Molecular Breeding

, Volume 32, Issue 4, pp 807–820 | Cite as

A genetic linkage map based on AFLP and SSR markers and mapping of QTL for dry-matter content in sweetpotato

  • Ning Zhao
  • Xiaoxia Yu
  • Qin Jie
  • Hui Li
  • Hua Li
  • Jun Hu
  • Hong Zhai
  • Shaozhen He
  • Qingchang Liu


We developed a genetic linkage map of sweetpotato using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers and a mapping population consisting of 202 individuals derived from a broad cross between Xushu 18 and Xu 781, and mapped quantitative trait loci (QTL) for the storage root dry-matter content. The linkage map for Xushu 18 included 90 linkage groups with 2077 markers (1936 AFLP and 141 SSR) and covered 8,184.5 cM with an average marker distance of 3.9 cM, and the map for Xu 781 contained 90 linkage groups with 1954 markers (1824 AFLP and 130 SSR) and covered 8,151.7 cM with an average marker distance of 4.2 cM. The maps described herein have the best coverage of the sweetpotato genome and the highest marker density reported to date. These are the first maps developed that have 90 complete linkage groups, which is in agreement with the actual number of chromosomes. Duplex and triplex markers were used to detect the homologous groups, and 13 and 14 homologous groups were identified in Xushu 18 and Xu 781 maps, respectively. Interval mapping was performed first and, subsequently, a multiple QTL model was used to refine the position and magnitude of the QTL. A total of 27 QTL for dry-matter content were mapped, explaining 9.0–45.1 % of the variation; 77.8 % of the QTL had a positive effect on the variation. This work represents an important step forward in genomics and marker-assisted breeding of sweetpotato.


Linkage map AFLP SSR QTL Dry-matter content Sweetpotato 



This work was supported by China Agriculture Research System (CARS-11, Sweetpotato) and the National “863 project” of China (no. 2012AA101204).

Supplementary material

11032_2013_9908_MOESM1_ESM.pdf (60 kb)
Supplementary material 1 (PDF 60 kb)
11032_2013_9908_MOESM2_ESM.pdf (57 kb)
Supplementary material 2 (PDF 56 kb)
11032_2013_9908_MOESM3_ESM.pdf (59 kb)
Supplementary material 3 (PDF 58 kb)
11032_2013_9908_MOESM4_ESM.pdf (58 kb)
Supplementary material 4 (PDF 58 kb)
11032_2013_9908_MOESM5_ESM.pdf (45 kb)
Supplementary material 5 (PDF 45 kb)
11032_2013_9908_MOESM6_ESM.pdf (42 kb)
Supplementary material 6 (PDF 42 kb)
11032_2013_9908_MOESM7_ESM.pdf (1.1 mb)
Supplementary material 7 (PDF 1132 kb)
11032_2013_9908_MOESM8_ESM.pdf (1.1 mb)
Supplementary material 8 (PDF 1093 kb)


  1. Alonso-Blanco C, Peeters AJM, Koorneef M, Lister C, Dean C, van den Bosh N, Pot J, Kuiper MTR (1998) Development of an AFLP based linkage map of Ler, Col and Cvi Arabidopsis thaliana ecotypes and construction of a Ler/Cvi recombinant inbred line population. Plant J 14:259–271PubMedCrossRefGoogle Scholar
  2. Andru S, Pan YB, Thongthawee S, Burner DM, Kimbeng CA (2011) Genetic analysis of the sugarcane (Saccharum spp.) cultivar ‘LCP 85-384’. I. Linkage mapping using AFLP, SSR, and TRAP markers. Theor Appl Genet 123:77–93PubMedCrossRefGoogle Scholar
  3. Barreneche T, Bodenes C, Lexer C, Trontin JF, Fluch S, Streiff R, Plomion C, Roussel G, Steinkellner H, Burg K, Favre JM, Glössl J, Kremer A (1998) A genetic linkage map of Quercus robur L. (pedunculate oak) based on RAPD, SCAR, microsatellite, minisatellite, isoenzyme and 5S rDNA markers. Theor Appl Genet 97:1090–1103CrossRefGoogle Scholar
  4. Becker J, Vos P, Kuiper M, Salamini F, Heun M (1995) Combined mapping of AFLP and RFLP markers in barley. Mol Gen Genet 249:65–73PubMedCrossRefGoogle Scholar
  5. Bhattramakki D, Dong J, Chhabra AK, Hart GE (2000) An integrated SSR and RFLP linkage map of Sorghum bicolor (L.) Moench. Genome 43:988–1002PubMedGoogle Scholar
  6. Buteler MI, Jarret RL, LaBonte DR (1999) Sequence characterization of microsatellites in diploid and polyploid Ipomoea. Theor Appl Genet 99:123–132CrossRefGoogle Scholar
  7. Buteler MI, LaBonte DR, Jarret RL, Macchiavelli RE (2002) Microsatellite-based paternity analysis in polyploidy sweetpotato. J Am Soc Hort Sci 127:392–396Google Scholar
  8. Carlier JD, Reis A, Duval MF, d’Eeckenbrugge GC, Leitão JM (2004) Genetic maps of RAPD, AFLP and ISSR markers in Ananas bracteatus and A. comosus using the pseudo-testcross strategy. Plant Breed 123:186–192CrossRefGoogle Scholar
  9. Cervantes-Flores JC, Yencho GC, Davis EL (2002) Host reactions of sweetpotato genotypes to root-knot nematodes and variation in virulence of Meloidogyne incognita populations. HortScience 37:1112–1116Google Scholar
  10. Cervantes-Flores JC, Yencho GC, Kriegner A, Pecota KV, Faulk MA, Mwanga ROM, Sosinski BR (2008) Development of a genetic linkage map and identification of homologous linkage groups in sweetpotato using multiple-dose AFLP markers. Mol Breed 21:511–532CrossRefGoogle Scholar
  11. Cervantes-Flores JC, Sosinski B, Pecota KV, Mwanga ROM, Catignani GL, Truong VD, Watkins RH, Ulmer MR, Yencho GC (2011) Identification of quantitative trait loci for dry-matter, starch, and β-carotene content in sweetpotato. Mol Breed 28:201–216CrossRefGoogle Scholar
  12. Chen JH, Lan JH, Wang H, Wang WW, Tian JC (2011) Genetic analysis on segregation distortion of molecular markers in wheat RIL population. J Triticeae Crop 31:407–410Google Scholar
  13. Cloutier S, Cappadocia M, Landry BS (1997) Analysis of RFLP mapping inaccuracy in Brassica napus L. Theor Appl Genet 95:83–91CrossRefGoogle Scholar
  14. Cloutier S, Ragupathy R, Niu Z, Duguid S (2011) SSR-based linkage map of flax (Linum usitatissimum L.) and mapping of QTLs underlying fatty acid composition traits. Mol Breed 28:437–451CrossRefGoogle Scholar
  15. da Silva JA, Sorrells ME (1996) Linkage análisis in polyploids using molecular markers. In: Jauhar PP (ed) Methods of genome analysis in plants. CRC Press, USAGoogle Scholar
  16. Danan S, Veyrieras JB, Lefebvre V (2011) Construction of a potato consensus map and QTL meta-analysis offer new insights into the genetic architecture of late blight resistance and plant maturity traits. BMC Plant Biol 11:1–16CrossRefGoogle Scholar
  17. Dhir SK, Oglesby J, Bhagsari AS (1998) Plant regeneration via somatic embryogenesis, and transient gene expression in sweetpotato protoplasts. Plant Cell Rep 17:665–669CrossRefGoogle Scholar
  18. FAOSTAT (2011) Food and agriculture organization of the United Nations, production statistics (
  19. Foisset N, Delourme R, Barret P, Hubert N, Landry BS, Renard M (1996) Molecular-mapping analysis in brassica napus using isozyme, RAPD and RFLF markers on a doubled-haploid progeny. Theor Appl Genet 93:1017–1025PubMedCrossRefGoogle Scholar
  20. Gebhardt C, Ritter E, Salamini F (1994) RFLP map of the potato. In: Phillips RL, Vastil IK (eds) DNA-based markers in plants. Kluwer, Dordrecht/Boston, pp 271–285CrossRefGoogle Scholar
  21. Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137:1121–1137PubMedGoogle Scholar
  22. Haanstra JPW, Wye C, Verbakel H, Meijer-Dekens F, Van Den Berg P, Odinot P, van Heusden AW, Tanksley S, Lindhout P, Peleman J (1999) An integrated high-density RFLP-AFLP map of tomato based on two Lycopersicon esculentum × L. pennellii F2 populations. Theor Appl Genet 99:254–271CrossRefGoogle Scholar
  23. Hackett CA, Broadfoot LB (2003) Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps. Heredity 90:33–38PubMedCrossRefGoogle Scholar
  24. Hermsen JG (1984) Nature, evolution and breeding of polyploids. Iowa State J Res 58:411–420Google Scholar
  25. Hwang SY, Tseng YT, Lo HF (2002) Application of simple sequence repeats in determining the genetic relationships of cultivars used in sweetpotato polycross breeding in Taiwan. Sci Hort 93:215–224CrossRefGoogle Scholar
  26. Isidore E, van Os H, Andrzejewski S, Bakker J, Barrena I, Bryan GJ, Caromel B, van Eck H, Ghareeb B, de Jong W, van Koert P, Lefebvre V, Milbourne D, Ritter E, van der Voort JR, Rousselle-Bourgeois F, van Vliet J, Waugh R (2003) Toward a marker-dense meiotic map of the potato genome: lessons from linkage group I. Genetics 165:2107–2116PubMedGoogle Scholar
  27. Jarret RL, Gawel N, Whittemore A (1992) Phylogenetic relationships of the sweetpotato [Ipomoea batatas (L.) Lam.]. J Am Soc Hort Sci 117:633–637Google Scholar
  28. Jie Q, Jiang W, Li H, Zhai H, Ma DF, Xie YP, Liu QQ (2008) Inheritance analysis and SCAR marker of the gene for stem nematode resistance in sweetpotato, Ipomoea batatas (L.) Lam. Mol Plant Breed 6:523–526Google Scholar
  29. Jie Q, Li H, Zhai H, Wang YP, Li Q, Ma DF, Xie YP, Liu QQ (2009) Development of AFLP markers linked to stem nematode resistance gene in sweetpotato (Ipomoea batatas (L.) Lam.). Chin J Agric Biotechnol 6:97–101CrossRefGoogle Scholar
  30. Jones A (1965) Cytological observations and fertility measurements of sweetpotato [Ipomoea batatas (L.) Lam.]. Proc Am Soc Hort Sci 86:527–537Google Scholar
  31. Jones A (1967) Theoretical segregation ratios of qualitatively inherited characters for hexaploid sweetpotato (Ipomoea batatas). Bull. No. 1368. USDA TechGoogle Scholar
  32. Keim P, Schupp JM, Travis SE, Clayton K, Zhu T, Shi L, Ferreira A, Webb DM (1997) A high density soybean genetic map based on AFLP markers. Crop Sci 37:537–543CrossRefGoogle Scholar
  33. Kriegner A, Cervantes JC, Burg K, Mwanga ROM, Zhang D (2003) A genetic linkage map of sweetpotato [Ipomoea batatas (L.) Lam.] based on AFLP markers. Mol Breed 11:169–185CrossRefGoogle Scholar
  34. Kubisiak TL, Nelson CD, Nance WL, Stine M (1995) RAPD linkage mapping in a long leaf pine × slash pine F1 family. Theor Appl Genet 90:1119–1127PubMedCrossRefGoogle Scholar
  35. Lacape JM, Nguyen TB, Thibivilliers S, Bojinov B, Courtois B, Cantrell RG, Burr B, Hau B (2003) A combined RFLP SSR AFLP map of tetraploid cotton based on a Gossypium hirsutum × Gossypium barbadense backcross population. Genome 46:612–626PubMedCrossRefGoogle Scholar
  36. Li XY, Ma DF, Li HM, Xie YP, Liu QC, Ma F (2003) Characterization and evaluation on breeding use of Xu 781, an advanced sweetpotato clone of high dry matter and high disease resistance. J Plant Genet Res 4:232–237Google Scholar
  37. Li AX, Liu QC, Wang QM, Zhang LM, Zhai H, Liu SZ (2010) Establishment of molecular linkage maps using SRAP markers in sweetpotato. Acta Agric Sin 36:1286–1295Google Scholar
  38. Luo HR (2004) Studies on EST-SSR markers and genetic transformation of sweetpotato (Ipomoea batatas (L.) Lam.). Dissertation. University of SichuanGoogle Scholar
  39. Ma DF, Li HM, Xie YP, Li XY, Zhu CW, Jiang XM (1997) Breeding of stem-nematode resistant varieties in sweetpotato. Crops 2:15–16Google Scholar
  40. Magoon ML, Krishnan R, Vijaya Bai K (1970) Cytological evidence on the origin of sweetpotato. Theor Appl Genet 40:360–366CrossRefGoogle Scholar
  41. Maheswaran M, Subudhi PK, Nandi S, Xu JC, Parco A, Yang DC, Huang N (1997) Polymorphism, distribution, and segregation of AFLP markers in a doubled haploid rice population. Theor Appl Genet 94:39–45PubMedCrossRefGoogle Scholar
  42. Marone D, Laido G, Gadaleta A, Colasuonno P, Ficco DBM, Giancaspro A, Giove S, Panio G, Russo MA, De Vita P, Cattivelli L, Papa R, Blanco A, Mastrangelo AM (2012) A high-density consensus map of A and B wheat genomes. Theor Appl Genet 125:1619–1638PubMedCrossRefGoogle Scholar
  43. Moreira FM, Madini A, Marino R, Zulini L, Stefanini M, Velasco R, Kozma P, Grando MS (2011) Genetic linkage maps of two interspecific grape crosses (Vitis spp.) used to localize quantitative trait loci for downy mildew resistance. Tree Genet Genomes 7:153–167CrossRefGoogle Scholar
  44. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200PubMedCrossRefGoogle Scholar
  45. Nishiyama I, Miyazaki T, Sakamoto S (1975) Evolutionary autopolyploidy in the sweetpotato (Ipomoea batatas (L.) Lam.) and its progenitors. Euphytica 24:197–208CrossRefGoogle Scholar
  46. Pérez-Vega E, Pañeda A, Rodríguez-Suárez C, Campa A, Giraldez R, Ferreira JJ (2010) Mapping of QTLs for morpho-agronomic and seed quality traits in a RIL population of common bean (Phaseolus vulgaris L.). Theor Appl Genet 120:1367–1380PubMedCrossRefGoogle Scholar
  47. Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238CrossRefGoogle Scholar
  48. Powell W, Thomas WTB, Baird E, Lawrence P, Booth A, Harrower B, McNicol JW, Waugh R (1997) Analysis of quantitative traits in barley by the use of amplified fragment length polymorphisms. Heredity 79:48–59CrossRefGoogle Scholar
  49. Ravindran V, Ravindran G, Sivakanesan R, Rajaguru SB (1995) Biochemical and nutritional assessment of tubers from 16 cultivars of sweetpotato (Ipomoea batatas L.). J Agric Food Chem 43:2646–2651CrossRefGoogle Scholar
  50. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barly: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8018PubMedCrossRefGoogle Scholar
  51. Santa-Maria M, Pecota KV, Yencho CG, Allen G, Sosinki B (2009) Rapid shoot regeneration in industrial ‘high starch’ sweetpotato (Ipomoea batatas L.) genotypes. Plant Cell Tissue Organ Cult 97:109–117CrossRefGoogle Scholar
  52. Shappley ZW, Jenkins JN, Meredith WR, McCarty JC Jr (1998) An RFLP linkage map of Upland cotton, Gossypium hirsutum L. Theor Appl Genet 97:756–761CrossRefGoogle Scholar
  53. Shiotani I, Kawase T (1989) Genomic structure of the sweetpotato and hexaploids in Ipomoea trifida (HBK) DON. Jpn J Breed 39:57–66CrossRefGoogle Scholar
  54. 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 121:731–739PubMedCrossRefGoogle Scholar
  55. Sinha S, Sharma SN (1992) Taxonomic significance of karyomorphology in Ipomoea spp. Cytologia 57:289–293CrossRefGoogle Scholar
  56. Sybenga J (1996) Chromosome pairing affinity and quadrivalent formation in polyploids: do segmental allopolyploids exist? Genome 39:1176–1184PubMedCrossRefGoogle Scholar
  57. Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27:205–233PubMedCrossRefGoogle Scholar
  58. Tanksley SD, Granal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Foulton TM, Giovannoni JJ, Grandillo S, Martin GB, Messeguer R, Miller JC, Miller L, Paterson AH, Pineda O, Röder MS, Wing RA, Wu W, Young ND (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141–1160PubMedGoogle Scholar
  59. Ting YC, Kehr AE (1953) Meiotic studies in the sweetpotato (Ipomoea batatas Lam.). J Hered 44:207–211Google Scholar
  60. Truco MJ, Antonise R, Lavelle D, Ochoa O, Kozik A, Witsenboer H, Fort SB, Jeuken MJW, Kesseli RV, Lindhout P, Michelmore RW, Peleman J (2007) A high-density, integrated genetic linkage map of lettuce (Lactuca spp.). Theor Appl Genet 115:735–746PubMedCrossRefGoogle Scholar
  61. Ubi BE, Fujimori M, Mano Y, Komatsu T (2004) A genetic linkage map of rhodesgrass based on an F1 pseudo-testcross population. Plant Breed 123:247–253CrossRefGoogle Scholar
  62. Ukoskit KT, Thompson PG (1997) Autopolyploidy versus allopolyploidy and low-density randomly amplified polymorphic DNA linkage maps of sweetpotato. J Am Soc Hort Sci 122:822–828Google Scholar
  63. van der Voort JR, Wolters P, Folkertsma R, Hutten R, van Zandvoort P, Vinke H, Kanyuka K, Bendahmane A, Jacobsen E, Janssen R, Bakker J (1997) Mapping of the cyst nematode resistance locus Gpa2 in potato using a strategy based on comigrating AFLP markers. Theor Appl Genet 95:874–880CrossRefGoogle Scholar
  64. van Eck HJ, van der Voort JR, Draaistra J, van Zandvoort P, van Enckevort E, Segers B, Peleman J, Jacobsen E, Helder J, Bakker J (1995) The inheritance and chromosomal localization of AFLP markers in a non-inbred potato offspring. Mol Breed 1:397–410CrossRefGoogle Scholar
  65. Van Ooijen JW (2004) MapQTL version 4.0 software for the mapping of quantitative trait loci in experimental populations. Kyazma, WageningenGoogle Scholar
  66. Van Ooijen JW, Voorrips RE (2001) JoinMap version 3.0 software for the calculation of genetic linkage maps. Kyazma, WageningenGoogle Scholar
  67. van Os H, Andrzejewski S, Bakker E, Barrena I, Bryan GJ, Caromel B, Ghareeb B, Isidore E, de Jong W, van Koert P, Lefebvre V, Milbourne D, Ritter E, van der Voort JNAMR, Rousselle-Bourgeois F, van Vliet J, Waugh R, Visser RGF, Bakker J, van Eck HJ (2006) Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 173:1075–1087PubMedCrossRefGoogle Scholar
  68. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78PubMedCrossRefGoogle Scholar
  69. Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414PubMedCrossRefGoogle Scholar
  70. Vuylsteke M, Mank R, Antonise R, Bastiaans E, Senior ML, Stuber CW, Melchinger AE, Lübberstedt T, Xia XC, Stam P, Zabeau M, Kuipe M (1999) Two high-density AFLP® linkage maps of Zea mays L.: analysis of distribution of AFLP markers. Theor Appl Genet 99:921–935CrossRefGoogle Scholar
  71. Young ND (1996) QTL mapping and quantitative disease resistance in plants. Annu Rev Phytopathol 34:479–501PubMedCrossRefGoogle Scholar
  72. Young WP, Schupp JM, Keim P (1999) DNA methylation and AFLP marker distribution in the soybean genome. Theor Appl Genet 99:785–790CrossRefGoogle Scholar
  73. Zang N, Zhai H, Gao S, Chen W, He SZ, Liu QC (2009) Efficient production of transgenic plants using the bar gene for herbicide resistance in sweetpotato. Sci Hort 122:649–653CrossRefGoogle Scholar
  74. Zhai H, Shang LL, Liu QC (2010) Construction of SSH cDNA library induced by ditylenchus destructor in sweetpotato and analysis of its expressed sequence tags. J Agric Biotechnol 18:141–148Google Scholar
  75. Zhang DP, Carbajulca D, Ojeda L, Rossel G, Milla S, Herrera C, Ghislain M (2001) Microsatellite analysis of genetic diversity in sweetpotato varieties from Latin America. CIP Program Report 1999–2000. International Potato Center, Lima, pp 295–301Google Scholar
  76. Zhao N, Zhai H, Yu XX, Liu ZS, He SZ, Li Q, Ma DF, Liu QC (2013) Development of SRAP markers linked to a gene for stem nematode resistance in sweetpotato, Ipomoea batatas (L.) Lam. J Integr Agric 12:414–419CrossRefGoogle Scholar
  77. Zhou Z, Wang X, Ma DF, Li HM, Xie YP, Li XY (2005) Identification of RAPD markers linked to stem-nematode resistant gene in sweetpotato. J Agric Biotechnol 13:549–552Google Scholar
  78. Zhou JQ, Guo YQ, Gao YF, Li JS, Yan JB (2011) A SSR linkage map of Maize × Teosinte F2 population and analysis of segregation distortion. Agric Sci China 10:166–174CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Ning Zhao
    • 1
  • Xiaoxia Yu
    • 1
  • Qin Jie
    • 1
  • Hui Li
    • 1
  • Hua Li
    • 1
  • Jun Hu
    • 1
  • Hong Zhai
    • 1
  • Shaozhen He
    • 1
  • Qingchang Liu
    • 1
  1. 1.Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina

Personalised recommendations