Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 16, 2006
Publication Date: January 30, 2007
Citation: Yoon, M.S., Song, Q.J., Choi, I.K., Specht, J.E., Cregan, P.B. 2007. Barcsoysnp23: a selected panel of snps for soybean cultivar identification. Theoretical and Applied Genetics. 114:885-899.
Interpretive Summary: For many decades soybean cultivars have been distinguished from one another using various morphological, pigmentation and biochemical traits. However, as the number of cultivars has increased, the circumstances whereby new cultivars are not distinguishable based upon these traits have increased. We analyzed 96 modern soybean cultivars from the U.S. and Korea with 58 single nucleotide polymorphism (SNP) DNA markers and developed an approach to select a subset of 23 markers that produced DNA fingerprints that were extremely efficient in distinguishing the 96 cultivars. Furthermore, this set of 23 SNP DNA markers readily distinguished an additional set of 36 cultivars that were completely indistinguishable based upon standard morphological and pigmentation traits. This set of 23 SNP markers will be useful to plant breeders who need to develop unique DNA fingerprints of newly developed soybean cultivars for purposes of obtaining Plant Variety Protection.
This report describes a set of 23 informative SNPs (BARCSoySNP23) distributed on 19 of the 20 soybean linkage groups that can be used for soybean cultivar identification. Selection of the set was made based upon the linkage map position of each SNP as well as the information provided by each SNP for distinguishing a diverse set of soybean genotypes. The genotypes included the ancestors of North American cultivars, modern North American cultivars, and a group of Korean cultivars. The procedure used to identify this subset of highly informative SNP markers resulted in a significant increase in the power of identification versus any other randomly selected set of equal number. This conclusion was supported by a simulation which indicated that the panel can uniquely distinguish 2200 soybean cultivars; in contrast, sets of 23 randomly selected SNPs which on average allowed the unique identification of only 50 cultivars. The panel can efficiently distinguish each of the genotypes within four sets of additional cultivars/lines with identical classical pigmentation and morphological traits. In comparison with the results from13 selected trinucleotide SSRs (BARCSoySSR13) in identifying 132 genotypes, the information provided by each SNP in BARCSoySNP23 was generally low, however, the analysis of bi-allelic SNP loci permits the rapid assay of many SNP loci, thereby compensating for their relatively low information content. Both BARCSoySNP23 and BARCSoySSR13 were highly consistent in identifying genotypes and estimating population genetic differences.