Skip to main content
SpringerLink
Log in

Chromosomal fragment deletion in APRR2-repeated locus modulates the dark stem color in Cucurbita pepo

  • Original Article
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Key message

Cp4.1LG15g03420 (CpDsc-1), which encodes a two-component response regulator-like protein (APRR2) in the nucleus, influences dark green stem formation in Cucurbita pepo by regulating the chlorophyll content.

Abstract

Stem color is an important agronomic trait in zucchini (Cucurbita pepo) for robust seeding and high yield. However, the gene controlling the stem color has not been characterized. In this study, we identified a single locus accounting for the dark green stem color of C. pepo (CpDsc-1). Genetic analysis of this trait in segregated populations derived from two parental lines (line 296 with dark green stems and line 274 with light green stems) revealed that stem color was controlled by a single dominant gene (dark green vs. light green). In bulked segregant analysis, CpDsc-1 was mapped to a 2.09-Mb interval on chromosome 15. This region was further narrowed to 65.2 kb using linkage analysis of the F2 population. Sequencing analysis revealed a 14 kb deletion between Cp4.1LG15g03420 and Cp4.1LG15g03360; these two genes both encoded a two-component response regulator-like protein (APRR2). The incomplete structures of the two APRR2 genes and abnormal chloroplasts in line 274 might be the main cause of the light green phenotype. Gene expression pattern analysis showed that only Cp4.1LG15g03420 was upregulated in line 296. Subcellular localization analysis indicated that Cp4.1LG15g03420 was a nuclear gene. Furthermore, a co-dominant marker, G4563 (93% accuracy rate), and a co-segregation marker, Fra3, were established in 111 diverse germplasms; both of these markers were tightly linked with the color trait. This study provided insights into chlorophyll regulation mechanisms and revealed the markers valuable for marker-assisted selection in future zucchini breeding.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Data availability

The data that supports the findings of this study are available in the article and supplementary materials.

References

  • Branham S, Vexler L, Meir A, Tzuri G, Frieman Z, Levi A, Wechter WP, Tadmor Y, Gur A (2017) Genetic mapping of a major codominant QTL associated with beta-carotene accumulation in watermelon. Mol Breed 37:146

    Google Scholar 

  • Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu XY, Ruden DM (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w(1118); iso-2; iso-3. Fly 6:80–92

    CAS  Google Scholar 

  • De Smet R, Van de Peer Y (2012) Redundancy and rewiring of genetic networks following genome-wide duplication events. Curr Opin Plant Biol 15:168–176

    Google Scholar 

  • Ding WQ, Wang YL, Qi C, Luo YS, Wang CJ, Xu WL, Qu SP (2021) Fine mapping identified the gibberellin 2-oxidase gene CpDw leading to a dwarf phenotype in squash (Cucurbita pepo L.). Plant Sci 306:110857

  • Esteras C, Nuez F, Pico B (2012) Genetic diversity studies in cucurbits using molecular tools. In: Behera TK (ed) Genetics Genomics & Breeding of Cucurbits, 1st edn. Science, New Hampshire, pp 140–198

    Google Scholar 

  • Farre EM, Liu T (2013) The PRR family of transcriptional regulators reflects the complexity and evolution of plant circadian clocks. Curr Opin Plant Biol 16:621–629

    CAS  Google Scholar 

  • Fekih R, Takagi H, Tamiru M, Abe A, Natsume S, Yaegashi H, Sharma S, Sharma S, Kanzaki H, Matsumura H, Saitoh H, Mitsuoka C, Utsushi H, Uemura A, Kanzaki E, Kosugi S, Yoshida K, Cano L, Kamoun S, Terauchi R (2013) MutMap plus: Genetic mapping and mutant identification without crossing in rice. PLoS ONE 8:e68529

    CAS  Google Scholar 

  • Fitter DW, Martin DJ, Copley MJ, Scotland RW, Langdale JA (2002) GLK gene pairs regulate chloroplast development in diverse plant species. Plant J 31:713–727

    CAS  Google Scholar 

  • Gao S, Gao J, Zhu XY, Song Y, Li ZP, Ren GD, Zhou X, Kuai BK (2016) ABF2, ABF3, and ABF4 Promote ABA-mediated chlorophyll degradation and leaf senescence by transcriptional activation of chlorophyll catabolic genes and senescence-associated genes in Arabidopsis. Mol Plant 9:1272–1285

    CAS  Google Scholar 

  • Guo J, Xu W, Hu Y, Huang J, Zhao Y, Zhang L, Huang CH, Ma H (2020) Phylotranscriptomics in Cucurbitaceae reveal multiple whole-genome duplications and key morphological and molecular innovations. Mol Plant 13:1117–1133

    CAS  Google Scholar 

  • Guo SG, Zhao SJ, Sun HH, Wang X, Wu S, Lin T, Ren Y, Gao L, Deng Y, Zhang J, Lu XQ, Zhang HY, Shang JL, Gong GY, Wen CL, He N, Tian SW, Li MY, Liu JP, Wang YP, Zhu YC, Jarrets R, Levi A, Zhang XP, Huang SW, Fei ZJ, Liu WG, Xu Y (2019) Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits. Nat Genet 51:1616-+

  • Hao N, Du YL, Li HY, Wang C, Wang C, Gong SY, Zhou SM, Wu T (2018) CsMYB36 is involved in the formation of yellow green peel in cucumber (Cucumis sativus L.). Theor Appl Genet 131:1659–1669

    CAS  Google Scholar 

  • Hill JT, Demarest BL, Bisgrove BW, Gorsi B, Su YC, Yost HJ (2013) MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq. Genome Res 23:687–697

    CAS  Google Scholar 

  • Hwang I, Kim Y, Han J, Nou IS (2016) Orange color is associated with CYC-B expression in tomato fleshy fruit. Mol Breed 36:42

    Google Scholar 

  • Inskeep WP, Bloom PR (1985) Extinction coefficients of chlorophyll a and b in n, n-dimethylformamide and 80 % acetone. Plant Physiol 77:483–485

    CAS  Google Scholar 

  • Jiang L, Fu YX, Tian XK, Ma YH, Chen FD, Wang GD (2022) The Anthurium APRR2-like gene promotes photosynthetic pigment accumulation in response to salt stress. Trop Plant Biol 15:12–21

    CAS  Google Scholar 

  • Jiao JQ, Liu HQ, Liu J, Cui MM, Xu J, Meng HW, Li YH, Chen SX, Cheng ZH (2017) Identification and functional characterization of APRR2 controlling green immature fruit color in cucumber (Cucumis sativus L.). Plant Growth Regul 83:233–243

    CAS  Google Scholar 

  • Kazminska K, Sobieszek K, Targonska-Karasek M, Korzeniewska A, Niemirowicz-Szczytt K, Bartoszewski G (2017) Genetic diversity assessment of a winter squash and pumpkin (Cucurbita maxima Duchesne) germplasm collection based on genomic Cucurbita-conserved SSR markers. Sci Hortic 219:37–44

    Google Scholar 

  • Kirkman LA, Deitsch KW (2012) Antigenic variation and the generation of diversity in malaria parasites. Cur Opin in Micro 15:456–462

    CAS  Google Scholar 

  • Li BB, Zhao SJ, Dou JL, Ali A, Gebremeskel H, Gao L, He N, Lu XQ, Liu WG (2019) Genetic mapping and development of molecular markers for a candidate gene locus controlling rind color in watermelon. Theor Appl Genet 132:2741–2753

    CAS  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760

    CAS  Google Scholar 

  • Li HR, Li YX, Deng H, Sun XC, Wang AQ, Tang XF, Gao YF, Zhang N, Wang LH, Yang SZ, Liu YS, Wang SH (2018) Tomato UV-B receptor SlUVR8 mediates plant acclimation to UV-B radiation and enhances fruit chloroplast development via regulating SlGLK2. Sci Rep 8:6097

    Google Scholar 

  • Liu C, Song GY, Zhou YH, Qu XF, Guo ZB, Liu ZW, Jiang DM, Yang DC (2015) OsPRR37 and Ghd7 are the major genes for general combining ability of DTH, PH and SPP in rice. Sci Rep 5:12803

    CAS  Google Scholar 

  • Lu ZH, Cao HH, Pan L, Niu L, Wei B, Cui GC, Wang LW, Yao JL, Zeng WF, Wang ZQ (2021) Two loss-of-function alleles of the glutathione S-transferase (GST) gene cause anthocyanin deficiency in flower and fruit skin of peach (Prunus persica). Plant J 107:1320–1331

    CAS  Google Scholar 

  • Makino S, Kiba T, Imamura A, Hanaki N, Nakamura A, Suzuki T, Taniguchi M, Ueguchi C, Sugiyama T, Mizuno T (2000) Genes encoding pseudo-response regulators: Insight into His-to-Asp phosphorelay and circadian rhythm in Arabidopsis thaliana. Plant Cell Physiol 41:791–803

    CAS  Google Scholar 

  • Metzker ML (2010) APPLICATIONS OF NEXT-GENERATION SEQUENCING Sequencing technologies - the next generation. Nat Rev Genet 11:31–46

    CAS  Google Scholar 

  • Montero-Pau J, Blanca J, Bombarely A, Ziarsolo P, Esteras C, Marti-Gomez C, Ferriol M, Gomez P, Jamilena M, Mueller L, Pico B, Canizares J (2018) De novo assembly of the zucchini genome reveals a whole-genome duplication associated with the origin of the Cucurbita genus. Plant Biotechnol J 16:1161–1171

    CAS  Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucl Acids Res 8(19):4321–4325

    CAS  Google Scholar 

  • Nadakuduti SS, Holdsworth WL, Klein CL, Barry CS (2014) KNOX genes influence a gradient of fruit chloroplast development through regulation of GOLDEN2-LIKE expression in tomato. Plant J 78:1022–1033

    CAS  Google Scholar 

  • Oren E, Tzuri G, Vexler L, Dafna A, Meir A, Faigenboim A, Kenigswald M, Portnoy V, Schaffer AA, Levi A, Buckler ES, Katzir N, Burger J, Tadmor Y, Gur A (2019) The multi-allelic APRR2 gene is associated with fruit pigment accumulation in melon and watermelon. J Exp Bot 70:3781–3794

    CAS  Google Scholar 

  • Pan Y, Bradley G, Pyke K, Ball G, Lu C, Fray R, Marshall A, Jayasuta S, Baxter C, van Wijk R, Boyden L, Cade R, Chapman NH, Fraser PD, Hodgman C, Seymour GB (2013) Network inference analysis identifies an APRR2-like gene linked to pigment accumulation in tomato and pepper fruits. Plant Physiol 161:1476–1485

    CAS  Google Scholar 

  • Paris HS (1996) Multiple Allelism at the D Locus in Squash. J Hered 87(5):391–395

    Google Scholar 

  • Paris HS, Hanan A, Baumkoler F (2013) Another gene affecting fruit and stem color in squash, Cucurbita pepo. Euphytica 191:99–107

    CAS  Google Scholar 

  • Pereira L, Ruggieri V, Perez S, Alexiou KG, Fernandez M, Jahrmann T, Pujol M, Garcia-Mas J (2018) QTL mapping of melon fruit quality traits using a high-density GBS-based genetic map. BMC Plant Biol 18:324

    CAS  Google Scholar 

  • Pomares-Viciana T, Del Rio-Celestino M, Roman B, Die J, Pico B, Gomez P (2019) First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.). BMC Plant Biol 19:61

  • Reumers J, De Rijk P, Zhao H, Liekens A, Smeets D, Cleary J, Van Loo P, Van Den Bossche M, Catthoor K, Sabbe B, Despierre E, Vergote I, Hilbush B, Lambrechts D, Del-Favero J (2012) Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing. Nat Biotechnolo 30:61-U103

    CAS  Google Scholar 

  • Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative C-T method. Nat Protoc 3:1101–1108

    CAS  Google Scholar 

  • Shi YZ, Zhang M, Shu Q, Ma W, Sun TZ, Xiang CG, Wang CL, Duan Y (2021) Genetic mapping and identification of the candidate gene for white seed coat in Cucurbita maxima. Int J Mol Sci 22:2972

    CAS  Google Scholar 

  • Sparkes IA, Runions J, Kearns A, Hawes C (2006) Rapid, transient expression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants. Nat Protoc 1:2019–2025

    CAS  Google Scholar 

  • Sun HH, Wu S, Zhang GY, Jiao C, Guo SG, Ren Y, Zhang J, Zhang HY, Gong GY, Jia ZC, Zhang F, Tian JX, Lucas WJ, Doyle JJ, Li HZ, Fei ZJ, Xu Y (2017) Karyotype stability and unbiased fractionation in the paleo-allotetraploid cucurbita genomes. Mol Plant 10:1293–1306

    CAS  Google Scholar 

  • Sun TH, Yuan H, Cao HB, Yazdani M, Tadmor Y, Li L (2018) Carotenoid metabolism in plants: The role of plastids. Mol Plant 11:58–74

    Google Scholar 

  • Tang HY, Dong X, Wang JK, Xia JH, Xie F, Zhang Y, Yao X, Xu YJ, Wan ZJ (2018) Fine mapping and candidate gene prediction for white immature fruit skin in cucumber (Cucumis sativus L.). Int J Mol Sci 19:1493

  • Urao T, Yakubov B, Yamaguchi-Shinozaki K, Shinozaki K (1998) Stress-responsive expression of genes for two-component response regulator-like proteins in Arabidopsis thaliana. FEBS Lett 427:175–178

    CAS  Google Scholar 

  • Wang Y, Qi C, Luo Y, Zhang F, Dai Z, Li M, Qu S (2021) Identification and mapping of CpPM10.1, a major gene involved in powdery mildew (race 2 France of Podosphaera xanthii) resistance in zucchini (Cucurbita pepo L.). Theor Appl Genet 134:2531–2545

    CAS  Google Scholar 

  • Wellburn AR (1994) The spectral determination of chlorophylls a and b, as well as total carotenoids, using various solvents with spectrophotometers of different resolution. J Plant Physiol 144:307–313

    CAS  Google Scholar 

  • Weng YQ, Garcia-Mas J, Levi A, Luan FS (2020) Editorial: Translational research for cucurbit molecular breeding: Traits, Markers, and Genes. Front Plant Sci 11

  • Xanthopoulou A, Montero-Pau J, Pico B, Boumpas P, Tsaliki E, Paris HS, Tsaftaris A, Kalivas A, Mellidou I, Ganopoulos I (2021) A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms. BMC Genomics 22:341

    CAS  Google Scholar 

  • Yue CN, Wang ZH, Yang PX (2021) Review: the effect of light on the key pigment compounds of photosensitive etiolated tea plant. Bot Stud 62:21

    CAS  Google Scholar 

  • Zhang J, Fengler KA, Van Hemert JL, Gupta R, Mongar N, Sun JD, Allen WB, Wang Y, Weers B, Mo H, Lafitte R, Hou ZL, Bryant A, Ibraheem F, Arp J, Swaminathan K, Moose SP, Li BL, Shen B (2019) Identification and characterization of a novel stay-green QTL that increases yield in maize. Plant Biotechnol J 17:2272–2285

    CAS  Google Scholar 

  • Zhao MH, Li X, Zhang XX, Zhang H, Zhao XY (2020) Mutation Mechanism of Leaf Color in Plants: A Review. Forests 11:851

    Google Scholar 

Download references

Acknowledgements

This research was supported by Major Public Welfare Project in Henan Province (201300111300), and Key Scientific Research Project of Colleges and Universities in Henan Province (22A210006).

Author information

Authors and Affiliations

  1. Henan Engineering Technology Research Center of Germplasm Innovation and Utilization of Melon Crops, Henan Agricultural University, Zhengzhou, China

    Lei Zhu, Yong Wang, Changsheng Ma, Luming Yang, Shouru Sun & Yanman Li

  2. International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China

    Lei Zhu, Zhenli Zhang, Deju Hu, Zanlin Wang, Jianbin Hu, Changsheng Ma, Luming Yang & Shouru Sun

Authors
  1. Lei Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yong Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zhenli Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Deju Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zanlin Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jianbin Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Changsheng Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Luming Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Shouru Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Yanman Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

LZ performed the experiments, SS, YW, and YL analyzed data. ZZ, YW, DH, ZW, and CM collected the phenotypic data. SS, YL, JH, and LY provided valuable research design. LZ and YL wrote the paper. All authors have read and approved the final manuscript.

Corresponding authors

Correspondence to Shouru Sun or Yanman Li.

Ethics declarations

Ethical approval

The authors declare that this study complies with the current laws of the countries in which the experiments were performed.

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Communicated by Yiqun Weng.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 157 kb)

Rights and permissions

Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhu, L., Wang, Y., Zhang, Z. et al. Chromosomal fragment deletion in APRR2-repeated locus modulates the dark stem color in Cucurbita pepo. Theor Appl Genet 135, 4277–4288 (2022). https://doi.org/10.1007/s00122-022-04217-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-022-04217-6

Search

Navigation