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United States Department of Agriculture

Agricultural Research Service

An Integrated Genetic Linkage Map of the Soybean
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March 2007

Soymap Link

Firefox and Safari users must download the Excel version of the SoyMap

The most recent published version of the soybean transcript map is located at this website.  In addition, a map is now being prepared that will contain 3792 Single Nucleotide Polymorphism (SNP) markers, 1009 Simple Sequence Repeat (SSR) markers and 664 Restriction Fragment Length Polymorphism (RFLP) markers.



Newly developed SSRs were mapped in one or more of the five soybean populations: Minsoy × Noir 1, Minsoy × Archer, Noir 1× Archer, Clark × Harosoy, and A81-356022 × PI468916. A JoinMap analysis resulted in a map with 20 linkage groups containing a total of 1849 markers, including 1015 SSRs, 709 RFLPs, 73 RAPDs, 23 classical traits and 29 others. Among these, 417 were new SSRs to the maps constructed by Cregan et al. (1999a). Two hundred of these new loci were developed in collaboration with the Monsanto Co. From 12 to 29 new SSR markers were added to each linkage group. Of the newly developed markers, 90 were positioned to 30 of the 36 gaps of 20 cM or more that had existed in the previous version of the map (Cregan et al. 1999).

Mapping populations:

Five widely used soybean mapping populations were used for SSR positioning:

USDA/Iowa State University Population (MS). This is a F2-derived mapping population from the interspecific cross of the A81-356022 (G. max) and PI468.916 (G. soja). The population consists of 59 F2 plant derivatives and has been described in detail (Keim et al. 1990; Shoemaker and Specht, 1995; Shoemaker and Olson, 1988).
Three Recombinant Inbred Line Populations from the University of Utah: These were derived by single seed descent from crosses of 'Minsoy' by 'Noir 1' (MN); Minsoy by 'Archer' (MA); and Noir 1 by Archer (NA). The MN, MA, and NA consist of 240, 233 and 240 F7-derived RILs, respectively, and have been described previously by Mansur et al. (1995, 1996).
University of Nebraska Population. (CH): This population is derived from the cross of near isogenic lines (NILs) of the important cultivars Clark and Harosoy. The population was used for mapping of classical genetic along with molecular loci. The population consists of derivatives of 57 F2 plants and previously was described by Shoemaker and Specht (1995).

DNA, Isozyme and Classical Markers:
Data sets containing 1017 SSR, 749 RFLP, 13 AFLP, 90 RAPD, 10 isozyme, and 30 classical markers mapped in at least one of the five populations CH, MS, MA, MN and NA were used for map integration. These include data of 598 SSR, 652 RFLP, 73 RAPD, 9 isozyme, and 24 other markers which were previously reported by Cregan et al. (1999) in at least one of three populations: MS, MN, and CH.

Linkage map construction:
An integrated linkage map of soybean based on the principle described by Stam (1993) was constructed. Integration of the data sets was performed using the JoinMap 3.0 program (Van Ooijen and Voorrips 2001). Initially, LOD scores and pairwise recombination frequencies between markers were calculated. A LOD of 5.0 was used to create groups in the MS, MA, NA populations and LOD 4.0 in the MN and CH populations. The map of each linkage group was then integrated. Recombination values were converted to genetic distances using the Kosambi mapping function. The linkage groups were named according to common markers shown on the map described by Cregan et al. (1999).


Cregan PB, Jarvik T, Bush AL, Shoemaker RC, Lark KG, Kahler AL, Kaya N, VanToai TT, Lohnes DG, Chung J, Specht JE (1999) An integrated genetic linkage map of the soybean. Crop Sci. 39:1464-1490.

Keim P, Diers BW, Olson TC, and Shoemaker RC (1990) RFLP mapping in soybean: association between marker loci and variation in quantitative traits. Genetics 126:735-742.

Mansur, LM, Orf JH, Chase K, Jarvik T, Cregan PB, Lark KG (1996) Genetic mapping of agronomic traits using recombinant inbred lines of soybean. Crop Sci. 36:1327-1336.

Mansur, LM and Orf J (1995) Evaluation of soybean recombinant inbreds for agronomic performance in northern USA and Chile. Crop Sci. 35:422-425.

Shoemaker, RC and Olson TC (1993) Molecular linkage map of soybean (Glycine max L. Merr.). p. 6.131-6.138. In O’Brien SJ (ed.) Genetic maps: Locus maps of complex genomes. Cold Spring Harbor Laboratory Press, New York.

Shoemaker, RC and Specht JE (1995) Integration of the soybean molecular and classical genetic linkage groups. Crop Sci. 35:436-446.

Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. The Plant Journal 3(5):739-744.

Van Ooijen, JW and Voorrips RE (2001) JoinMap 3.0 software for the calculation of genetic linkage maps. Plant Research Internation, Wageningen, the Netherlands.

Last Modified: 1/31/2012
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