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Genetic analyses of bolting in bulb onion (Allium cepa L.)

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Abstract

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We present the first evidence for a QTL conditioning an adaptive trait in bulb onion, and the first linkage and population genetics analyses of candidate genes involved in photoperiod and vernalization physiology.

Abstract

Economic production of bulb onion (Allium cepa L.) requires adaptation to photoperiod and temperature such that a bulb is formed in the first year and a flowering umbel in the second. ‘Bolting’, or premature flowering before bulb maturation, is an undesirable trait strongly selected against by breeders during adaptation of germplasm. To identify genome regions associated with adaptive traits we conducted linkage mapping and population genetic analyses of candidate genes, and QTL analysis of bolting using a low-density linkage map. We performed tagged amplicon sequencing of ten candidate genes, including the FT-like gene family, in eight diverse populations to identify polymorphisms and seek evidence of differentiation. Low nucleotide diversity and negative estimates of Tajima’s D were observed for most genes, consistent with purifying selection. Significant population differentiation was observed only in AcFT2 and AcSOC1. Selective genotyping in a large ‘Nasik Red × CUDH2150’ F2 family revealed genome regions on chromosomes 1, 3 and 6 associated (LOD > 3) with bolting. Validation genotyping of two F2 families grown in two environments confirmed that a QTL on chromosome 1, which we designate AcBlt1, consistently conditions bolting susceptibility in this cross. The chromosome 3 region, which coincides with a functionally characterised acid invertase, was not associated with bolting in other environments, but showed significant association with bulb sucrose content in this and other mapping pedigrees. These putative QTL and candidate genes were placed on the onion map, enabling future comparative studies of adaptive traits.

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Abbreviations

SD:

Short-day

LD:

Long-day

DH:

Doubled-haploid

CAPS:

Cleaved amplified polymorphic sequence

AMAL:

Alien monosomic addition line

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Acknowledgments

This research was funded by the NZ Ministry for Business, Innovation and Employment. We gratefully acknowledge provision of germplasm by the EU Allium Genebank (University Of Warwick) and Cornell University Department of Plant Breeding and of monosomic alien addition line DNA samples by Masayoshi Shigyo (Yamaguchi University, Japan). Field trialling support was provided by Enza-Zaden NZ Ltd, Allium Solutions Ltd., Seminis NZ Ltd and FruitFed Supplies. We thank Zygem Corp (Hamilton, New Zealand) for provision of reagents.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. New Zealand Institute for Plant and Food Research, Private Bag, 4704, Christchurch, New Zealand

    Samantha Baldwin, Roopashree Revanna, Meeghan Pither-Joyce, Martin Shaw, Kathryn Wright, Susan Thomson, Leire Moya & John McCallum

  2. Biochemistry Department, University of Otago, Dunedin, New Zealand

    Robyn Lee & Richard Macknight

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  1. Samantha Baldwin
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  2. Roopashree Revanna
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  3. Meeghan Pither-Joyce
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  4. Martin Shaw
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  10. John McCallum
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Correspondence to John McCallum.

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Communicated by A. E. Melchinger.

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Baldwin, S., Revanna, R., Pither-Joyce, M. et al. Genetic analyses of bolting in bulb onion (Allium cepa L.). Theor Appl Genet 127, 535–547 (2014). https://doi.org/10.1007/s00122-013-2232-4

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  • DOI: https://doi.org/10.1007/s00122-013-2232-4

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