염색체 도식화와 imputation에 의한 GBS 기반 여교잡 회복률 계산 정확도 증진 방법
Method for Improving Marker Selection Efficiency through a Graphical Representation of Molecular Markers
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초록
Marker-assisted backcrossing is a powerful method for developing new cultivars. To develop genomic-wide markers, genotyping-by-sequencing(GBS) can be an efficient method. However, unrefined low-quality markers and missing data between markers can contribute to hamperingthe marker selection process, particularly in multi-way crosses. In this study, we aimed to calculate the recovery rate of offspring individualsand minimize errors that occur among a large number of markers. Initially, missing data were imputed by comparing samples using the k-nearestneighbor (k-NN) algorithm. Thereafter, low-quality single-nucleotide polymorphisms (SNPs) were corrected by applying the graphical representationmethod based on the k-NN algorithm in order of the SNPs in a chromosome designed for a multi-parental population. Four-way cross anddouble-backcrossed tomato BC1F1 (230 lines) and BC2F1 (96 lines) populations were genotyped by GBS. The genotype of samples of theBC1F1 and BC2F1 populations was determined based on the parental haplotype. Thus, the method of visualizing the genotype of offspringindividuals, generated via crosses of multiple parents, not only improves estimation of the recovery rate but also facilitates easier selectionin breeding programs.
Abstract
Marker-assisted backcrossing is a powerful method for developing new cultivars. To develop genomic-wide markers, genotyping-by-sequencing(GBS) can be an efficient method. However, unrefined low-quality markers and missing data between markers can contribute to hamperingthe marker selection process, particularly in multi-way crosses. In this study, we aimed to calculate the recovery rate of offspring individualsand minimize errors that occur among a large number of markers. Initially, missing data were imputed by comparing samples using the k-nearestneighbor (k-NN) algorithm. Thereafter, low-quality single-nucleotide polymorphisms (SNPs) were corrected by applying the graphical representationmethod based on the k-NN algorithm in order of the SNPs in a chromosome designed for a multi-parental population. Four-way cross anddouble-backcrossed tomato BC1F1 (230 lines) and BC2F1 (96 lines) populations were genotyped by GBS. The genotype of samples of theBC1F1 and BC2F1 populations was determined based on the parental haplotype. Thus, the method of visualizing the genotype of offspringindividuals, generated via crosses of multiple parents, not only improves estimation of the recovery rate but also facilitates easier selectionin breeding programs.
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