Skip to main content

Advertisement

SpringerLink
Log in

An SSR-based linkage map of Capsicum annuum

  • ORIGINAL PAPER
  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

There are five cultivated species of pepper, of which Capsicum annuum is the most widely cultivated as a vegetable or spice and the main experimental material of most pepper breeding programs. However, the number of simple sequence-repeat (SSR) markers known for C. annuum is limited. To develop SSR markers for Capsicum species, we constructed four SSR-enriched libraries from the genomic DNA of C.␣annuum, sequenced 1873 clones, and isolated 626 unique SSR clones. A higher percentage of these SSR markers were taken from dinucleotide motif libraries than from trinucleotide motif libraries. Primer pairs for the 626 SSR clones were synthesized and tested for polymorphisms; 594 amplified products were detected with the expected size. However, only 153 products were polymorphic between the parents of our mapping population. Using 106 highly reproducible pairs from the primer pairs, we constructed a linkage map of C. annuum in an intraspecific doubled haploid population (n=117) that contains nine previously reported SSRs as well as AFLP, CAPS, and RAPD markers and the trait of fruit pungency. The map contains 374 markers, including 106 new SSR markers distributed across all 13 linkage groups, and covers 1042 cM. The polymorphism information content (PIC) of these new SSR markers was calculated using 14 lines of Capsicum species. The average number of alleles per locus was 2.9 and the average PIC value was 0.46, even within C. annuum. The SSR markers developed in this study will be useful for mapping and marker-assisted selection in pepper breeding, and the linkage map provides a reference genetic map for Capsicum species.

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

Similar content being viewed by others

References

  • Areshchenkova T, Ganal MW (1999) Long tomato microsatellites are predominantly associated with centromeric regions. Genome 42:536–544

    Article  PubMed  CAS  Google Scholar 

  • Ben Chaim A, Grube RC, Lapidot M, Jahn M (2001) Identification of quantitative trait loci associated with resistance to cucumber mosaic virus in Capsicum annuum. Theor Appl Genet 102:1213–1220

    Article  CAS  Google Scholar 

  • Blair MW, Pedraza F, Buendia HF, Gaitan-Solis E, Beebe SE, Gepts P, Tohme J (2003) Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.). Theor Appl Genet 107:1362–1374

    Article  PubMed  CAS  Google Scholar 

  • Bradeen JM, Staub JE, Wye C, Antonise R, Peleman J (2001) Towards an expanded and integrated linkage map of cucumber (Cucumis sativus L.). Genome 44:111–119

    Article  PubMed  CAS  Google Scholar 

  • Broun P, Tanksley SD (1996) Characterization and genetic mapping of simple repeat sequences in the tomato genome. Mol Gen Genet 250:39–49

    Article  PubMed  CAS  Google Scholar 

  • Cai HW, Yuyama N, Tamaki H, Yoshizawa A (2003) Isolation and characterization of simple sequence repeat markers in the hexaploid forage grass timothy (Phleum pratense L.). Theor Appl Genet 107:1337–1349

    Article  PubMed  CAS  Google Scholar 

  • Caranta C, Pflieger S, Lefebvre V, Daubeze AM, Thabuis A, Palloix A (2002) QTLs involved in the restriction of cucumber mosaic virus (CMV) long-distance movement in pepper. Theor Appl Genet 104:586–591

    Article  PubMed  CAS  Google Scholar 

  • Chiba N, Suwabe K, Nunome T, Hirai M (2003) Development of microsatellite markers in melon (Cucumis melo L.) and their application to major cucurbit crops. Breed Sci 53:21–27

    Article  CAS  Google Scholar 

  • Ghislain M, Spooner DM, Rodriguez F, Villamon F, Nunez J, Vasquez C, Waugh R, Bonierbale M (2004) Selection of highly informative and user-friendly microsatellites (SSRs) for genotyping of cultivated potato. Theor Appl Genet 108:881–890

    Article  PubMed  CAS  Google Scholar 

  • Goldstein DB, Schloetterer C (1999) Microsatellite evolution and applications. Oxford University Press, Oxford

    Google Scholar 

  • Inazuka M, Tahira T, Hayashi K (1996) One-tube post-PCR fluorescent labeling of DNA fragments. Genome Res 6:551–557

    Article  PubMed  CAS  Google Scholar 

  • Jones ES, Dupal MP, Kolliker R, Drayton MC, Forster JW (2001) Development and characterisation of simple sequence repeat (SSR) markers for perennial ryegrass (Lolium perenne L.). Theor Appl Genet 102:405–415

    Article  CAS  Google Scholar 

  • Jones ES, Dupal MP, Dumsday JL, Hughes LJ, Forster JW (2002) A SSR-based genetic linkage map for perennial ryegrass (Lolium perenne L.). Theor Appl Genet 105:577–584

    Article  PubMed  CAS  Google Scholar 

  • Kang BC, Nahm SH, Hhu JH, Yoo HS, Yu UW, Lee MH, Kim BD (2001) An interspecific (Capsicum annuum  ×  C. chinense) F2 linkage map in pepper using RFLP and AFLP markers. Theor Appl Genet 102:531–539

    Article  CAS  Google Scholar 

  • Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175

    Google Scholar 

  • Lagercrantz U, Ellegren H, Andersson L (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res 21:1111–1115

    Article  PubMed  CAS  Google Scholar 

  • Lee JM, Nahm SH, Kim YM, Kim BD (2004) Characterization and molecular genetic mapping of microsatellite loci in pepper. Theor Appl Genet 108:619–627

    Article  PubMed  CAS  Google Scholar 

  • Lefebvre V, Palloix A, Caranta C, Pochard E (1995) Construction of an intraspecific integrated linkage map of pepper using molecular markers and doubled-haploid progenies. Genome 38:112–121

    PubMed  CAS  Google Scholar 

  • Lefebvre V, Pflieger S, Thabuis A, Caranta C, Blattes A, Chauvet JC, Daubeze AM, Palloix A (2002) Towards the saturation of the pepper linkage map by alignment of three intraspecific maps including known-function genes. Genome 45:839–854

    Article  PubMed  CAS  Google Scholar 

  • Livingstone KD, Lackney VK, Blauth JR, van Wijk R, Jahn MK (1999) Genome mapping in Capsicum and the evolution of the genome structure in the Solanaceae. Genetics 152:1183–1202

    PubMed  CAS  Google Scholar 

  • Maughan PJ, Saghai Maroof MA, Buss GR, Huestis GM (1996) Amplified fragment length polymorphism (AFLP) in soybean: species diversity, inheritance, and near-isogenic line analysis. Theor Appl Genet 93:392–401

    Article  CAS  Google Scholar 

  • Mba REC, Stephenson P, Edwards K, Melzer S, Nkumbira J, Gullberg U, Apel K, Gale M, Tohme J, Fregene M (2001) Simple sequence repeat (SSR) markers survey of the cassava (Manihot esculenta Crantz) genome: towards an SSR-based molecular genetic map of cassava. Theor Appl Genet 102:21–31

    Article  CAS  Google Scholar 

  • Milbourne D, Meyer RC, Collins AJ, Ramsay LD, Gebhardt C, Waugh R (1998) Isolation, characterization and mapping of simple sequence repeat loci in potato. Mol Gen Genet 259:233–245

    Article  PubMed  CAS  Google Scholar 

  • Minamiyama Y, Kinoshita S, Inaba K, Inoue M (2005) Development of a cleaved amplified polymorphic sequence (CAPS) marker linked to pungency in pepper. Plant Breed 124:288–291

    Article  CAS  Google Scholar 

  • Moury B, Pflieger S, Blattes A, Lefebvre V, Palloix A (2000) A CAPS marker to assist selection of tomato spotted wilt virus (TSWV) resistance in pepper. Genome 43:137–142

    Article  PubMed  CAS  Google Scholar 

  • Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323

    Article  PubMed  CAS  Google Scholar 

  • Nunome T, Ishiguro K, Yoshida T, Hirai M (2001) Mapping of fruit shape and color development traits in eggplant (Solanum melongena L.) based on RAPD and AFLP markers. Breed Sci 51:19–26

    Article  CAS  Google Scholar 

  • Nunome T, Suwabe K, Iketani H, Hirai M (2003) Identification and characterization of microsatellites in eggplant. Plant Breed 122:256–262

    Article  CAS  Google Scholar 

  • Paran I, Rouppe van der Voort J, Lefebvre V, Jahn M, Landry L, van Schriek M, Tanyolac B, Caranta C, Ben Chaim A, Livingstone K, Palloix A, Peleman J (2004) An integrated genetic linkage map of pepper (Capsicum spp.). Mol Breed 13:251–261

    Article  CAS  Google Scholar 

  • Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier MH, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023

    PubMed  Google Scholar 

  • Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726

    Article  CAS  Google Scholar 

  • Shen YJ, Jiang H, Jin JP, Zhang ZB, Xi B, He YY, Wang G, Wang C, Qian L, Li X (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol 135:1198–1205

    Article  PubMed  CAS  Google Scholar 

  • Smulders MJM, Bredemeijer G, Rus-Kortekaas W, Arens P, Vosman B (1997) Use of short microsatellites from database sequences to generate polymorphism among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species. Theor Appl Genet 97:264–272

    Article  Google Scholar 

  • Suwabe K, Iketani H, Nunome T, Kage T, Hirai M (2002) Isolation and characterization of microsatellites in Brassica rapa L. Theor Appl Genet 104:1092–1098

    Article  PubMed  CAS  Google Scholar 

  • Thabuis A, Palloix A, Pflieger S, Daubeze AM, Caranta C, Lefebvre V (2003) Comparative mapping of Phytophthora resistance loci in pepper germplasm: evidence for conserved resistance loci across Solanaceae and for a large genetic diversity. Theor Appl Genet 106:1473–1485

    PubMed  CAS  Google Scholar 

  • Torjek O, Berger D, Meyer RC, Mussig C, Schmid KJ, Sorensen TR, Weisshaar B, Mitchell-Olds T, Altmann T (2003) Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis. Plant J 36:122–140

    Article  PubMed  CAS  Google Scholar 

  • Van Ooijen JW, Voorrips RE (2001) JoinMap 3.0, software for the calculation of genetic linkage maps. Plant Research International, Wageningen

    Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijians M, Lee T, van de Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    Article  CAS  Google Scholar 

  • Yang W, Bai X, Kabelka E, Eaton C, Kamoun S, van der Knaap E, Francis D (2004) Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags. Mol Breed 14:21–34

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank Drs. T. Nunome and H. Fukuoka for their valuable suggestions. We are also grateful to Ms. T. Ohta and Ms. W. Okai for their technical assistance.

Author information

Author notes

  1. Masato Tsuro

    Present address: Faculty of Agriculture, Meijo University, Shiogamaguchi, Tenpaku, Nagoya, 468-8502, Japan

Authors and Affiliations

  1. Kyoto Prefectural Institute of Agricultural Biotechnology, 74, Oji, Kitainayazuma, Seika, Soraku, Kyoto, 619-0244, Japan

    Yasuhiro Minamiyama, Masato Tsuro & Masashi Hirai

  2. Graduate School of Agriculture, Kyoto Prefectural University, 74, Oji, Kitainayazuma, Seika, Soraku, Kyoto, 619-0244, Japan

    Masashi Hirai

Authors
  1. Yasuhiro Minamiyama
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Masato Tsuro
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Masashi Hirai
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yasuhiro Minamiyama.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Minamiyama, Y., Tsuro, M. & Hirai, M. An SSR-based linkage map of Capsicum annuum . Mol Breeding 18, 157–169 (2006). https://doi.org/10.1007/s11032-006-9024-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11032-006-9024-3

Keywords

Search

Navigation