Submitted to: Theoretical and Applied Genetics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 12/20/2003
Publication Date: 12/20/2003
Citation: Song, Q.J., Marek, L.F., Shoemaker, R.C., Lark, K.G., Consibido, V.C., Delannay, X., Specht, J.E., Cregan, P.B. 2003. A new integrated genetic linkage map of the soybean. Theoretical and Applied Genetics. v. 109. p. 122-128. Interpretive Summary: DNA markers serve as genetic landmarks and are interspersed among the 50,000 or more genes throughout the chromosomes (also know as the genome) of the soybean. If a marker is located near a gene of interest, the marker can be used to select for the desired form of the gene. For example, the soybean breeder can use a DNA marker to identify plants that carry the form of the gene that gives resistance to a disease rather than the form that leads to susceptibility. It was the objective of this work to report the genome map position of 391 new DNA markers of a type called "simple sequence repeat" or SSR markers, so as to make these DNA markers available to the soybean research community. Many of the SSR markers were developed with the express purpose of positioning new markers in 'gaps' in the previous version of the genome map that we published in 1999. The resulting map has a total of 1849 genetic markers with only two small gaps in which no SSR marker is present. This new version of the SSR-based soybean genome map will greatly improve the ability to define the genome position of genes that control soybean traits of interest. Furthermore, the markers on the new genome map will be of use in 'marker assisted selection' to identify soybean breeding lines that possess improved characteristics. The new and augmented version of the soybean genome map will be of particular use to soybean geneticists and soybean breeders.
Technical Abstract: 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 BAC-end sequences were developed. In contrast to SSRs derived from EST sequence, 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 2523.6 cM of Kosambi map distance across 20 linkage groups that contained1849 markers, including 1015 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.