ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2022
Development of a genome-wide marker design workflow for onions and its application in target amplicon sequencing-based genotyping.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Recent progress in DNA marker-assisted selection for vegetable breeding in Japan.Breeding science · 2026Article
- Genomic insights into pigeon breeding: GWAS for economic traits and the development of a high-throughput liquid phase array chip.Poultry science · 2025Article
- Development and application of a 1K functional liquid chip for lactation performance in Bactrian camels.Frontiers in veterinary science · 2024Article
- Development and Validation of a 54K Genome-Wide Liquid SNP Chip Panel by Target Sequencing for Dairy Goat.Genes · 2023Article
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10 authors.
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Abstract
Onions are one of the most widely cultivated vegetables worldwide; however, the development and utilization of molecular markers have been limited because of the large genome of this plant. We present a genome-wide marker design workflow for onions and its application in a high-throughput genotyping method based on target amplicon sequencing. The efficiency of the method was evaluated by genotyping of F2 populations. In the marker design workflow, unigene and genomic sequence data sets were constructed, and polymorphisms between parental lines were detected through transcriptome sequence analysis. The positions of polymorphisms detected in the unigenes were mapped onto the genome sequence, and primer sets were designed. In total, 480 markers covering the whole genome were selected. By genotyping an F2 population, 329 polymorphic sites were obtained from the estimated positions or the flanking sequences. However, missing or sparse marker regions were observed in the resulting genetic linkage map. We modified the markers to cover these regions by genotyping the other F2 populations. The grouping and order of markers on the linkages were similar across the genetic maps. Our marker design workflow and target amplicon sequencing are useful for genome-wide genotyping of onions owing to their reliability, cost effectiveness, and flexibility.
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