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Agronomy 2018, 8(9), 179;

Varietal Identification of Open-Pollinated Onion Cultivars Using a Nanofluidic Array of Single Nucleotide Polymorphism (SNP) Markers

Center for Horticultural Seed Development of GSP, Jeonnam, Suncheon 57922, Korea
Department of Horticulture, Sunchon National University, Suncheon 57922, Korea
Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
These authors contributed equally to this work.
Author to whom correspondence should be addressed.
Received: 15 August 2018 / Revised: 5 September 2018 / Accepted: 7 September 2018 / Published: 10 September 2018
(This article belongs to the Section Crop Breeding and Genetics)
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Onions (Allium cepa L.) are a medicinally and economically important vegetable species rich in sulphur compounds, polyphenols, and antioxidants. In Korea, most of the onion cultivars are of the open-pollinated, heterozygous, short duration, and early spring type, which are generally harvested in April. Precise varietal identification is crucially important to warrant the authenticity of supreme onion genotypes, which aid in affirming the genetic identity of breeding materials at both the breeders and farmers levels. A set of markers identified from the double-digest restriction-site associated DNA sequencing (ddRAD-seq) database of Allium cepa L. and involving single nucleotide polymorphisms (SNPs) were deployed for genotyping deoxyribonucleic acid (DNA) samples extracted from seven genetically diverse onion cultivars collected in Korea and Japan. The validation process led us to designating 43 SNPs out of 48 that unequivocally identified all seven genotypes with high statistical validity (p < 0.001). Phylogenetic relationships and varietal identity among the cultivars were ascertained by Bayesian clustering and ordination analyses. Two genotypes, Singsingball and Taegeukhwang of Korean origin, showed a greater genetic distance from the five other onion cultivars. The SNP markers deployed in this study effectively authenticated the DNA fingerprints of the early spring onion cultivars utilizing a high-throughput genotyping protocol. The method exploited in this study provides an efficient pathway of verifying genetic identity of onion genotypes for their quality control. The markers developed are highly useful in the management and conservation of elite onion breeding materials at the farmers’ level. View Full-Text
Keywords: onion; nanofluidic array; varietal identification; SNP markers onion; nanofluidic array; varietal identification; SNP markers

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Lee, J.-H.; Robin, A.H.K.; Natarajan, S.; Jung, H.-J.; Nou, I.-S. Varietal Identification of Open-Pollinated Onion Cultivars Using a Nanofluidic Array of Single Nucleotide Polymorphism (SNP) Markers. Agronomy 2018, 8, 179.

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