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High-throughput genotyping in onion reveals structure of genetic diversity and informative SNPs useful for molecular breeding

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Abstract

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.

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Acknowledgments

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).”

Funding

This study was funded by Italian Ministry of Agriculture.

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Authors and Affiliations

  1. Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy

    Clizia Villano, Salvatore Esposito, Francesca Carucci, Luigi Frusciante, Domenico Carputo & Riccardo Aversano

  2. Plants for Human Health Institute, Department of Horticultural Sciences, North Carolina State University, Kannapolis, NC, USA

    Massimo Iorizzo

Authors
  1. Clizia Villano
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  2. Salvatore Esposito
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  3. Francesca Carucci
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  4. Massimo Iorizzo
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  5. Luigi Frusciante
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  6. Domenico Carputo
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  7. Riccardo Aversano
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Correspondence to Riccardo Aversano.

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Supplementary Figure 1

The ΔK method result. (DOCX 30 kb)

Supplementary Figure 2

Genetic variation among populations of onion in the expected and observed groups. For each population, the expected heterozygosity (HE), observed heterozygosity (HO), and fixation index (F) are reported. (PNG 104 kb)

High Resolution Image (TIF 496 kb)

Supplementary Figure 3

Genetic variation among onion populations of two groups (expected and observed) calculated using a filtered set of markers. For each population, the expected heterozygosity (HE), observed heterozygosity (HO), and fixation index (F) are reported. (DOCX 112 kb)

Supplementary Table 1

List of the onion genotypes used in the present study. For each genotype, common name, species, production area, bulbing photoperiod (SD = short day; ID = intermediate day; LD = long day), bulb shape and bulb color are listed. (XLSX 14 kb)

Supplementary Table 2

List of SNP markers (Duangjit et al. 2013) used for the present study. For each marker, identification number, assigned function, sequence, position, alleles (X and Y), and linkage group (LG) are reported. (XLSX 141 kb)

Supplementary Table 3

SNP results obtained in 73 genotypes of onion species. (XLSX 210 kb)

Supplementary Table 4

Statistical analysis of 389 SNPs of 73 different genotypes of Allium spp. For each locus, the major allele frequency (MAF) and polymorphic information content (PIC) values are reported. (XLSX 25 kb)

Supplementary Table 5

List of SNP loci associated with bulbing photoperiod, bulb shape and bulb color. LG = linkage group. (DOC 77 kb)

Supplementary Table 6

List of SNP pairs in linkage disequilibrium and related coefficients. For each pair, the ID of the two co-inherited SNPs (named SNP_A and SNP_B), the linkage group location (LG), the measure of LD (r2), and the coefficient of LD (D′) are reported. (DOCX 19 kb)

Supplementary Table 7

List of SNP pairs in linkage disequilibrium and associated with a phenotypic traits (S = bulb shape; C = bulb color; P = bulbing photoperiod). (DOCX 13 kb)

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Villano, C., Esposito, S., Carucci, F. et al. High-throughput genotyping in onion reveals structure of genetic diversity and informative SNPs useful for molecular breeding. Mol Breeding 39, 5 (2019). https://doi.org/10.1007/s11032-018-0912-0

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