.
Plant Breeding, Wageningen University & Research, Wageningen, Netherlands.
Front Genet. 2019 Apr 16;10:335. doi: 10.3389/fgene.2019.00335. eCollection 2019.
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.
DNA序列读数包含位于单条染色体上的基因组变异信息。通过利用读数之间的重叠来提取和扩展此信息，可以获得个体的单倍型。利用群体中的亲子关系可以显著提高从短读数获得的单倍型质量，因为系谱信息可用于校正虚假重叠（由于测序错误）和重叠不足（由于短读长、低基因组变异和低覆盖度）。我们开发了一种新方法PopPoly，通过考虑单倍型从亲本到后代的传递，从短序列数据估计F1群体中的多倍体单倍型。此外，该信息还用于改善基因型剂量估计并在群体中调用缺失的基因型。通过模拟，我们将PopPoly与其他单倍型分型方法进行比较，并展示了其更好的性能。我们通过将PopPoly应用于涉及块茎形成的九个基因组区域的四倍体马铃薯杂交种来评估PopPoly。
