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a USDA-ARS, Soybean and Alfalfa Research Lab., Beltsville, MD 20705 USA
b Dep. of Biology, Univ. of Utah, Salt Lake City, UT 84112 USA
c USDA-ARS-CICG, Dep. of Agronomy, Iowa State Univ., Ames, IA 50011 USA
d Biogenetic Services Inc., 801 32 Ave., Brookings, SD 57006 USA
e Yuzuncu Yil Univ., College of Agriculture, 65080-Van, Turkey
f USDA-ARS, Soil Drainage Unit, 590 Woody Hayes Drive, Columbus, OH 43210 USA
g Dep. of Horticulture and Crop Science, The Ohio State Univ. and the Ohio Agric. Res. and Dev. Center, Wooster, OH 44691 USA
h Dep. of Agronomy, Gyeong Sang National Univ., Chinju, South Korea 660-701
i Dep. of Agronomy, Univ. Nebraska, Lincoln, NE 68583-0915 USA
pcregan{at}nal.usda.gov
A number of molecular genetic maps of the soybean [Glycine max (L.) Merr.] have been developed over the past 10 yr. These maps are primarily based on restriction fragment length polymorphism (RFLP) markers. Parental surveys have shown that most RFLP loci have only two known alleles. However, because the soybean is an ancient polyploid, RFLP probes typically hybridize and map to more than one position in the genome. Thus, the polymorphic potential of an RFLP probe is primarily a function of the frequency of the two alleles at each locus the probe detects. In contrast, simple sequence repeat (SSR) markers are single locus markers with multiple alleles. The polymorphic potential of an SSR marker is dependent on the number of alleles and their frequencies. Single locus markers provide an unambiguous means of defining linkage group homology across mapping populations. The objective of the work reported here was to develop and map a large set of SSR markers. A total of 606 SSR loci were mapped in one or more of three populations: the USDA/Iowa State G. max x G. soja F2 population, the Univ. of Utah Minsoy x Noir 1 recombinant inbred population, and the Univ. of Nebraska Clark x Harosoy F2 population. Each SSR mapped to a single locus in the genome, with a map order that was essentially identical in all three populations. Many SSR loci were segregating in two or all three populations. Thus, it was relatively simple to align the 20+ linkage groups derived from each of the three populations into a consensus set of 20 homologous linkage groups presumed to correspond to the 20 pairs of soybean chromosomes. On the basis of in situ segregation or linkage reports in the literature all but one of the classical linkage groups can now be assigned to a corresponding molecular linkage group.
Abbreviations: AFLP, amplified fragment length polymorphism • BAC, bacterial artificial chromosome • CLG, classical linkage group • cM, centimorgan • MLG, molecular linkage group • NIL, near isogenic line • PCR, polymerase chain reaction • QTL, quantitative trait loci • RAPD, random amplified polymorphic DNA • RIL, recombinant inbred line • RFLP, restriction fragment length polymorphism • SSR, simple sequence repeat
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