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

Abstract

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.

Exploring the genetic and phenotypic diversity within and between onion (Allium cepa L.) ecotypes in Morocco

“…Several molecular markers like ISSR, RAPD, and SSR have been used to study the genetic diversity in the Allium genus and also to characterize the genetic relationship between the species [16,26,27]. In more recent years, different molecular markers have been introduced to characterize onion populations, like SNP, RAPD, AFPL, ISSR, and SSR [26][27][28][29][30][31]. into the population structure.…”

Conservation and Global Distribution of Onion (Allium cepa L.) Germplasm for Agricultural Sustainability

“…The worldwide genepool of onion is estimated to be over 20,000, and this can be subdivided into three distinct groups: common group, aggregatum group, and ever-ready group [ 61 ]. Members of the common onion group comprise open-pollinated traditional and modern cultivars, hybrids, and local landraces under cultivation across the globe [ 62 ]. Thus, there is a wide diversity within bulbous or common onion groups and much variation across different countries [ 10 , 63 ].…”