Development of simple sequence repeat markers and construction of a high-density linkage map of Capsicum annuum

Molecular Breeding

Volumn 31, Issue 4, 2013, Pages 909-920

  Sugita, Toru ^a   Semi, Yukari ^a,d   Sawada, Hiromasa ^b,e   Utoyama, Yumi ^a,f   Hosomi, Yuko ^b   Yoshimoto, Eri ^b   Maehata, Yuki ^a   Fukuoka, Hiroyuki ^c   Nagata, Ryutaro ^a   Ohyama, Akio ^c  

^a Miyazaki Agricultural Research Institute   (Japan)

^b Kochi Prefectural Agriculture Research Center   (Japan)

^c NATIONAL INSTITUTE OF VEGETABLE AND TEA SCIENCE   (Japan)

^d Miyazaki Prefectural Higashiusuki Agricultural Community Development Bureau   (Japan)

^e Kochi Agricultural College   (Japan)

^f Miyazaki Prefectural Nishiusuki Branch Office   (Japan)

Author keywords

Capsicum; Linkage map; SSR; Tomato genome

Indexed keywords

BIOMARKERS; DNA SEQUENCES; FRUITS; LIBRARIES; OLIGONUCLEOTIDES; PLANTS (BOTANY);

CAPSICUM; CAPSICUM ANNUUM; DOUBLED HAPLOID; GENETIC ANALYSIS; LINKAGE MAP; MARKER-ASSISTED BREEDING; ORTHOLOGS; SIMPLE SEQUENCE REPEATS; SIMPLE SEQUENCE-REPEAT MARKERS; TOMATO GENOMES;

GENES;

CAPSICUM; CAPSICUM ANNUUM; CAPSICUM FRUTESCENS; LYCOPERSICON ESCULENTUM;

EID: 84875759848     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-013-9844-x     Document Type: Article

References (59)

1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. Borovsky Y, Paran I (2011) Characterization of fs10. 1, a major QTL controlling fruit elongation in Capsicum. Theor Appl Genet 123: 657-665.
8. 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.
9. 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.
10. 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.
11. 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.
12. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
13. 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.
14. 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.
15. m-shift genotyping method. Breed Sci 58: 461-464.
16. 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.
17. Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8: 195-202.
18. Iwata H, Ninomiya S (2006) AntMap: constructing genetic linkage maps using an ant colony optimization algorithm. Breed Sci 56: 371-377.
19. 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.
20. 2 linkage map in pepper using RFLP and AFLP markers. Theor Appl Genet 102: 531-539.
21. 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.
22. 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.
23. 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.
24. 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.
25. Lander ES, Botstein D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
26. 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.
27. 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.
28. 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.
29. 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.
30. 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.
31. 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.
32. 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.
33. 8 RILs of pepper (Capsicum annuum L.). Mol Cell. doi: 10. 1007/s10059-012-0018-1.
34. 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.
35. 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.
36. Minamiyama Y, Tsuro M, Hirai M (2006) An SSR-based linkage map of Capsicum annuum. Mol Breed 18: 157-169.
37. 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.
38. 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.
39. 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.
40. 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.
41. 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.
42. 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.
43. 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.
44. 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.
45. 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.
46. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
47. 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.
48. 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.
49. 3 gene in Capsicum. Breed Sci 54: 111-115.
50. 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.
51. 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.
52. 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.
53. 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.
54. 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.
55. Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641.
56. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93: 77-78.
57. 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.
58. 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.
59. 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.