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Dissected Leaf 1 encodes an MYB transcription factor that controls leaf morphology in potato

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Abstract

Key message

The transcription factor StDL1 regulates dissected leaf formation in potato and the genotype frequency of recessive Stdl1/Stdl1, which results in non-dissected leaves, has increased in cultivated potatoes.

Abstract

Leaf morphology is a key trait of plants, influencing plant architecture, photosynthetic efficiency and yield. Potato (Solanum tuberosum L.), the third most important food crop worldwide, has a diverse leaf morphology. However, despite the recent identification of several genes regulating leaf formation in other plants, few genes involved in potato leaf development have been reported. In this study, we identified an R2R3 MYB transcription factor, Dissected Leaf 1 (StDL1), regulating dissected leaf formation in potato. A naturally occurring allele of this gene, Stdl1, confers non-dissected leaves in young seedlings. Knockout of StDL1 in a diploid potato changes the leaf morphology from dissected to non-dissected. Experiments in N. benthamiana and yeast show that StDL1 is a transcriptional activator. Notably, by calculating the genotype frequency of the Stdl1/Stdl1 in 373-potato accessions, we found that it increases significantly in cultivated potatoes. This work reveals the genetic basis of dissected leaf formation in potato and provides insights into plant leaf morphology.

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Data availability

The BSA-seq data are available at NCBI with BioProject accession number PRJNA877053 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA877053).

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Acknowledgements

We appreciate the advice from Dr. Sanwen Huang (Agricultural Genomics Institute at Shenzhen) on this work. The work was supported by China National Key Research and Development Program (2019YFE0120500 to C. Z.), Guangdong Major Project of Basic and Applied Basic Research (2021B0301030004), the Agricultural Science and Technology Innovation Program (CAAS‐ZDXT2018004), China Postdoctoral Science Foundation (2022M723462), the National Science Fund of Yunnan for Distinguished Young Scholars (202001AV070003) and Yunnan Fundamental Research Project (202001AV070003).

Funding

The work was supported by China National Key Research and Development Program (2019YFE0120500 to C. Z.), Guangdong Major Project of Basic and Applied Basic Research (2021B0301030004), the Agricultural Science and Technology Innovation Program (CAAS‐ZDXT2018004), China Postdoctoral Science Foundation (2022M723462), the National Science Fund of Yunnan for Distinguished Young Scholars (202001AV070003) and Yunnan Fundamental Research Project (202001AV070003).

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Author notes

  1. Dawei Li and Xiaoyue Lu have contributed equally to this work.

Authors and Affiliations

  1. Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China

    Dawei Li, Xiaoyue Lu, Duoduo Qian, Pei Wang, Dié Tang, Yang Zhong & Chunzhi Zhang

  2. State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China

    Duoduo Qian

  3. Shenzhen Research Institute of Henan University, Shenzhen, 518120, China

    Duoduo Qian

  4. Yunnan Key Laboratory of Potato Biology, The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650000, China

    Yi Shang & Guangtao Zhu

  5. Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China

    Han Guo

  6. School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China

    Zhen Wang

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  1. Dawei Li
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Contributions

CZ and GZ conceived and designed the project. DL and XL performed molecular experiments. DL conducted the bioinformatics analyses. ZW, HG, DQ and YZ assisted in molecular experiments. DT assisted in the bioinformatics analyses. PW contributed to the greenhouse work. YS coordinated the project. DL wrote the manuscript. CZ and DL revised the final manuscript.

Corresponding authors

Correspondence to Guangtao Zhu or Chunzhi Zhang.

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The authors declare no competing interests.

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Communicated by Herman J. van Eck.

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Supplementary Information

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122_2023_4430_MOESM1_ESM.jpg

Supplemental Fig. S1: Statistics of leaflet number of DL and EL plants at different leaf positions. NS: not significant, *P < 0.05, **P < 0.01, ***P < 0.001 (Student’s t test). n = 5.

122_2023_4430_MOESM2_ESM.jpg

Supplemental Fig. S2: Knockout of C gene and overexpression of StDL1 in tomato. a and b, Phenotypes of tomato cultivar "Ailsa Craig" (wild type) and three SlDL1 knockout lines. c, The mutant genotypes of the three knockout lines. "-" means deletion. The position of insertion is indicated using a blue arrow. d and e, Phenotypes of tomato seedlings (d) and leaves (e) in TS-21 (wild type) and three StDL1 overexpression lines. f, Expression level of StDL1 in tomato young and mature leaves of TS-21 and three overexpression lines. n = 3

122_2023_4430_MOESM3_ESM.jpg

Supplemental Fig. S3: Arabidopsis wild type (left) and transgenic lines overexpressing StDL1 (right). The Arabidopsis COL-0 was used for transgenic experiment. No obvious changes in leaves are found between COL-0 and overexpression lines.

122_2023_4430_MOESM4_ESM.jpg

Supplemental Fig. S4: Subcellular localization of Stdl1. The nuclei were stained with DAPI. The empty vector was used as a negative control. Scale bar = 20 µm.

122_2023_4430_MOESM5_ESM.jpg

Supplemental Fig. S5: Sequence alignment of RAX family proteins in Arabidopsis, tomato and potato. The red box indicates the MYB domain. Variations between StDL1 and Stdl1 are marked with red arrows. The sequence alignment was conducted using Jalview software. The different colors indicate the amino acid conservation based on Clustal X color scheme.

Supplemental Table 1: Potential candidate genes within the mapping interval. (XLSX 10 KB)

Supplemental Table 2: List of primers used in this study. (XLSX 10 KB)

Supplemental Table 3: The 10 polymorphic mutation sites of StDL1 in 373-potato accessions. (XLSX 33 KB)

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Li, D., Lu, X., Qian, D. et al. Dissected Leaf 1 encodes an MYB transcription factor that controls leaf morphology in potato. Theor Appl Genet 136, 183 (2023). https://doi.org/10.1007/s00122-023-04430-x

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