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Architecture design of cucurbit crops for enhanced productivity by a natural allele

Nature Plants volume 8, pages 1394–1407 (2022)Cite this article

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Abstract

Increasing production efficiency is a top priority in agriculture. Optimal plant architecture is the biological basis of dense planting, high crop yield and labour cost savings, and is thus critical for improving agricultural productivity. In cucurbit crops, most species have elongated internodes, but the path to architecture improvement is still not clear. Here we identified a pumpkin accession with a dominant bushy trait, and found that the associated Bush locus harbours a cucurbit-conserved cis-regulatory element in the 5’ untranslated region of a transcription factor gene YABBY1. In cucurbit crops, various B-region deletions enhance the translation of YABBY1, with consequent proportional suppression of stem length in a dose-dependent manner. Depending on different cultivation patterns, the precise deployment of these alleles has significant effects on yield improvement or labour cost saving. Our findings demonstrate that the engineering of the YABBY1 B-region is an efficient strategy to customize plant architecture in cucurbit crops.

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Fig. 1: Characterization of the SXHD82 phenotype.
Fig. 2: Identification of the Bu locus by map-based cloning.
Fig. 3: CRISPR/Cas9 targeting of the CmoYABBY1 5’ UTR B-region generated a range of reduced stem lengths in transgenic pumpkin.
Fig. 4: CRISPR/Cas9-engineered deletion in the YABBY1 5’ UTR resulted in shortened stem length in cucumber and watermelon.
Fig. 5: Editing the YABBY1 5’ UTR enables higher yield and labour cost saving in cucurbit crops.
Fig. 6: Model for ideal plant architecture in cucurbit crops.

Data availability

Relevant data can be found in the Supplementary Tables. Source data, including raw data for all quantifications, are provided with this paper.

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Acknowledgements

We thank H. Chen (Hunan Vegetable Research Institute, Hunan Academy of Agricultural Sciences) for providing cucumber seeds used in transformation; J. Wang (Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences) for providing information on watermelon and melon accessions; and X. Zhang (Xinjiang Academy of Agricultural Sciences) for providing melon seeds. This work was supported by the National Natural Science Foundation of China (31701914 to S.W.), the National Key R&D Program of China (2019YFA0906200), the National Natural Science Foundation of China (31922076 to X.Y.), the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-ASTIP) and the Science and Technology Innovation Team of Shaanxi (2021TD-32).

Author information

Author notes

  1. These authors contributed equally: Shenhao Wang, Kun Wang, Zheng Li.

Authors and Affiliations

  1. Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China

    Shenhao Wang, Kun Wang, Bowen Wang, Tongxu Xin, Haojie Tian & Xueyong Yang

  2. College of Horticulture, Northwest A&F University, Yangling, China

    Shenhao Wang, Zheng Li, Yangyang Li & Jiao He

  3. Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China

    Hongbo Li & Sanwen Huang

  4. Beijing Vegetable Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China

    Jiaxing Tian, Guoyu Zhang & Haizhen Li

Authors
  1. Shenhao Wang
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Contributions

S.W., X.Y. and S.H. designed the research; K.W., Y.L., J.H., T.X. and H.T. performed genetic transformation; Hongbo Li and S.W. designed the markers; S.W., Y.L., B.W. and K.W. performed vectors construction and most experiments. J.T., G.Z. and Haizhen Li helped to collect seeds; S.W., X.Y., Z.L. and Haizhen Li performed data analysis; S.W. and X.Y. wrote the paper, which was approved by all authors.

Corresponding author

Correspondence to Xueyong Yang.

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Nature Plants thanks Qiang Xu and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Stem length of Daluo and the bushy SXHD82 accession at 10-week-old stage.

Data are presented as mean ± standard deviation (s.d.) (n = 10 plants). Exact P values are shown (two-tailed, two sample Student’s t-test).

Source data

Extended Data Fig. 2 The weight of a single fruit from Daluo and SXHD82 two weeks after pollination.

Data are presented as mean ± SD (n = 12 fruits). Exact P values are shown (two-tailed, two sample Student’s t-test).

Source data

Extended Data Fig. 3 CmoCh15G012090 belongs to YABBY transcriptional factor family.

CmoCh15G012090 encodes a protein with a zinc finger-like domain in the N terminus and a YABBY domain in the C terminus.

Extended Data Fig. 4 Quantification of GUS activity of leaves from CmoYABBY1Pro-WT5’ UTR:GUS and CmoYABBY1Pro-Bu5’ UTR:GUS transgenic pumpkin plants.

Data are presented as mean ± SD (n = 4 plants). Exact P values are shown (two-tailed, two sample Student’s t-test).

Source data

Extended Data Fig. 5 The specificity of CmoYABBY1 polyclonal antibodies was validated by Western blot analysis.

a, The specific short peptide is selected to design polyclonal antibodies for CmoYABBY1. There are two YABBY1 genes in pumpkin, and CmoCh15G012090 is designated as CmoYABBY1 while CmoCh02G015970 is designated as CmoYABBY1b. The specific short peptide with red underline is selected to design polyclonal antibodies for CmoYABBY1. b, The pCAMBIA 1300-CmoYABBY1-5×myc, 1300-CmoYABBY1b-5×myc, and the corresponding empty vector were transiently expressed in leaves of tobacco (N. benthamiana). Total protein extracted was performed for immunoblotting using the anti-CmoYABBY1 and antic-Myc antibodies. Experiments were repeated independently three times (b).

Source data

Extended Data Fig. 6 The protein expression level of CmoYABBY1 detected at different developmental periods of leaves in wildtype pumpkin.

a, The leaves of the three developmental periods from the pumpkin Daluo. Bar = 10 cm. b, The protein expression level of CmoYABBY1 was detected at different developmental periods of leaves in wildtype pumpkin Daluo. Experiments were repeated independently three times (b).

Source data

Extended Data Fig. 7 Alignments of YABBY1 5’UTR sequences from species mentioned in Fig.4 (a).

The B-region sequences in the red box are conserved in Cucurbitaceae plants.

Extended Data Fig. 8 Comparison of yield per plant for edited pumpkin.

a, Comparison of yield per plant for WT and edited pumpkin (CmoM-1, CmoM-2, CmoM-3 and CmoM-4) under ample cultivation space conditions. Data are presented as mean ± SD (n = 8 plants). Different letters indicate significant differences (P < 0.05, one-way ANOVA and Tukey’s test). b, The fruits of WT and edited pumpkin (CmoM-1, CmoM-2, CmoM-3 and CmoM-4) under ample cultivation space conditions. Bars = 8 cm.

Source data

Extended Data Fig. 9 The editing mutant CmoM-4 enables labor cost saving in greenhouse.

a, WT pumpkin and edited CmoM-4 mutant planted in greenhouse in Beijing, China, in 2021. The CmoM-4 plants showed an upright bushy growth habit without hanging vines, while the WT plants with long and trailing vines require hanging vines and holding fruits. b, Comparison of labor cost time per 100 plants between WT and CmoM-4 in greenhouse (n = 3 biological replicates). Data are presented as mean ± SD. c, Comparison of fruit yield per 100 m2 between WT and CmoM-4 plants in greenhouse (n = 3 biological replicates). Data are presented as mean ± SD. Exact P values are shown (two-tailed, two sample Student’s t-test).

Source data

Extended Data Fig. 10 The predicted secondary structures of YABBY1 B-region in cucurbits.

The secondary structures of B-region of CmoYABBY1 (a), CsYABBY1 (b) and ClYABBY1 (c) were predicted by using UNAFold software. (d) Two mutant constructs were used to detect the effect of predicted stem-loop structure on protein translation by determining the LUC/REN activity and mRNA levels. The modified-1 mutant construct was designed to enhance the stem-loop, and the modified-2 mutant construct was designed to destroy the stem-loop. A wild type (WT) construct and those carrying modified-1 or modified-2 constructs were expressed in Cucurbita moschata cotyledons. The mean LUC/REN activity and mRNA levels conferred by each mutant construct were normalized to those of WT control (n = 8 biological replicates). Data are presented as mean ± SD. Different letters indicate significant differences (P < 0.05, one-way ANOVA and Tukey’s test). (e) The secondary structure of mutant B-region (modified-1) of CmoYABBY1 was predicted by UNAFold software.

Source data

Supplementary information

Supplementary Information

Supplementary Figs. 1–11.

Reporting Summary

Supplementary Tables 1–9

Supplementary Table 1 List of pumpkin accessions. Table 2 List of watermelon accessions. Table 3 List of melon accessions. Table 4 Stem length of pumpkin, watermelon and melon accessions. Table 5 Information regarding molecular markers used for fine mapping of Bu. Table 6 Primers used for qPCR. Table 7 Primers used for the construction of native pro::WT/Bu-5’UTR::GUS fusion genes. Table 8 Primers for vector construction of dual-luciferase assay. Table 9 Primers used for CRISPR-Cas9 vector construction in pumpkin, cucumber and watermelon.

Source data

Source Data Fig. 1

Statistical source data.

Source Data Fig. 2

Statistical source data.

Source Data Fig. 3

Statistical source data and unprocessed western blots.

Source Data Fig. 4

Statistical source data.

Source Data Fig. 5

Statistical source data.

Source Data Extended Data Fig. 1

Statistical source data.

Source Data Extended Data Fig. 2

Statistical source data.

Source Data Extended Data Fig. 4

Statistical source data.

Source Data Extended Data Fig. 5

Unprocessed western blots.

Source Data Extended Data Fig. 6

Unprocessed western blots.

Source Data Extended Data Fig. 8

Statistical source data.

Source Data Extended Data Fig. 9

Statistical source data.

Source Data Extended Data Fig. 10

Statistical source data.

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Wang, S., Wang, K., Li, Z. et al. Architecture design of cucurbit crops for enhanced productivity by a natural allele. Nat. Plants 8, 1394–1407 (2022). https://doi.org/10.1038/s41477-022-01297-6

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