High-throughput genotyping in onion reveals structure of genetic diversity and informative SNPs useful for molecular breeding
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Onion is an economically important crop cultivated worldwide since ancient times. Over the centuries, domestication and outbreeding have had a significant influence on its genetic pool, leading to a high degree of biodiversity. In this study, using kompetitive allele-specific PCR (KASP) genotyping technology, we explored the genetic variation of 73 onion accessions (including wild species, commercial, and local varieties) from different areas of the world. The SNP dataset inspection returned 375 polymorphic loci with a very low percentage of non-calling sites (0.03%). Eight-nine percent of the onions amplified all polymorphic loci and were considered for a population structure analysis. The ΔK method suggested four populations and enabled the identification of genepools, reflecting the geographical origin of the samples. Through statistical studies, our SNP set has proven to be successful, revealing population-specific alleles and potential candidates for use in future breeding programs. Notably, 74 loci were associated with phenotypic traits (bulbing photoperiod, bulb shape, or bulb color), and 3 loci were identified as putative targets of selection associated with onion improvement. Fifty-three pairs of SNPs were co-inherited, and among them, 17 were both trait-associated and in linkage disequilibrium. In conclusion, the data generated in this study allowed the survey of genetic variability in a heterogeneous and scantily examined germplasm, with repercussions on its exploitation in breeding programs.
KeywordsAllium sp. KASP SNPs Population structure
We are grateful to Mr. Raffaele Garramone for his technical assistance and to Marti OhMok Pottorff for manuscript editing. This research was carried out in the frame of the project “Definizione di firme geochimiche e molecolari per la tracciabilità e l’autenticazione di produzioni agrarie di pregio (FIRMA).”
This study was funded by Italian Ministry of Agriculture.
- Bölter B, Nada A, Fulgosi H, Soll J (2006) A chloroplastic inner envelope membrane protease is essential for plant development. FEBS Letters 580(3):789-794Google Scholar
- Jakse J, Martin W, McCallum J, Havey MJ (2005) Single nucleotide polymorphisms, indels, and simple sequence repeats for onion cultivar identification. J Am Soc Hortic Sci 130(6):912–917Google Scholar
- Khar A, Jakse J, Havey MJ (2008) Segregations for onion bulb colors reveal that red is controlled by at least three loci. J Am Soc Hortic Sci 133(1):42–47Google Scholar
- Kisha TJ, Cramer CS (2011) Determining redundancy of short-day onion accessions in a germplasm collection using microsatellite and targeted region amplified polymorphic markers. J Am Soc Hortic Sci 136(2):129–134Google Scholar
- McCallum J, Thomson S, Pither-Joyce M, Kenel F, Clarke A, Havey MJ (2008) Genetic diversity analysis and single–nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tag–simple sequence repeat markers. J Am Soc Hortic Sci 133:810–818Google Scholar
- Rashid MHA, Massiah AJ, Thomas B (2016) Genetic regulation of day length adaptation and bulb formation in onion (Allium cepa L). In: VII International Symposium on Edible Alliaceae, vol 1143, pp 7–14Google Scholar
- Saxena RK, Varma Penmetsa R, Upadhyaya HD, Kumar A, Carrasquilla-Garcia N, Schlueter JA, Farmer A, Whaley AM, Sarma BK, May GD, Cook DR, Varshney RK (2012) Large-scale development of cost-effective single-nucleotide polymorphism marker assays for genetic mapping in pigeonpea and comparative mapping in legumes. DNA Res 19(6):449–461CrossRefGoogle Scholar
- Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Molecular Breeding 33(1):1-14. https://doi.org/10.1007/s11032-013-9917-x
- Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt S (2004) mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. The Plant Journal 37(6):914-939. https://doi.org/10.1111/j.1365-313X.2004.02016.x