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QTL-seq and marker development for resistance to head splitting in cabbage

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Abstract

Head splitting is a major physiological disease in cabbage. The most effective approach for controlling head splitting is to deploy genetic resistance by breeding cabbage cultivars with stable resistance. However, the genetic mechanisms regulating head-splitting resistance in cabbage remain largely unknown. Here, we employed the whole-genome resequencing-based approach (QTL-seq) to discover genomic regions, candidate genes, and diagnostic markers for head-splitting resistance in an F2 segregation population derived from a cross between two inbred lines G274 (head-splitting susceptible) and G279 (head-splitting resistant). Single nucleotide polymorphism index (SNP-index) analysis indicated that one candidate genomic region spanning 5.6 Mb on chromosome 3 was responsible for head-splitting resistance. A candidate gene, Bol016058, was identified in this region, which is a homologue of proline-rich protein 4 (PRP4) and encodes a structural cell wall protein in Arabidopsis. This target gene was highly expressed in leaves, with four SNPs and one insertion-deletion (InDel) between G274 and G279. Moreover, a diagnostic InDel marker was successfully developed from this gene and validated on a set of breeding materials and could accelerate the selection of head-splitting resistant cabbage cultivars.

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Funding

This research was funded by the Agricultural Development Program through Science and Technology of Shanghai (2022-02-08-00-12-F01099), the Agricultural Field Project of Shanghai Science and Technology Innovation Action Plan (21N51900400), the China Agriculture Research System (Grant No. CARS-25).

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Authors and Affiliations

  1. Shanghai Key Lab of Protected Horticultural Technology, Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China

    **aowei Zhu, **ang Tai, Yunying Ren, Min Wang, **xiu Chen & Tianyue Bo

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  1. **aowei Zhu
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  2. **ang Tai
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  3. Yunying Ren
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  4. Min Wang
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  5. **xiu Chen
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  6. Tianyue Bo
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Contributions

XZ conceptualised and designed the experiments and wrote the manuscript; XZ, XT, YR, MW, JC, and TB performed the experiments and analysed the data.

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Correspondence to **xiu Chen or Tianyue Bo.

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Online resource 1

Candidate genes based on functional annotation of the SNPs with a minimum read depth of 10, and an SNP-index near 1 (≥ 0.7) and 0 (≤ 0.3) in R-bulk and S-bulk, respectively. Online resource 2 Genomic DNA sequences alignment of the Bol016058 in G274 and G279. Online resource 3 Genotypes of the diagnostic marker in inbred lines with different resistances to head splitting.Online resource 4 Primers used in this study (RAR 45 kb)

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Zhu, X., Tai, X., Ren, Y. et al. QTL-seq and marker development for resistance to head splitting in cabbage. Euphytica 218, 41 (2022). https://doi.org/10.1007/s10681-022-02982-5

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