Abstract
To facilitate marker-assisted breeding and genetic analyses of pepper (Capsicum annuum), we developed non-redundant 2- or 3-base simple sequence repeat (SSR) markers from enriched C. annuum genomic libraries and from C. annuum cDNA sequences in public databases. The SSR-enriched libraries were constructed using combinations of three restriction enzymes (AluI, HaeIII, and RsaI) and two biotinylated oligonucleotides [b(GA)15 and b(CA)15]. Ultimately, we obtained 1,736 genomic SSR markers and 1,344 cDNA-derived SSR markers from 6,528 clones and 13,003 sequences, respectively. We mapped 597 markers, including 265 of the newly developed SSR markers, onto a linkage map by using doubled-haploid (DH) lines derived from an intraspecific cross of two pure lines of C. annuum (K9-11 × MZC-180). The map, designated as the KL-DH map, consisted of 12 linkage groups. The map covered a genetic distance of 2,028 cM, and the average distance between markers was less than 4 cM. The frame structure of the KL-DH map was compared with the published standard conserved ortholog set II (COSII) map, which was derived from an interspecific F2 population (C. frutescens × C. annuum), by using tomato (Solanum lycopersicum) chromosomal sequences to bridge the two maps. The intraspecific KL-DH map constructed in this study and the interspecific COSII map were similar in map length and marker distribution, suggesting that the KL-DH map covers nearly the whole genome of C. annuum.
Similar content being viewed by others
References
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Arnedo-Andres S, Gil-Ortega R, Luis-Arteaga M, Hormaza I (2002) Development of RAPD and SCAR markers linked to the Pvr4 locus for resistance to PVY in pepper (Capsicum annuum L.). Theor Appl Genet 105:1067–1074
Barchi L, Bonnet J, Boudet C, Signoret P, Nagy I, Lanteri S, Palloix A, Lefebvre V (2007) A high-resolution, intraspecific linkage map of pepper (Capsicum annuum L.) and selection of reduced recombinant inbred line subsets for fast mapping. Genome 50:51–60
Barchi L, Lefebvre V, Sage-Palloix AM, Lanteri S, Palloix A (2009) QTL analysis of plant development and fruit traits in pepper and performance of selective phenotyping. Theor Appl Genet 118:1157–1171
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
Bonnet J, Danan S, Boudet C, Barchi L, Sage-Palloix AM, Caromel B, Palloix A, Lefebvre V (2007) Are the polygenic architectures of resistance to Phytophthora capsici and P. parasitica independent in pepper? Theor Appl Genet 115:253–264
Borovsky Y, Paran I (2011) Characterization of fs10.1, a major QTL controlling fruit elongation in Capsicum. Theor Appl Genet 123:657–665
Caranta C, Thabuis A, Palloix A (1999) Development of a CAPS marker for the Pvr4 locus: a tool for pyramiding potyvirus resistance genes in pepper. Genome 42:1111–1116
Chaim AB, Borovsky Y, De Jong W, Paran I (2003) Linkage of the A locus for the presence of anthocyanin and fs10.1, a major fruit-shape QTL in pepper. Theor Appl Genet 106:889–894
Djian-Caporalino C, Fazari A, Arguel MJ, Vernie T, VandeCasteele C, Faure I, Brunoud G, Pijarowski L, Palloix A, Lefebvre V, Abad P (2007) Root-knot nematode (Meloidogyne spp.) Me resistance genes in pepper (Capsicum annuum L.) are clustered on the P9 chromosome. Theor Appl Genet 114:473–486
Efrati A, Eyal Y, Paran I (2005) Molecular mapping of the chlorophyll retainer (cl) mutation in pepper (Capsicum spp.) and screening for candidate genes using tomato ESTs homologous to structural genes of the chlorophyll catabolism pathway. Genome 48:347–351
Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194
Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185
Fukuoka H, Nunome T, Minamiyama Y, Kono I, Namiki N, Kojima A (2005) Read2Marker: a data processing tool for microsatellite marker development from a large data set. Biotechniques 39:472–476
Fukuoka H, Miyatake K, Negoro S, Nunome T, Ohyama A, Yamaguchi H (2008) Development of a routine procedure for single nucleotide polymorphism marker design based on the Tm-shift genotyping method. Breed Sci 58:461–464
Fukuoka H, Miyatake K, Nunome T, Negoro S, Shirasawa K, Isobe S, Asamizu E, Yamaguchi H, Ohyama A (2012) Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets. Theor Appl Genet 125:47–56
Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8:195–202
Iwata H, Ninomiya S (2006) AntMap: constructing genetic linkage maps using an ant colony optimization algorithm. Breed Sci 56:371–377
Jahn M, Paran I, Hoffmann K, Radwanski ER, Livingstone KD, Grube RC, Aftergoot E, Lapidot M, Moyer J (2000) Genetic mapping of the Tsw locus for resistance to the Tospovirus Tomato spotted wilt virus in Capsicum spp. and its relationship to the Sw-5 gene for resistance to the same pathogen in tomato. Mol Plant Microbe Interact 13:673–682
Kang BC, Nahm SH, Huh JH, Yoo HS, Yu JW, Lee MH, Kim BD (2001) An interspecific (Capsicum annuum × C. chinese) F2 linkage map in pepper using RFLP and AFLP markers. Theor Appl Genet 102:531–539
Kim DS, Kim DH, Yoo JH, Kim BD (2006) Cleaved amplified polymorphic sequence and amplified fragment length polymorphism markers linked to the fertility restorer gene in chili pepper (Capsicum annuum L.). Mol Cell 21:135–140
Kim HJ, Baek KH, Lee SW, Kim J, 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
Kim HJ, Han JH, Kwon JK, Park M, Kim BD, Choi D (2010) Fine mapping of pepper trichome locus 1 controlling trichome formation in Capsicum annuum L. CM334. Theor Appl Genet 120:1099–1106
Kong Q, Zhang G, Chen W, Zhang Z, Zou X (2012) Identification and development of polymorphic EST-SSR markers by sequence alignment in pepper, Capsicum annuum (Solanaceae). Am J Bot 99:e59–e61
Lander ES, Botstein D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199
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
Lee HR, Cho MC, Kim HJ, Park SW, Kim BD (2008) Marker development for erect versus pendant-orientated fruit in Capsicum annuum L. Mol Cell 26:548–553
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 Cell 27:21–37
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
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
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
Lu FH, Cho MC, Park YJ (2012a) Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68. Mol Biol Rep 39:3327–3335
Lu FH, Kwon SW, Yoon MY, Kim KT, Cho MC, Yoon MK, Park YJ (2012b) SNP marker integration and QTL analysis of 12 agronomic and morphological traits in F8 RILs of pepper (Capsicum annuum L.). Mol Cell. doi:10.1007/s10059-012-0018-1
Mimura Y, Inoue T, Minamiyama Y, Kubo N (2012) An SSR-based genetic map of pepper (Capsicum annuum L.) serves as an anchor for the alignment of major pepper maps. Breed Sci 62:93–98
Min WK, Kim S, Sung SK, Kim BD, Lee S (2009) Allelic discrimination of the Restorer-of-fertility gene and its inheritance in peppers (Capsicum annuum L.). Theor Appl Genet 119:1289–1299
Minamiyama Y, Tsuro M, Hirai M (2006) An SSR-based linkage map of Capsicum annuum. Mol Breed 18:157–169
Nagy I, Stagel A, Sasvari Z, Roder M, Ganal M (2007) Development, characterization, and transferability to other Solanaceae of microsatellite markers in pepper (Capsicum annuum L.). Genome 50:668–688
Nunome T, Negoro S, Miyatake K, Yamaguchi H, Fukuoka H (2006) Protocol for the construction of microsatellite enriched genomic library. Plant Mol Biol Rep 24:305–312
Ogundiwin EA, Berke TF, Massoudi M, Black LL, Huestis G, Choi D, Lee S, Prince JP (2005) Construction of 2 intraspecific linkage maps and identification of resistance QTLs for Phytophthora capsici root-rot and foliar-blight diseases of pepper (Capsicum annuum L.). Genome 48:698–711
Ohyama A, Asamizu E, Negoro S, Miyatake K, Yamaguchi H, Tabata S, Fukuoka H (2009) Characterization of tomato SSR markers developed using BAC-end and cDNA sequences from genome databases. Mol Breed 23:685–691
Paran I, van der Voort JR, Lefebvre V, Jahn M, Landry L, van Schriek M, Tanyolac B, Caranta C, Chaim AB, Livingstone K, Palloix A, Peleman J (2004) An integrated genetic linkage map of pepper (Capsicum spp.). Mol Breed 13:251–261
Portis E, Nagy I, Sasvari Z, Stagel A, Barchi L, Lanteri S (2007) The design of Capsicum spp. SSR assays via analysis of in silico DNA sequence, and their potential utility for genetic mapping. Plant Sci 172:640–648
Prince JP, Pochard E, Tanksley SD (1993) Construction of a molecular linkage map of pepper and a comparison of synteny with tomato. Genome 36:404–417
Quackenbush J, Liang F, Holt I, Pertea G, Upton J (2000) The TIGR gene indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Res 28(1):141–145
Rao GU, Ben Chaim A, Borovsky Y, Paran I (2003) Mapping of yield-related QTLs in pepper in an interspecific cross of Capsicum annuum and C. frutescens. Theor Appl Genet 106:1457–1466
Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386
Sanwen H, Baoxi Z, Milbourne D, Cardle L, Guimei Y, Jiazhen G (2001) Development of pepper SSR markers from sequence databases. Euphytica 117:163–167
Stewart C Jr, Kang BC, Liu K, Mazourek M, Moore SL, Yoo EY, Kim BD, Paran I, Jahn MM (2005) The Pun1 gene for pungency in pepper encodes a putative acyltransferase. Plant J 42:675–688
Sugita T, Yamaguchi K, Sugimura Y, Nagata R, Yuji K, Kinoshita T, Todoroki A (2004) Development of SCAR markers linked to L 3 gene in Capsicum. Breed Sci 54:111–115
Sugita T, Kinoshita T, Kawano T, Yuji K, Yamaguchi K, Nagata R, Shimizu A, Chen LZ, Kawasaki S, Todoroki A (2005) Rapid construction of a linkage map using high-efficiency genome scanning/AFLP and RAPD, based on an intraspecific, doubled-haploid population of Capsicum annuum. Breed Sci 55:287–295
Sugita T, Yamaguchi K, Kinoshita T, Yuji K, Sugimura Y, Nagata R, Kawasaki S, Todoroki A (2006) QTL analysis for resistance to phytophthora blight (Phytophthora capsici Leon.) using an intraspecific doubled-haploid population of Capsicum annuum. Breed Sci 56:137–145
Tam SM, Mhiri C, Vogelaar A, Kerkveld M, Pearce SR, Grandbastien MA (2005) Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theor Appl Genet 110:819–831
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
Thorup TA, Tanyolac B, Livingstone KD, Popovsky S, Paran I, Jahn M (2000) Candidate gene analysis of organ pigmentation loci in the Solanaceae. Proc Natl Acad Sci USA 97:11192–11197
Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641
Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78
Wu F, Eannetta NT, Xu Y, Durrett R, Mazourek M, Jahn MM, 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
Yi G, Lee JM, Lee S, Choi D, Kim BD (2006) Exploitation of pepper EST-SSRs and an SSR-based linkage map. Theor Appl Genet 114:113–130
Zygier S, Chaim AB, Efrati A, Kaluzky G, Borovsky Y, Paran I (2005) QTLs mapping for fruit size and shape in chromosomes 2 and 4 in pepper and a comparison of the pepper QTL map with that of tomato. Theor Appl Genet 111:437–445
Acknowledgments
We thank N. Fukushima and Y. Kitamura of NIVTS for their technical assistance. This work was supported by grants from the Ministry of Agriculture, Forestry, and Fisheries of Japan (Research and Development Projects for Application in Promoting New Policy of Agriculture, Forestry and Fisheries, grants 18047 and 22064).
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Sugita, T., Semi, Y., Sawada, H. et al. Development of simple sequence repeat markers and construction of a high-density linkage map of Capsicum annuum . Mol Breeding 31, 909–920 (2013). https://doi.org/10.1007/s11032-013-9844-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11032-013-9844-x