A selected set of trinucleotide simple sequence repeat markers for soybean cultivar identification

Q. J. Song, C. V. Quigley, R. L. Nelson, T. E. Carter, H. R. Boerma, J. L. Strachan, P. B. Cregan

Research output: Contribution to journalArticlepeer-review


Soybean [Glycine max (L.) Merr.] cultivars are described for purposes of Plant Variety Protection (PVP) by standard pigmentation and morphological traits. However, many commercial soybeans arise from a limited number of elite lines and are often indistinguishable based on these traits. A system based on DNA markers could provide unique DNA profiles or fingerprints of cultivars. Simple Sequence Repeat (SSR) or microsatellite allele size profiling is used in human forensics to provide unique DNA fingerprints of an individual. Allele sizing technologies are well established and can be readily used to size SSR alleles from any organism. The purpose of the work presented here was to select and evaluate a small set of trinucleotide SSR markers with maximum reliability and repeatability that would provide a high level of discriminatory power to distinguish soybean genotypes. A total of 48 fluorescently labelled SSR primer sets was used to amplify genomic DNA of the 35 ancestors of N. American soybeans as well as a diverse group of elite N. American soybean cultivars. Only loci with allele size ranges that showed no overlap in size over a series of analyses and in which adjacent alleles differed by at least three basepairs were maintained for further statistical analysis via a clustering procedure. Cluster analysis was performed on the remaining loci and resulted in the identification of a subset of 13 loci, from 12 different linkage groups, that easily produced unique SSR allele size profiles for each of the 66 elite N. American soybean cultivars. This set of 13 loci was used to characterise four independent sets of elite cultivars that were selected based upon identical maturity, morphological, and pigmentation traits. Based upon these analyses, all cultivars could be distinguished using the set of 13 selected SSR loci. This set of loci is proposed as a standard set for use in DNA profiling of soybean cultivars for purposes of obtaining PVP.

Original languageEnglish (US)
Pages (from-to)207-220
Number of pages14
JournalPlant Varieties and Seeds
Issue number3
StatePublished - 1999

ASJC Scopus subject areas

  • Plant Science
  • Horticulture


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