Skip to main content
SpringerLink
Log in

An EST-based linkage map reveals chromosomal translocation in Capsicum

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

To facilitate marker-assisted breeding and analysis of the structure and/or organization of Capsicum (pepper) genomes, this study utilized expressed sequence tags (ESTs) to develop single-nucleotide polymorphism (SNP) markers. Three different types of PCR-based markers derived from pepper ESTs were developed: intron-based polymorphic markers (IBPs), conserved ortholog sets (COSIIs), and eSNPs (EST–SNPs). For scanning and detection of SNPs, high-resolution melting analysis was performed and the resultant markers were used for linkage analysis. A total of 512 markers, comprising 214 IBP, 143 COSII, 48 eSNP, and 107 previously reported markers, were mapped on 12 linkage groups (LGs) of the “AC99” F2 population. This newly constructed interspecific map (AC2) covered 2,335.6 cM with an average marker interval distance of 4.5 cM and was aligned directly with another interspecific map (AF) for validation. Most LGs showed collinear relationships, except for the alignment of chromosomes 1 and 8 of the AC2 map to LG P1 of the AF map. Using our newly developed SNP markers, we generated chromosome-specific markers, and the previously predicted reciprocal translocation event between chromosomes 1 and 8 was revealed between wild and cultivated Capsicum by fluorescent in situ hybridization analysis. The results from this study will promote subsequent evolutionary studies of 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.

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • An SJ, Pandeya D, Park SW, Li J, Kwon JK, Koeda S, Hosokawa M, Paek NC, Choi D, Kang BC (2010) Characterization and genetic analysis of a low-temperature-sensitive mutant, sy-2, in Capsicum chinense. Theor Appl Genet 122:459–470

    Article  PubMed  Google Scholar 

  • Ashirafi H, Hill T, Stoffel K, Kozik A, Yao J, Chin-Wo SR, Van Deynze A (2012) De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes. BMC Genomics 13:571

    Article  Google Scholar 

  • Aza-González C, Núñez-Palenius HG, Ochoa-Alejo N (2011) Molecular biology of capsaicinoid biosynthesis in chilli pepper (Capsicum spp.). Plant Cell Rep 30:695–706

    Article  PubMed  Google Scholar 

  • Ben-Chaim A, Borovsky Y, Falise M, Mazourek M, Kang BC, Paran I, Jahn M (2006) QTL analysis for capsaicinoid content in Capsicum. Theor Appl Genet 113:1481–1490

    Article  PubMed  CAS  Google Scholar 

  • Chagné D, Gasic K, Crowhurst RN, Han Y, Bassett HC, Bowatte DR, Lawrence TJ, Rikkerink EH, Gardiner SE, Korban SS (2008) Development of a set of SNP markers present in expressed genes of the apple. Genomics 92:353–358

    Article  PubMed  Google Scholar 

  • Hearnden PR, Eckermann PJ, McMichael GL, Hayden MJ, Eglinton JK, Chalmers KJ (2007) A genetic map of 1,000 SSR and DArT markers in a wide barley cross. Theor Appl Genet 115:383–391

    Article  PubMed  CAS  Google Scholar 

  • Hong HT, Kim KT, Kim S, Chae Y, Park JH, Oh DG, Cho MC (2010) Comparative mapping of consensus SSR markers in an intraspecific F8 recombinant inbred line population in Capsicum. Hort Environ Biotechnol 51:193–206

    Google Scholar 

  • Jeong HJ, Kwon JK, Pandeya D, Hwang J, Hoang NH, Bae JH, Kang BC (2011) A survey of natural and ethyl methane sulfonate-induced variations of eIF4E using high-resolution melting analysis in Capsicum. Mol Breeding 29:349–360

    Article  Google Scholar 

  • Jung JK, Park SW, Liu WY, Kang BC (2010) Discovery of single nucleotide polymorphism in Capsicum and SNP markers for cultivar identification. Euphytica 175:91–107

    Article  CAS  Google Scholar 

  • Kim S, Misra A (2007) SNP genotyping: technologies and biomedical applications. Annu Rev Biomed Eng 9:289–320

    Article  PubMed  CAS  Google Scholar 

  • Kim HJ, Baek KH, Lee SW, Kim JE, Lee BW, Cho HS, Kim WT, Choi D, Hur CG (2008) Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome. BMC Plant Biol 8:101

    Article  PubMed  PubMed Central  Google Scholar 

  • Kim S, Park M, Yeom S, Kim Y-M, Lee JM, Lee H-A, Seo E, Choi J, Cheong K, Kim K-T, Jung K, Lee G-W, Oh S-G, Bae C-Y, Kim S-B, Lee H-Y, Kim S-Y, Kim M-S, Kang B-C, Jo YD, Yang H-B, Jeong H-J, Kang W-H, Kwon J-K, Shin C, Lim JY, Park JH, Huh JH, Kim J-S, Kim B-D, Cohen O, Paran I, Suh MC, Lee SB, Kim Y-K, Shin Y, Noh S-J, Park J, Seo YS, Kwon S-Y, Kim HA, Park JM, Kim H-J, Choi S-B, Bosland PW, Reeves G, Jo S-W, Lee B-W, Cho H-T, Choi H-S, Lee M-S, Yu Y, Choi YD, Park B-S, van Deynze A, Ashrafi H, Hill T, Kim WT, Pai H-S, Ahn HK, Yeam I, Giovannoni JJ, Rose JKC, Sørensen I, Lee S-J, Kim RW, Choi I-Y, Choi B-S, Lim J-S, Lee Y-H, Choi D (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46:270–278

    Article  PubMed  CAS  Google Scholar 

  • Koo DH, Jo S-H, Bang J-W, Park H-M, Lee SH, Choi D (2008) Integration of cytogenetic and genetic linkage maps unveils the physical architecture of tomato chromosome 2. Genetics 179:1211–1220

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Koumbaris GL, Bass HW (2003) A new single-locus cytogenetic mapping system for maize (Zea mays L.): overcoming FISH detection limits with marker-selected sorghum (S. propinquum L.) BAC clones. Plant J 35:647–659

    Article  PubMed  CAS  Google Scholar 

  • Kwon J-K, Kim BD (2009) Localization of 5S and 25S rRNA genes on Somatic and meiotic chromosomes in Capsicum species of chili pepper. Mol Cells 27:205–209

    Article  PubMed  CAS  Google Scholar 

  • Lanteri S, Pickersgill B (1993) Chromosomal structural-changes in Capsicum annuum L. and C. chinense Jacq. Euphytica 67:155–160

    Article  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 

  • Lee HR, Bae IH, Park SW, Kim HJ, Min WK, Han JH, Kim KT, Kim BD (2009) Construction of an Integrated Pepper Map Using RFLP, SSR, CAPS, AFLP, WRKY, rRAMP, and BAC End Sequences. Mol Cells 27:21–37

    Article  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 

  • Lehmensiek A, Sutherland MW, McNamara RB (2008) The use of high resolution melting HRM to map single nucleotide polymorphism markers linked to a covered smut resistance gene in barley. Theor Appl Genet 117:721–728

    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 genome structure in the Solanaceae. Genetics 152:1183–1202

    PubMed  CAS  PubMed Central  Google Scholar 

  • Lu FH, Kwon SW, Yoon MY, Kim KT, Cho MC, Yoon MK, Park YJ (2012) SNP marker integration and QTL analysis of 12 agronomic and morphological traits in F8 RILs of pepper (Capsicum annuum L.). Mol and Cells 34:25–34

    Article  CAS  Google Scholar 

  • Miller RT, Christoffels AG, Gopalakrishnan C, Burke J, Ptitsyn AA, Broveak TR, Hide WA (1999) A comprehensive approach to clustering of expressed human gene sequence: the sequence tag alignment and consensus knowledge base. Genome Res 9:1143–1155

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Park YK, Kim BD, Kim BS, Armstrong KC, Kim NS (1999) Karyotyping of the chromosomes and physical mapping of the 5S rRNA and 18S-26S rRNA gene families in five different species in Capsicum. Genes Genet Syst 74:149–157

    Article  Google Scholar 

  • Park SW, An SJ, Yang HB, Kwon JK, Kang BC (2009) Optimization of high resolution melting analysis and discovery of single nucleotide polymorphism in Capsicum. Hort Environ Biotechnol 50:31–39

    CAS  Google Scholar 

  • Pickersgill B (1971) Relationships between weedy and cultivated forms in some species of chilli peppers (genus Capsicum). Evolution 25:683–691

    Article  Google Scholar 

  • Piquemal J, Cinquin E, Couton F, Rondeau C, Seignoret E, Doucet I, Perret D, Villeger MJ, Vincourt P, Blanchard P (2005) Construction of an oilseed rape (Brassica napus L.) genetic map with SSR markers. Theor Appl Genet 111:1514–1523

    Article  PubMed  CAS  Google Scholar 

  • Pochard E (1970) Description of trisomic individuals of Capsicum annuum L. obtained in progeny of a haploid plant. Ann Amel Plantes 20:233–256

    Google Scholar 

  • Prince JP, Pochard E, Tanksley SD (1993) Construction of molecular linkage map of pepper and a comparison of synteny with tomato. Genome 36:404–417

    Article  PubMed  CAS  Google Scholar 

  • Reed GH, Wittwer CT (2004) Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin Chem 50:1748–1754

    Article  PubMed  CAS  Google Scholar 

  • Ririe KM, Rasmussen RP, Wittwer CT (1997) Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal Biochem 245:154–160

    Article  PubMed  CAS  Google Scholar 

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Bioinformatics Methods and Protocols 132:365–386

    Article  CAS  Google Scholar 

  • Schiex T, Gaspin C (1997) CARTHAGENE: constructing and joining maximum likelihood genetic maps. Proc Int Conf Intell Syst Mol Biol 5:258–267

    PubMed  CAS  Google Scholar 

  • Shirasawa K, Asamizu E, Fukuoka H, Ohyama A, Sato S, Nakamura Y, Tabata S, Sasamoto S, Wada T, Kishida Y, Tsuruoka H, Fujishiro T, Yamada M, Isobe S (2010) An interspecific linkage map of SSR and intronic polymorphism markers in tomato. Theor Appl Genet 121:731–739

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Sugita T, Semi Y, Sawada H, Utoyama Y, Hosomi Y, Yoshimoto E, Maehata Y, Fukuoka H, Nagata R, Ohyama A (2013) Development of simple sequence repeat markers and construction of a high-density linkage map of Capsicum annuum. Mol Breeding 31:909–920

    Article  CAS  Google Scholar 

  • Tanksley SD (1984) Linkage relationships and chromosomal locations of enzyme-coding genes in pepper, Capsicum annuum. Chromosoma 89:352–360

    Article  CAS  Google Scholar 

  • Tanksley SD, Bernatzky R, Lapitan NL, Prince JP (1988) Conservation of gene repertoire but not gene order in pepper and tomato. Proc Natl Acad Sci USA 85:6419–6423

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Van Deynze A, Stoffel K, Buell CR, Kozik A, Liu J, Van der Knaap E, Francis D (2007) Diversity in conserved genes in tomato. BMC Genom 8:465

    Article  Google Scholar 

  • Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ (2003) High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem 49:853–860

    Article  PubMed  CAS  Google Scholar 

  • Wu F, Mueller LA, Crouzillat D, Petiard V, Tanksley SD (2006) Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics 174:1407–1420

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Wu F, Eannetta NT, Xu Y, Durrett R, Mazourek M, Jahn MK, Tanksley SD (2009) A COSII genetic map of the pepper genome provides a detailed picture of synteny with tomato and new insights into recent chromosome evolution in the genus Capsicum. Theor Appl Genet 118:1279–1293

    Article  PubMed  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 Breeding 14:21–24

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by the grants from the Golden Seed Project (213002-04-1-CG910), Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), Rural Development Administration (RDA) and Korea Forest Service (KFS), the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ00906501), Rural Development Administration, and the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (2012R1A1A3015216) Republic of Korea.

Author information

Authors and Affiliations

  1. Department of Plant Science, Plant Genomics and Breeding Institute, Vegetable Breeding Research Center, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 151-921, Korea

    Soung-Woo Park, Eun-A Choi, Jin-Kyung Kwon, Jin-Ho Kang & Byoung-Cheorl Kang

  2. Research Institute and Experiment, National Agricultural Products Quality Management Service, Seoul, 150-043, Korea

    Jin-Kee Jung

  3. College of Agriculture and Life Sciences, University of Wisconsin, Madison, Wisconsin, WI, 53706, USA

    Molly Jahn

Authors
  1. Soung-Woo Park
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jin-Kee Jung
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Eun-A Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jin-Kyung Kwon
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jin-Ho Kang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Molly Jahn
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Byoung-Cheorl Kang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Byoung-Cheorl Kang.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Park, SW., Jung, JK., Choi, EA. et al. An EST-based linkage map reveals chromosomal translocation in Capsicum . Mol Breeding 34, 963–975 (2014). https://doi.org/10.1007/s11032-014-0089-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11032-014-0089-0

Keywords

Search

Navigation