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Candidate gene analysis of watermelon stripe pattern locus ClSP ongoing recombination suppression

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Abstract

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Using two segregating population, watermelon stripe pattern underlying gene ClSP was delimited to a 611.78 Kb region, consisting of four discrete haploblocks and ongoing recombination suppression.

Abstract

Stripe pattern is an important commodity trait in watermelon, displaying diverse types. In this study, two segregating populations were generated for genetic mapping the single dominant locus ClSP, which was finally delimited to a 611.78 Kb interval with suppression of recombination. According to polymorphism sites detected among genotypes, four discrete haploblocks were characterized in this target region. Based on reference genomes, 81 predicted genes were annotated in the ClSP interval, including seven transcription factors namely as candidate No1-No7. Meanwhile, the ortholog gene of cucumber ist responsible for the irregular stripes was considered as candidate No8. Strikingly, gene structures of No1-No5 completely varied from their reference descriptions and subsequently re-annotated. For instance, the original adjacent distribution candidates No2 and No3 were re-annotated as No2_3, while No4 and No5 were integrated as No4_5. Sequence analysis demonstrated the third polymorphism in CDS of re-annotated No4_5 resulting in truncated proteins in non-stripe plants. Furthermore, only No4_5 was down-regulated in light green stripes relative to dark green stripes. Transcriptome analysis identified 356 DEGs between dark green striped and light green striped peels, with genes involved in photosynthesis and chloroplast development down-regulated in light green stripes but calcium ion binding related genes up-regulated. Additionally, 38 DEGs were annotated as transcription factors, with the majority up-regulated in light green stripes, such as ERFs and WRKYs. This study not only contributes to a better understanding of the molecular mechanisms underlying watermelon stripe development, but also provides new insights into the genomic structure of ClSP locus and valuable candidates.

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Acknowledgements

This work was supported by funding from the National Natural Science Foundation of China [Grant No. 31701939] and the National Natural Science Foundation of Shaanxi Province, China [No. 2019JQ-324].

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Authors and Affiliations

  1. State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A and F University, Yangling, 712100, Shaanxi, China

    Zhen Yue, Rongxue Ma, Denghu Cheng, Xing Yan, Yaping He, Chunxia Wang, Xiaona Pan, Lijuan Yin, Xian Zhang & Chunhua Wei

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  1. Zhen Yue
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  2. Rongxue Ma
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  3. Denghu Cheng
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  4. Xing Yan
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  5. Yaping He
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  6. Chunxia Wang
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  7. Xiaona Pan
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  8. Lijuan Yin
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  9. Xian Zhang
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  10. Chunhua Wei
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Contributions

CW designed the experiment and wrote the manuscript, with help from XZ. ZY performed the major experiments and analyzed the data. RM, DC, and XY participated in DNA extraction and phenotypic record. YH and CW contributed to gene cloning and sequence analysis. XP and LY participated in RNA extraction. All authors have read and approved the final manuscript.

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Correspondence to Chunhua Wei.

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The authors declare that there is no conflict of interest.

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Communicated by Sanwen Huang.

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Yue, Z., Ma, R., Cheng, D. et al. Candidate gene analysis of watermelon stripe pattern locus ClSP ongoing recombination suppression. Theor Appl Genet 134, 3263–3277 (2021). https://doi.org/10.1007/s00122-021-03891-2

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