Abstract
Single nucleotide polymorphisms (SNPs) play important roles as molecular markers in plant genomics and breeding studies. Although onion (Allium cepa L.) is an important crop globally, relatively few molecular marker resources have been reported due to its large genome and high heterozygosity. Genotyping-by-sequencing (GBS) offers a greater degree of complexity reduction followed by concurrent SNP discovery and genotyping for species with complex genomes. In this study, GBS was employed for SNP mining in onion, which currently lacks a reference genome. A segregating F2 population, derived from a cross between ‘NW-001’ and ‘NW-002,’ as well as multiple parental lines were used for GBS analysis. A total of 56.15 Gbp of raw sequence data were generated and 1,851,428 SNPs were identified from the de novo assembled contigs. Stringent filtering resulted in 10,091 high-fidelity SNP markers. Robust SNPs that satisfied the segregation ratio criteria and with even distribution in the mapping population were used to construct an onion genetic map. The final map contained eight linkage groups and spanned a genetic length of 1,383 centiMorgans (cM), with an average marker interval of 8.08 cM. These robust SNPs were further analyzed using the high-throughput Fluidigm platform for marker validation. This is the first study in onion to develop genome-wide SNPs using GBS. The resulting SNP markers and developed linkage map will be valuable tools for genetic mapping of important agronomic traits and marker-assisted selection in onion breeding programs.
Highlights
Onion (Allium cepa L.) is one of the most widely cultivated vegetable crops grown in tropical, temperate and boreal regions around the world
The high frequency of Single nucleotide polymorphisms (SNPs) retained after the initial quality check in our study indicates the importance of generating genome-wide SNPs, TABLE 4 | Summary of the onion genetic map constructed using SNP markers
Assembled filtering procedures and quality checks resulted in high fidelity SNPs which were subsequently applied for genetic map construction and Fluidigm validation
Summary
Onion (Allium cepa L.) is one of the most widely cultivated vegetable crops grown in tropical, temperate and boreal regions around the world. With the advent of nextgeneration sequencing (NGS) technologies, SNP markers were generated from the expressed regions of the genome of an inbred onion population and used to construct a genetic map (Duangjit et al, 2013). A study used an interspecific F1 hybrid and a set of onion cultivars to develop transcriptomederived SNP markers and a genetic map, which were used to identify quantitative trait locus for resistance to Botrytis leaf blight (Scholten et al, 2016). Large numbers of new molecular markers are still required to construct saturated consensus genetic linkage maps for onion and to significantly improve marker-assisted selection for both research and breeding objectives
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