Informativeness of single nucleotide polymorphisms and relationships among onion populations from important world production regions

Authors: Havey, Michael; GHAVAMI, FARHAD - Eurofins Scientific, Inc

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/21/2017
Publication Date: 1/5/2018
Citation: Havey, M.J., Ghavami, F. 2018. Informativeness of single nucleotide polymorphisms and relationships among onion populations from important world production regions. Journal of the American Society for Horticultural Science. 143(1):34-44. https://doi.org/10.21273/JASHS04277-17.
DOI: https://doi.org/10.21273/JASHS04277-17

Interpretive Summary: Single nucleotide polymorphisms (SNPs) were scored using a high-density array and DNAs from individual plants from important onion populations from major production regions world-wide and from the likely progenitor of onion, Allium vavilovii. Genotypes at 1226 SNPs were used to estimate genetic relationships among these populations and revealed close associations among onions grown in Europe and those in North and South America and Eastern Asia, supporting paths of introduction from Europe to the Americas and Asia. A population grown on the Indian sub-continent was divergent from onions of European origins. Frequencies of SNPs among and within populations were used as a measure of informativeness. A set of 199 commonly polymorphic SNPs distributed across the eight chromosomes of onion were identified. This research will be useful for onion breeders and seed companies for estimation of relatedness among onion populations, mapping of important traits, fingerprinting of inbred lines and hybrids, and quality control of seed lots.

Technical Abstract: Single nucleotide polymorphisms (SNPs) were genotyped using a high-density array and DNAs from individual plants from important onion populations from major production regions world-wide and the likely progenitor of onion, Allium vavilovii. Genotypes at 1226 SNPs were used to estimate genetic relationships among these populations and revealed close associations among onions grown in Europe and those in North and South America and Eastern Asia, supporting paths of introduction from Europe to the Americas and Asia. Nasik Red is a population grown on the Indian sub-continent and was divergent from onions of European origins. Frequencies of SNPs among and within populations were used as a measure of informativeness. A set of 199 commonly polymorphic SNPs distributed across the eight chromosomes of onion were identified, which will be useful for estimation of relatedness among a broader collection of onion populations, mapping of important phenotypes, fingerprinting of inbred lines and hybrids, and quality control of seed lots.