Theoretical and Applied Genetics

, Volume 109, Issue 1, pp 122–128 | Cite as

A new integrated genetic linkage map of the soybean

  • Q. J. Song
  • L. F. Marek
  • R. C. Shoemaker
  • K. G. Lark
  • V. C. Concibido
  • X. Delannay
  • J. E. Specht
  • P. B. Cregan
Original Paper


A total of 391 simple sequence repeat (SSR) markers designed from genomic DNA libraries, 24 derived from existing GenBank genes or ESTs, and five derived from bacterial artificial chromosome (BAC) end sequences were developed. In contrast to SSRs derived from EST sequences, those derived from genomic libraries were a superior source of polymorphic markers, given that the mean number of tandem repeats in the former was significantly less than that of the latter (P<0.01). The 420 newly developed SSRs were mapped in one or more of five soybean mapping populations: ‘Minsoy’ × ‘Noir 1’, ‘Minsoy’ × ‘Archer’, ‘Archer’ × ‘Noir 1’, ‘Clark’ × ‘Harosoy’, and A81-356022 × PI468916. The JoinMap software package was used to combine the five maps into an integrated genetic map spanning 2,523.6 cM of Kosambi map distance across 20 linkage groups that contained 1,849 markers, including 1,015 SSRs, 709 RFLPs, 73 RAPDs, 24 classical traits, six AFLPs, ten isozymes, and 12 others. The number of new SSR markers added to each linkage group ranged from 12 to 29. In the integrated map, the ratio of SSR marker number to linkage group map distance did not differ among 18 of the 20 linkage groups; however, the SSRs were not uniformly spaced over a linkage group, clusters of SSRs with very limited recombination were frequently present. These clusters of SSRs may be indicative of gene-rich regions of soybean, as has been suggested by a number of recent studies, indicating the significant association of genes and SSRs. Development of SSR markers from map-referenced BAC clones was a very effective means of targeting markers to marker-scarce positions in the genome.


Linkage Group Restriction Fragment Length Polymorphism Bacterial Artificial Chromosome Simple Sequence Repeat Marker Bacterial Artificial Chromosome Clone 
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 wish to thank Edward Fickus for excellent technical assistance. The financial support of the United Soybean Board (grant nos. 1243 and 2212) and the Monsanto Company is gratefully acknowledged.

Supplementary material

supp2.pdf (260 kb)
Soybean SSR information (PDF 266 KB)
supp1.pdf (192 kb)
Soybean Consensus Linkage Groups (PDF 196 KB)


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Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Q. J. Song
    • 1
  • L. F. Marek
    • 2
  • R. C. Shoemaker
    • 2
    • 3
  • K. G. Lark
    • 4
  • V. C. Concibido
    • 5
  • X. Delannay
    • 5
  • J. E. Specht
    • 6
  • P. B. Cregan
    • 1
  1. 1.Soybean Genomics and Improvement LaboratoryUSDA-ARSBeltsvilleUSA
  2. 2.Department of Agronomy, USDA-ARS-CICGIowa State UniversityAmesUSA
  3. 3.Department of AgronomyIowa State UniversityAmesUSA
  4. 4.Department of BiologyUniversity of UtahSalt Lake CityUSA
  5. 5.Monsanto CompanySt. LouisUSA
  6. 6.Department of AgronomyUniversity of NebraskaLincolnUSA

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