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Fine mapping of the pleiotropic locus B for black spine and orange mature fruit color in cucumber identifies a 50 kb region containing a R2R3-MYB transcription factor

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Abstract

In cucumber, Cucumis sativus L., the spine and skin colors are two important fruit quality traits for variety improvement. In this study, we investigated the inheritance of spine and mature fruit skin colors in F2 and F3 populations derived from a cross between two inbred lines WI7200 (black spine and orange fruit skin colors) and WI7201 (white spine and creamy fruit skin colors). We confirmed that a single, dominant gene, B, controlled both black spine color and orange mature fruit color. Initial framework mapping with microsatellite markers located the B locus in the distal region of the short arm of cucumber chromosome 4. Fine mapping was conducted with draft genome scaffold-assisted chromosome walking and stepwise increase of mapping population sizes, which allowed for the assignment of the B locus to a 50 kb genomic DNA region with two flanking markers that were 0.06 and 0.09 cM, respectively, from the B locus in a mapping population of 2,001 F2 plants. Gene annotation of this 50 kb region identified six genes including one encoding for a R2R3-MYB transcription factor. Sequence alignment of the R2R3-MYB homologs between the two parent inbreds identified a 1 bp deletion in the third intron of this gene in WI 7201. A molecular marker based on this indel was co-segregating with the spine and fruit colors. Quantitative RT-PCR revealed higher level of expression of this R2R3-MYB gene in WI7200 than in WI7201 in both immature and mature fruits. This R2R3-MYB gene seems to be the best candidate gene for the B locus conditioning black spine and orange mature fruit colors of cultivated cucumber.

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References

  • Alverson AJ, Rice DW, Dickinson S, Barry K, Palmer JD (2011) Origins and recombination of the bacterial-sized multi-chromosomal mitochondrial genome of cucumber (Cucumis sativus). Plant Cell 23:2499–2513

    Article  PubMed  CAS  Google Scholar 

  • Azuma A, Yakushiji H, Koshita Y, Kobayashi S (2012) Flavonoid biosynthesis-related genes in grape skin are differentially regulated by temperature and light conditions. Planta 236:1067–1080

    Article  PubMed  CAS  Google Scholar 

  • Cavagnaro PF, Senalik DA, Yang LM, Simon PW, Harkins TT, Kodira CD, Huang SW, Weng Y (2010) Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics 11:569

    Article  PubMed  Google Scholar 

  • Cowen NM, Helsel DB (1983) Inheritance of two genes for spine color and linkages in a cucumber cross. J Hered 74:308–310

    Google Scholar 

  • da Maia LC, Palmieri DA, de Souza VQ, Kopp MM, de Carvalho FIF, Oliveira AC (2008) SSR Locator: tool for simple sequence repeat discovery integrated with primer design and PCR simulation. Int J Plant Genomics: 412696

  • Espley RV, Brendolise C, Chagné D, Kutty-Amma S, Green S, Volz R, Putterill J, Schouten HJ, Gardiner SE, Hellens RP, Allan AC (2009) Multiple repeats of a promoter segment causes transcription factor autoregulation in red apples. Plant Cell 21:168–183

    Article  PubMed  CAS  Google Scholar 

  • Fanourakis NE, Simon PW (1987) Analysis of genetic linkage in the cucumber. J Hered 78:238–242

    Google Scholar 

  • Feller A, Machemer K, Braun EL, Grotewold E (2011) Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. Plant J 64:94–116

    Article  Google Scholar 

  • Feng SQ, Wang YL, Yang S, Xu YT, Chen XS (2010) Anthocyanin biosynthesis in pears is regulated by a R2R3-MYB transcription factor PyMYB10. Planta 232:245–255

    Article  PubMed  CAS  Google Scholar 

  • Gaudet M, Fara AG, Sabatti M, Kuztninsky E, Mugnozza GS (2007) Single-reaction for SNP genotyping on agarose gel by allele-specific PCR in black poplar (Populus nigra L.). Plant Mol Biol Report 25:1–9

    Article  CAS  Google Scholar 

  • Guan Y (2008) Mapping and cloning of related gene for fruit spines formation in cucumber. Ph.D. thesis of Shanghai Jiaotong University (in Chinese with English abstract)

  • Havey MJ, McCreight JD, Rhodes B, Taurick G (1998) Differential transmission of the Cucumis organellar genomes. Theor Appl Genet 97:122–128

    Article  CAS  Google Scholar 

  • Hichri I, Barrieu F, Bogs J, Kappel C, Delrot S, Lauvergeat V (2011) Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway. J Exp Bot 62:2465–2483

    Article  PubMed  CAS  Google Scholar 

  • Huang S, Li RQ, Zhang ZH, Li L, Gu XF, Fan W, Lucas WJ, Wang XW et al (2009) The genome of the cucumber, Cucumis sativus L. Nat Genet 41:1275–1281

    Article  PubMed  CAS  Google Scholar 

  • Hutchins AE (1940) Inheritance in the cucumber. J Agric Res 60:117–128

    Google Scholar 

  • Kobayashi S, Goto-Yamamoto N, Hirochika H (2004) Retrotransposon-induced mutations in grape skin color. Science 304:982

    Article  PubMed  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    Article  PubMed  CAS  Google Scholar 

  • Li YH, Yang LM, Pathak M, Li DW, He XM, Weng Y (2011a) Fine genetic mapping of cp: a recessive gene for compact (dwarf) plant architecture in cucumber, Cucumis sativus L. Theor Appl Genet 123:973–983

    Article  PubMed  Google Scholar 

  • Li Z, Zhang ZH, Yan PC, Huang SW, Fei ZJ, Lin K (2011b) RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics 12:540

    Article  PubMed  CAS  Google Scholar 

  • Li Q, Zhang CJ, Li J, Wang LN, Ren ZH (2012) Genome-wide identification and characterization of R2R3MYB family in Cucumis sativus. PLoS ONE 7:e47576

    Article  PubMed  CAS  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25:402–408

    Article  PubMed  CAS  Google Scholar 

  • Miao H, Zhang SP, Wang XW, Zhang ZH, Li M, Mu SQ, Cheng ZC, Zhang RW, Huang SW, Xie BY, Fang ZY, Zhang ZX, Weng Y, Gu XF (2011) A linkage map of cultivated cucumber (Cucumis sativus L.) with 248 microsatellite marker loci and seven genes for horticulturally important traits. Euphytica 172:167–176

    Article  Google Scholar 

  • Michaels SD, Amasino RM (1998) A robust method for the detecting single-nucleotide changes as polymorphic markers by PCR. Plant J 14:381–385

    Article  PubMed  CAS  Google Scholar 

  • Neff MM, Neff JD, Chory J, Pepper AE (1998) dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J 14:387–392

    Article  PubMed  CAS  Google Scholar 

  • Neff MM, Turk E, Kalishman M (2002) Web-based primer design for single nucleotide polymorphism analysis. Trends Genet 18:613–615

    Article  PubMed  CAS  Google Scholar 

  • Peterson GC, Pike LM (1992) Inheritance of green mature seed-stage fruit color in Cucumis sativus L. J Am Soc Hortic Sci 117:643–645

    Google Scholar 

  • Pierce LK, Wehner TC (1990) Review of genes and linkage groups in cucumber. HortScience 25:605–615

    CAS  Google Scholar 

  • Piero ARL, Puglisi I, Rapisarda P, Petrone G (2005) Anthocyanins accumulation and related gene expression in red orange fruit induced by low temperature storage. J Agric Food Chem 53:9083–9088

    Article  PubMed  Google Scholar 

  • Pitchaimuthu M, Dutta OP, Swamy KRM, Souravi K (2012) Mode of inheritance of bitterness and spine color in cucumber fruits (Cucumis sativus L.). In: Sari N, Solmaz I, Aras V (eds) Cucurbitaceae 2012, Proceedings of the 10th EUCARPIA meeting on genetics and breeding of Cucurbitaceae, Antalya, Turkey, 15–18 October 2012, pp 70–73

  • Ren Y, Zhang ZH, Liu JH, Staub JE, Han YH, Cheng ZC, Li XF, Lu JY, Miao H, Kang HX, Xie BY, Gu XF, Wang XW, Du YC, Jin WW, Huang SW (2009) An integrated genetic and cytogenetic map of the cucumber genome. PLoS ONE 4:e5795

    Article  PubMed  Google Scholar 

  • Salamov AA, Solovyev VV (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10:516–522

    Article  PubMed  CAS  Google Scholar 

  • Sebastian P, Schaefer H, Telford IRH, Renner SS (2010) Cucumber (Cucumis sativus) and melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia. Proc Natl Acad Sci USA 107:14269–14273

    Article  PubMed  CAS  Google Scholar 

  • Shanmugasundarum SP, Williams PH, Peterson CE (1971) Inheritance of fruit spine color in cucumber. HortScience 6:213–214

    Google Scholar 

  • Strong WJ (1931) Breeding experiments with the cucumber (Cucumis sativus L.). Sci Agric 11:333–346

    Google Scholar 

  • Tanaka Y, Sasaki N, Ohmiya A (2008) Biosynthesis of plant pigments: anthocyanins, betalains and carotenoids. Plant J 54:733–749

    Article  PubMed  CAS  Google Scholar 

  • Telias A, Lin-Wang K, Stevenson DE, Cooney JM, Hellens RP, Allan AC, Hoover EE, Bradeen JM (2011) Apple skin patterning is associated with differential expression of MYB10. BMC Plant Biol 11:93

    Article  PubMed  CAS  Google Scholar 

  • Tkachenko NN (1935) Preliminary results of a genetic investigation of the cucumber, Cucumis sativus L. Bull Appl Plant Breed (Ser 2) 9:311–356

    Google Scholar 

  • Ubi BE, Honda C, Bessho H, Kondo S, Wada M, Kobayashi S, Moriguchi T (2006) Expression analysis of anthocyanin biosynthetic genes in apple skin: effect of UV-B and temperature. Plant Sci 170:571–578

    Article  CAS  Google Scholar 

  • Vakalounakis DJ (1992) Heart leaf, a recessive leaf shape markers in cucumber: linkage with disease resistance and other traits. J Hered 83:217–220

    Google Scholar 

  • Walters SA, Shetty NV, Wehner TC (2001) Segregation and linkage of several genes in cucumber. J Am Soc Hortic Sci 126:442–450

    CAS  Google Scholar 

  • Wan H, Zhao Z, Qian C, Sui Y, Malik A, Chen J (2010) Selection of appropriate reference genes for gene expression studies by quantitative real-time polymerase chain reaction in cucumber. Anal Biochem 399:257–261

    Article  PubMed  CAS  Google Scholar 

  • Weng Y, Johnson S, Staub JE, Huang S (2010) An extended microsatellite genetic map of cucumber, Cucumis sativus L. HortScience 45:880–886

    Google Scholar 

  • Woycicki R, Witkowicz J, Gawronski P et al (2011) The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. PLoS ONE 6:e22728

    Article  PubMed  CAS  Google Scholar 

  • Xia XJ, Wang YJ, Zhou YH, Tao Y, Mao WH, Shi K, Asami T, Chen Z, Yu JQ (2009) Reactive oxygen species are involved in brassinosteroid-induced stress tolerance in cucumber. Plant Physiol 150:801–814

    Article  PubMed  CAS  Google Scholar 

  • Yang SJ, Miao H, Zhang SP, Cheng ZC, Zhou J, Dong SY, Wehner TC, Gu XF (2011) Genetic analysis and mapping of gl-2 gene in cucumber (Cucumis sativus L.). Acta Hortic Sin 38:1685–1692

    CAS  Google Scholar 

  • Yang L, Koo DH, Li Y, Zhang X, Luan F, Havey MJ, Jiang J, Weng Y (2012) Chromosome rearrangements during domestication of cucumber as revealed from high-density genetic mapping and draft genome assembly. Plant J 71:895–906

    Article  PubMed  CAS  Google Scholar 

  • Yhaushiji H, Kobayashi S, Goto-Yamamoto N, Jeong ST et al (2006) A skin color mutation of grapevine from black-skinned Pinot Noir to white skinned Pinot Blanc, is cause by deletion of the functional VvmybA1 allele. Biosci Biotechnol Biochem 70:1506–1508

    Article  Google Scholar 

  • Yuan XJ, Pan JS, Cai R, Guan Y, Liu LZ et al (2008) Genetic mapping and QTL analysis of fruit and flower related traits in cucumber (Cucumis sativus L.) using recombinant inbred lines. Euphytica 164:473–491

    Article  CAS  Google Scholar 

  • Zhang WW, He HL, Guan Y, Du H, Yuan LH, Li Z, Yao DQ, Pan JS, Cai R (2010) Identification and mapping of molecular markers linked to the tuberculate fruit gene in the cucumber (Cucumis sativus L.). Theor Appl Genet 91:53–61

    Google Scholar 

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Acknowledgments

The authors thank Linda Crubaugh for technical help, and Michael J. Havey for critical reading of the manuscript. This research was supported by a Grant from USDA-SCRI (Project #2011-51181-30661) to YW. YL’s work was partly supported by the National Natural Science Foundation of China (Project #31171955). CW’s research was sponsored by the China Scholarship Council.

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Authors and Affiliations

  1. Horticulture College, Northwest A&F University, Yangling, 712100, China

    Yuhong Li

  2. Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA

    Yuhong Li, Changlong Wen & Yiqun Weng

  3. Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China

    Changlong Wen

  4. Vegetable Crops Research Unit, USDA-ARS, 1575 Linden Drive, Madison, WI, 53706, USA

    Yiqun Weng

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  1. Yuhong Li
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Correspondence to Yiqun Weng.

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Communicated by I. Paran.

Y. Li and C. Wen contributed equally to this work.

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Li, Y., Wen, C. & Weng, Y. Fine mapping of the pleiotropic locus B for black spine and orange mature fruit color in cucumber identifies a 50 kb region containing a R2R3-MYB transcription factor. Theor Appl Genet 126, 2187–2196 (2013). https://doi.org/10.1007/s00122-013-2128-3

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