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QTL for horticulturally important traits associated with pleiotropic andromonoecy and carpel number loci, and a paracentric inversion in cucumber

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Abstract

The legendary cucumber inbred line WI2757 possesses a rare combination of resistances against nine pathogens, which is an important germplasm for cucumber breeding. However, WI2757 flowers late and does not perform well under field conditions. The genetic basis for horticulturally important traits other than disease resistances in WI2757 is largely unknown. In this study, we conducted QTL mapping using F2 and recombinant inbred line (RIL) populations from the WI2757 × True Lemon cross that were segregating for multiple traits. Phenotypic data were collected in replicated field trials across multiple years for seven traits including fruit carpel number (CN) and sex expression. A high-density SNP-based genetic map was developed with genotyping by sequencing of the RIL population, which revealed a region on chromosome 1 with strong recombination suppression. The reduced recombination in this region was due to a ~ 10-Mbp paracentric inversion in WI2757 that was confirmed with additional segregation and cytological (FISH) analyses. Thirty-six QTL were detected for flowering time, fruit length (FL), fruit diameter (FD), fruit shape (LD), fruit number (FN), CN, and powdery mildew resistance. Five moderate- or major-effect QTL for FL, FD, LD, and FN inside the inversion are likely the pleiotropic effects of the andromonoecy (m), or the cn locus. The major-effect flowering time QTL ft1.1 was also mapped inside the inversion, which seems to be different from the previously assigned delayed flowering in WI2757. Implications of these findings on the use of WI2757 in cucumber breeding are discussed.

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Acknowledgements

This research was supported by the Agriculture and Food Research Initiative Competitive Grants under award Numbers 2015-51181-24285 and 2017-67013-26195 from the US Department of Agriculture National Institute of Food and Agriculture (to Y. Weng). USDA is an equal opportunity provider and employer.

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Authors and Affiliations

  1. College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China

    Yupeng Pan & Yuhong Li

  2. Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA

    Yupeng Pan, Changlong Wen, Yuhui Wang, Yuhong Li, Sen Li, Xiaomao Cheng & Yiqun Weng

  3. Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China

    Changlong Wen

  4. Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China

    Yonghua Han

  5. Horticulture College, Shanxi Agricultural University, Taigu, 030801, China

    Sen Li

  6. USDA-ARS Vegetable Crops Research Unit, 1575 Linden Dr., Madison, WI, 53706, USA

    Yiqun Weng

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  1. Yupeng Pan
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  2. Changlong Wen
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Contributions

YP conducted majority of the reported research. CW genotyped the RIL population with SLAF-Seq. YHW conducted GBS data analysis and linkage analysis with SNP markers. YH performed FISH analysis. XC, SL, and YL participated in phenotypic data collection in different experiments. YW conceived and supervised the research and wrote the manuscript with YP.

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Correspondence to Yiqun Weng.

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Pan, Y., Wen, C., Han, Y. et al. QTL for horticulturally important traits associated with pleiotropic andromonoecy and carpel number loci, and a paracentric inversion in cucumber. Theor Appl Genet 133, 2271–2290 (2020). https://doi.org/10.1007/s00122-020-03596-y

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