Theoretical and Applied Genetics

, Volume 111, Issue 6, pp 1060–1071 | Cite as

A microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae)

  • M. C. MoretzsohnEmail author
  • L. Leoi
  • K. Proite
  • P. M. Guimarães
  • S. C. M. Leal-Bertioli
  • M. A. Gimenes
  • W. S. Martins
  • J. F. M. Valls
  • D. Grattapaglia
  • D. J. Bertioli
Original Paper


Cultivated peanut (Arachis hypogaea) is an important crop, widely grown in tropical and subtropical regions of the world. It is highly susceptible to several biotic and abiotic stresses to which wild species are resistant. As a first step towards the introgression of these resistance genes into cultivated peanut, a linkage map based on microsatellite markers was constructed, using an F2 population obtained from a cross between two diploid wild species with AA genome (A. duranensis and A. stenosperma). A total of 271 new microsatellite markers were developed in the present study from SSR-enriched genomic libraries, expressed sequence tags (ESTs), and by “data-mining” sequences available in GenBank. Of these, 66 were polymorphic for cultivated peanut. The 271 new markers plus another 162 published for peanut were screened against both progenitors and 204 of these (47.1%) were polymorphic, with 170 codominant and 34 dominant markers. The 80 codominant markers segregating 1:2:1 (P<0.05) were initially used to establish the linkage groups. Distorted and dominant markers were subsequently included in the map. The resulting linkage map consists of 11 linkage groups covering 1,230.89 cM of total map distance, with an average distance of 7.24 cM between markers. This is the first microsatellite-based map published for Arachis, and the first map based on sequences that are all currently publicly available. Because most markers used were derived from ESTs and genomic libraries made using methylation-sensitive restriction enzymes, about one-third of the mapped markers are genic. Linkage group ordering is being validated in other mapping populations, with the aim of constructing a transferable reference map for Arachis.


Linkage Group Simple Sequence Repeat Marker Arachis Linkage Group Distorted Marker 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors thank Raphael FTM Oliveira, Aryanne G Amaral, and Juliana Dias for their technical assistance. This research is part of the Ph.D. Thesis of Marcio de Carvalho Moretzsohn and has been supported by the European Union: INCO-DEV, Contract ICA4-CT-2001-10072 Project “ARAMAP” and by the World Bank and EMBRAPA “The Agricultural Technology Development Project for Brazil” (PRODETAB), project 004/01/01.

Supplementary material

122_2005_28_MOESM1_ESM.xls (138 kb)
Supplementary material


  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefPubMedGoogle Scholar
  2. Barzen E, Mechelke W, Ritter E, Schulte-Kappert E, Salamini F (1995) An extended map of the sugar beet genome containing RFLP and RFLP loci. Theor Appl Genet 90:189–193Google Scholar
  3. Bennet MD, Leitch IJ (2005) Nuclear DNA amounts in angiosperms: progress, problems and prospects. Ann Bot 95:45–90CrossRefPubMedGoogle Scholar
  4. Berry ST, Leon AJ, Hanfrey CC, Challis P, Burkholz A, Barnes SJ, Rufener GK, Lee M, Caligari PDS (1995) Molecular marker analysis of Helianthus annuus L. 2. Construction of an RFLP linkage map for cultivated sunflower. Theor Appl Genet 91:195–199CrossRefGoogle Scholar
  5. Bravo JP, Hoshino AA, Angelici CMLCD, Lopes CR, Gimenes MA (2005) Analysis of genetic variability in germplasm of Arachis section Arachis by using microsatellites. Gen Mol Biol (in press)Google Scholar
  6. Burow MD, Simpson CE, Paterson AH, Starr JL (1996) Identification of peanut (Arachis hypogaea L.) RAPD markers diagnostic of root-knot nematode (Meloidogyne arenaria (Neal) Chitwood) resistance. Mol Breed 2:369–379CrossRefGoogle Scholar
  7. Burow MD, Simpson CE, Starr JL, Paterson AH (2001) Transmission genetics of chromatin from a synthetic amphidiploid to cultivated peanut (Arachis hypogaea L.): broadening the gene pool of a monophyletic polyploid species. Genetics 159:823–837PubMedGoogle Scholar
  8. Burstin J, Deniot G, Potier J, Weinachter C, Aubert G, Baranger A (2001) Microsatellite polymorphism in Pisum sativum. Plant Breed 120:311–317CrossRefGoogle Scholar
  9. Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156:847–854PubMedGoogle Scholar
  10. Castelo A, Martins WS, Gao G (2002) TROLL: tandem repeat occurrence locator. Bioinformatics J 18:634–636Google Scholar
  11. Chavarriaga-Aguirre P, Maya MM, Bonierbale MW, Kresovich S, Fregene MA, Tohme J, Kochert G (1998) Microsatellites in Cassava (Manihot esculenta Crantz): discovery, inheritance and variability. Theor Appl Genet 97:493–501Google Scholar
  12. Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice ( Oryza sativa L.). Theor Appl Genet 100:713–722Google Scholar
  13. Cordeiro GM, Casu R, McIntyre CL, Manners JM, Henry RJ (2001) Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant Sci 160:1115–1123CrossRefPubMedGoogle Scholar
  14. Creste S, Tulmann Neto A, Figueira A (2001) Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver staining. Plant Mol Biol Rep 19:299–306Google Scholar
  15. Eujayl I, Sledge MK, Wang L, May GD, Chekhovskiy K, Zwonitzer JC, Mian MAR (2004) Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. Theor Appl Genet 108:414–422PubMedGoogle Scholar
  16. Eujayl I, Sorrells ME, Baum M, Wolters P, Powell W (2002) Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor Appl Genet 104:399–407CrossRefPubMedGoogle Scholar
  17. Ferguson ME, Burow MD, Schulze SR, Bramel PJ, Paterson AH, Kresovich S, Mitchell S (2004) Microsatellite identification and characterization in peanut (A. hypogaea L.). Theor Appl Genet 108:1064–1070PubMedGoogle Scholar
  18. Gao LF, Jing RL, Huo NX, Li Y, Li XP, Zhou RH, Chang XP, Tang JF, Ma ZY, Jia JZ (2004) One hundred and one new microsatellite loci derived from ESTs (EST-SSRs) in bread wheat. Theor Appl Genet 108:1392–1400PubMedGoogle Scholar
  19. Gao LF, Tang JF, Li HW, Jia JZ (2003) Analysis of microsatellites in major crops assessed by computational and experimental approaches. Mol Breed 12:245–261CrossRefGoogle Scholar
  20. Garcia GM, Stalker HT, Kochert G (1995) Introgression analysis of an interspecific hybrid population in peanuts (Arachis hypogaea L.) using RFLP and RAPD markers. Genome 38:166–176PubMedGoogle Scholar
  21. Garcia GM, Stalker HT, Shroeder E, Kochert G (1996) Identification of RAPD, SCAR, and RFLP markers tightly linked to nematode resistance genes introgressed from Arachis cardenasii into Arachis hypogaea. Genome 39:836–845PubMedCrossRefGoogle Scholar
  22. Gimenes MA, Hoshino AA, Barbosa AVG, Palmieri DA, Bravo JP, Lopes CR (2005) Characterization and transferability of microsatellite markers from the cultivated peanut (Arachis hypogaea L.). Bot J Linn Soc (in press)Google Scholar
  23. 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
  24. Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Gen Genomics 270:315–323CrossRefGoogle Scholar
  25. Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185CrossRefGoogle Scholar
  26. Halward TM, Stalker HT, Kochert G (1993) Development of an RFLP linkage map in diploid peanut species. Theor Appl Genet 87:379–384Google Scholar
  27. Halward TM, Stalker HT, Larue EA, Kochert G (1991) Genetic variation detectable with molecular markers among unadapted germ-plasm resources of cultivated peanut and related wild species. Genome 34:1013–1020Google Scholar
  28. He G, Meng R, Newman M, Gao G, Pittman RN, Prakash CS (2003) Microsatellites as DNA markers in cultivated peanut (A. hypogaea L.). BMC Plant Biol 3:3.
  29. Herselman L, Thwaites R, Kimmins FM, Courtois B, van der Merwe PJA, Seal SE (2004) Identification and mapping of AFLP markers linked to peanut (Arachis hypogaea L.) resistance to the aphid vector of groundnut rosette disease. Theor Appl Genet 109:1426–1433PubMedGoogle Scholar
  30. Hopkins MS, Casa AM, Wang T, Mitchell SE, Dean R, Kochert GD, Kresovich S (1999) Discovery and characterization of polymorphic Simple Sequence Repeats (SSRs) in peanut. Crop Sci 39:1243–1247CrossRefGoogle Scholar
  31. Hulbert SH, Ilott TW, Legg EJ, Lincoln SE, Lander ES, Michelmore RW (1988) Genetic analysis of the fungus, Bremia lactucae, using Restriction Fragment Length Polymorphisms. Genetics 120:947–958PubMedGoogle Scholar
  32. Jenczewski E, Gherardi M, Bonnin I, Prosperi JM, Olivieri I, Huguet T (1997) Insight on segregation distortions in two intraspecific crosses between annual species of Medicago (Leguminosae). Theor Appl Genet 94:682–691Google Scholar
  33. Kantety RV, La Rota M, Matthews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501–510CrossRefPubMedGoogle Scholar
  34. Khlestkina EK, Than MH, Pestsova EG, Roder MS, Malyshev SV, Korzun V, Borner A (2004) Mapping of 99 new microsatellite-derived loci in rye (Secale cereale L.) including 39 expressed sequence tags. Theor Appl Genet 109:725–732PubMedGoogle Scholar
  35. Krapovickas A, Gregory WC (1994) Taxonomía del género Arachis (Leguminosae) Bonplandia 8:1–186Google Scholar
  36. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic maps of experimental and natural populations. Genomics 1:174–181CrossRefPubMedGoogle Scholar
  37. Li YC, Korol AB, Fahima T, Nevo E (2004) Microsatellites within genes: structure, function, and evolution. Mol Biol Evol 21:991–1007CrossRefPubMedGoogle Scholar
  38. Metzgar D, Bytof J, Wills C (2000) Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res 10:72–80PubMedGoogle Scholar
  39. Moretzsohn MC, Hopkins MS, Mitchell SE, Kresovich S, Valls JFM, Ferreira ME (2004) Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome. BMC Plant Biol 4:11.
  40. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200CrossRefPubMedGoogle Scholar
  41. Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323PubMedzbMATHADSGoogle Scholar
  42. Paik-Ro OG, Smith RL, Knauft DA (1992) Restriction fragment length polymorphism evaluation of six peanut species within the Arachis section. Theor Appl Genet 84:201–208CrossRefGoogle Scholar
  43. Palmieri DA, Hoshino AA, Bravo JP, Lopes CR, Gimenes MA (2002) Isolation and characterization of microsatellite loci from the forage species Arachis pintoi (Genus Arachis). Mol Ecol Notes 2:551–553CrossRefGoogle Scholar
  44. Palmieri DA, Bechara MD, Curi RA, Gimenes MA, Lopes CR (2005) Novel polymorphic microsatellite markers in section Caulorrhizae (Arachis, Fabaceae). Mol Ecol Notes 5:77–79CrossRefGoogle Scholar
  45. Prasad M, Varshney RK, Roy JK, Balyan HS, Gupta PK (2000) The use of microsatellites for detecting DNA polymorphism genotype identification and genetic diversity in wheat. Theor Appl Genet 100:584–592Google Scholar
  46. Provan J, Powell W, Waugh R (1996) Microsatellite analysis of relationships within cultivated potato (Solanum tuberosum). Theor Appl Genet 92:1078–1084Google Scholar
  47. Quillet MC, Madjidian N, Griveau Y, Serieys H, Tersac M, Lorieux M, Bervillé A (1995) Mapping genetic factors controlling pollen viability in an interspecific cross in Helianthus sect. Helianthus. Theor Appl Genet 91:1195–1202Google Scholar
  48. Rafalski JA, Vogel JM, Morgante M, Powel W, Andre C, Tingey SV (1996) Generating and using DNA markers in plants. In: Birren B, Lai E (eds) Analysis of non-mammalian genomes — a practical guide. Academic, New York, pp 75–134Google Scholar
  49. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning — A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, New YorkGoogle Scholar
  50. Scott KD, Eggler P, Seaton G, Rosetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726CrossRefGoogle Scholar
  51. Song QJ, Marek LF, Shoemaker RC, Lara KG, Concibido VC, Delannay X, Specht JE, Cregan PB (2004) A new integrated genetic linkage map of the soybean. Theor Appl Genet 109:122–128CrossRefPubMedGoogle Scholar
  52. Staden R, Judge DP, Bonfield JK (2003) Managing sequencing projects in the GAP4 environment. In: Krawetz SA, Womble DD (eds) Introduction to Bioinformatics. A Theoretical and practical approach. Human Press Inc, TotawaGoogle Scholar
  53. Tian AG, Wang J, Cui P, Han YJ, Xu H, Cong LJ, Huang XG, Wang XL, Jiao YZ, Wang BJ, Wang YJ, Zhang JS, Chen SY (2004) Characterization of soybean genomic features by analysis of its expressed sequence tags. Theor Appl Genet 108:903–913CrossRefPubMedGoogle Scholar
  54. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422PubMedGoogle Scholar
  55. Thomas MR, Scott NS (1993) Microsatellite repeats in grapevine reveal DNA polymorphisms when analyzed as sequence-tagged sites (STSs). Theor Appl Genet 86:985–990Google Scholar
  56. Udupa SM, Robertson LD, Weigand F, Baum M, Kahl G (1999) Allelic variation at (TAA)n microsatellite loci in a world collection of chickpea (Cicer arietinum L.) germplasm. Mol Gen Genet 261:354–363CrossRefPubMedGoogle Scholar
  57. Varshney RK, Thiel T, Stein N, Langridge P, Graner A (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 7:537–546PubMedGoogle Scholar
  58. Wang Z, Weber JL, Zhong G, Tanksley SD (1994) Survey of plant short tandem DNA repeats. Theor Appl Genet 88:1–6Google Scholar
  59. Weber JL (1990) Informativeness of human (dC-dA)n (dG-dT)n polymorphisms. Genomics 7:524–530CrossRefPubMedGoogle Scholar
  60. Young ND, Weeden NF, Kochert G (1996) Genome mapping in legumes (Family Fabaceae). In: Paterson AH (ed) Genome mapping in plants. RG Landes, Austin, TXGoogle Scholar

Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • M. C. Moretzsohn
    • 1
    • 2
    Email author
  • L. Leoi
    • 3
  • K. Proite
    • 1
    • 2
  • P. M. Guimarães
    • 1
  • S. C. M. Leal-Bertioli
    • 1
  • M. A. Gimenes
    • 4
  • W. S. Martins
    • 5
  • J. F. M. Valls
    • 1
  • D. Grattapaglia
    • 1
    • 2
    • 3
  • D. J. Bertioli
    • 3
  1. 1.Embrapa Recursos Genéticos e BiotecnologiaBrasíliaBrazil
  2. 2.Departamento de Biologia CelularIB - Universidade de Brasília (UnB)BrasíliaBrazil
  3. 3.Universidade Católica de BrasíliaBrasíliaBrazil
  4. 4.Departamento de GenéticaIB-UNESP BotucatuBrazil
  5. 5.Departamento de Ciência da ComputaçãoUniversidade Católica de GoiásGoiâniaBrazil

Personalised recommendations