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Fine mapping of major QTL qshgd1 for spontaneous haploid genome doubling in maize (Zea mays L.)

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A large-effect QTL was fine mapped, which revealed 79 gene models, with 10 promising candidate genes, along with a novel inversion.


In commercial maize breeding, doubled haploid (DH) technology is arguably the most efficient resource for rapidly developing novel, completely homozygous lines. However, the DH strategy, using in vivo haploid induction, currently requires the use of mutagenic agents which can be not only hazardous, but laborious. This study focuses on an alternative approach to develop DH lines—spontaneous haploid genome duplication (SHGD) via naturally restored haploid male fertility (HMF). Inbred lines A427 and Wf9, the former with high HMF and the latter with low HMF, were selected to fine-map a large-effect QTL associated with SHGD—qshgd1. SHGD alleles were derived from A427, with novel haploid recombinant groups having varying levels of the A427 chromosomal region recovered. The chromosomal region of interest is composed of 45 megabases (Mb) of genetic information on chromosome 5. Significant differences between haploid recombinant groups for HMF were identified, signaling the possibility of mapping the QTL more closely. Due to suppression of recombination from the proximity of the centromere, and a newly discovered inversion region, the associated QTL was only confined to a 25 Mb region, within which only a single recombinant was observed among ca. 9,000 BC1 individuals. Nevertheless, 79 gene models were identified within this 25 Mb region. Additionally, 10 promising candidate genes, based on RNA-seq data, are described for future evaluation, while the narrowed down genome region is accessible for straightforward introgression into elite germplasm by BC methods.

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The datasets generated and the figures/tables created with R software have been made available in the following public Github repository:


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Funding for this work was provided by USDA’s National Institute of Food and Agriculture (NIFA) Project, No. IOW04314, IOW01018, and IOW05510; NIFA award 2018–51181-28419; and the National Science Foundation under Grant No. DGE-1545453. Funding for this work was also provided by the R.F. Baker Center for Plant Breeding, Plant Sciences Institute, and K.J. Frey Chair in Agronomy at Iowa State University.

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Project conceptualization: L.G., M.K.M., U.K.F., and T.H.L.; Data collection: T.H.L, L.G., and M.K.M.; Data analysis: T.L.F.; Data interpretation: T.L.F., S.P., S.D., Y.C., A.S.S, M.B.H.; Manuscript writing: T.L.F and T.H.L with input from the other authors.

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Correspondence to Tyler L. Foster.

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The authors have not disclosed any competing interests. The authors have no relevant financial or non-financial interests to disclose.

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Communicated by Annaliese S Mason.

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Foster, T.L., Kloiber-Maitz, M., Gilles, L. et al. Fine mapping of major QTL qshgd1 for spontaneous haploid genome doubling in maize (Zea mays L.). Theor Appl Genet 137, 117 (2024).

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