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Construction of a high density integrated genetic map for cucumber (Cucumis sativus L.)

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Abstract

The high-density consensus map was constructed based on the GY14 × PI 183967 map from an inter-subspecific cross and the extended S94 × S06 map from an intra-subspecific cross. The consensus map was composed of 1,369 loci, including 1,152 SSR loci, 192 SRAP loci, 21 SCAR loci and one STS locus as well as three gene loci of fruit external quality traits in seven chromosomes, and spanned 700.5 cM, of which 682.7 cM (97.5%) were covered by SSR markers. The average genetic distance and physical interval between loci were 0.51 cM and ~268 kbp, respectively. Additionally, the physical position of the sequence-associated markers aligned along the assembled cucumber genome sequence established a relationship between genetic maps and cucumber genome sequence and to a great extent validated the order of markers in individual maps and consensus map. This consensus map with a high marker density and well-ordered markers is a saturated and reliable linkage map for genetic analysis of cucumber or the Cucurbitaceae family of plants.

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Abbreviations

SSR:

Simple sequence repeat

SRAP:

Sequence-related amplified polymorphism

SCAR:

Sequence characterized amplified region

STS:

Sequence tagged site

RIL:

Recombinant inbred lines

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Acknowledgments

This work was supported by grants from the National Natural Science Foundation of China (No. 30671111, 30871707), the Shanghai Leading Academic Discipline Project (No. B209), the Chinese Ministry of Agriculture (948 Program: 2008-Z42), the Shanghai Municipal Scientific and Technological Commission Project (No. 09JC1407300) and the National Basic Research Program of China (973 Program, Grant No. 2012CB113902).

Author information

Authors and Affiliations

  1. School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China

    Wei-Wei Zhang, Jun-Song Pan, Huan-Le He, Chi Zhang, Zheng Li, Jun-Long Zhao, Xiao-Jun Yuan & Run Cai

  2. Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, 201602, China

    Wei-Wei Zhang

  3. The State Key Laboratory of Plant Genomics and National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China

    Li-Huang Zhu

  4. Key Laboratory of Horticultural Crops Genetic Improvement of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics Technology, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    San-Wen Huang

Authors
  1. Wei-Wei Zhang
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  2. Jun-Song Pan
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  3. Huan-Le He
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  4. Chi Zhang
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  5. Zheng Li
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  6. Jun-Long Zhao
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  7. Xiao-Jun Yuan
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  8. Li-Huang Zhu
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  9. San-Wen Huang
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  10. Run Cai
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Corresponding authors

Correspondence to San-Wen Huang or Run Cai.

Additional information

Communicated by M. Havey.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Material S1: The primer sequences of SRAP markers. (DOC 32 kb)

122_2011_1701_MOESM2_ESM.xls

Supplementary material S2: Information of marker loci in SS map. Excel spreadsheet contains a list of all marker loci in extended SS map, including the genetic and physical position of each locus in chromosomes, marker types and distorted segregation marker loci. Loci names with an asterisk indicate significant distorted segregation (P < 0.05), and single asterisk and double asterisks indicate the preferential transmission from the alleles of S94 and S06, respectively. (XLS 172 kb)

122_2011_1701_MOESM3_ESM.xls

Supplementary material S3: Information of marker loci in GP map. Excel spreadsheet contains a list of all marker loci in GP map, including the genetic and physical position of each locus in chromosomes, marker types and distorted segregation marker loci. Loci names with an asterisk indicate significant distorted segregation (P < 0.05), and single asterisk and double asterisks indicate the preferential transmission from the alleles of GY14 and PI183067, respectively. (XLS 240 kb)

122_2011_1701_MOESM4_ESM.xls

Supplementary Material S4: Information of marker loci in consensus map. Excel spreadsheet contains a list of all marker loci in consensus map and their features, including the genetic and physical position of each locus in chromosomes, source of each marker locus, marker types, bridging markers and multi-copy marker details. Blue color represents well-orders markers regions; Red color represents regions of likely structural rearrangement. (XLS 426 kb)

Supplementary Material S5: The sequences of the sequence-associated markers. (DOC 651 kb)

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Zhang, WW., Pan, JS., He, HL. et al. Construction of a high density integrated genetic map for cucumber (Cucumis sativus L.). Theor Appl Genet 124, 249–259 (2012). https://doi.org/10.1007/s00122-011-1701-x

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  • DOI: https://doi.org/10.1007/s00122-011-1701-x

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