Journal of Science Education and Technology

, Volume 18, Issue 1, pp 48–59 | Cite as

Gene Polymorphism Studies in a Teaching Laboratory



I present a laboratory procedure for illustrating transcription, post-transcriptional modification, gene conservation, and comparative genetics for use in undergraduate biology education. Students are individually assigned genes in a targeted biochemical pathway, for which they design and test polymerase chain reaction (PCR) primers. In this example, students used genes annotated for the steroid biosynthesis pathway in soybean. The authoritative Kyoto encyclopedia of genes and genomes (KEGG) interactive database and other online resources were used to design primers based first on soybean expressed sequence tags (ESTs), then on ESTs from an alternate organism if soybean sequence was unavailable. Students designed a total of 50 gene-based primer pairs (37 soybean, 13 alternative) and tested these for polymorphism state and similarity between two soybean and two pea lines. Student assessment was based on acquisition of laboratory skills and successful project completion. This simple procedure illustrates conservation of genes and is not limited to soybean or pea. Cost per student estimates are included, along with a detailed protocol and flow diagram of the procedure.


Undergraduate Genes Genetics PCR EST Soybean Comparative genetics Exons 



Expressed sequence tag


Kyoto encyclopedia of genes and genomes


National center for biotechnology information


Polymerase chain reaction


Randomly amplified polymorphic DNA


Untranslated region



I gratefully acknowledge Jeffry Ray and James Smith from the United States Department of Agriculture (Stoneville, MS) for the provision of soybean DNA and Clarice Coyne, also from the USDA (Pullman, WA) for the provision of Pea DNA. I also wish to thank Jeffrey Yule for critical review of the manuscript. The continued support of the Louisiana Tech University College of Applied and Natural Sciences and the Student Technology Fee Board is greatly appreciated.

Supplementary material

10956_2008_9131_MOESM1_ESM.doc (1.5 mb)
MOESM1 (DOC 1529 kb)
10956_2008_9131_MOESM2_ESM.doc (1016 kb)
MOESM2 (DOC 1015 kb)
10956_2008_9131_MOESM3_ESM.doc (286 kb)
MOESM3 (DOC 286 kb)


  1. Choi IY, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, Chase K, Lark KG, Reiter RS, Yoon MS, Hwang EY, Yi SI, Young ND, Shoemaker RC, van Tassell CP, Specht JE, Cregan PB (2007) A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176:685–696CrossRefGoogle Scholar
  2. CIRTL (2008) Center for the integration of research, teaching and learning [Online]. Verified 02 October
  3. GRIN (2008) Germplasm resources information network.
  4. Handelsman J, Ebert-May D, Beichner R, Bruns P, Chang A, DeHaan R, Gentile J, Lauffer S, Stewart J, Tilghman SM, Wood WB (2004) Education, scientific teaching. Science 304:521–522. doi: 10.1126/science.1096022 CrossRefGoogle Scholar
  5. Lee SH, Walker DR, Cregan PB, Boerma HR (2004) Comparison of four flow cytometric SNP detection assays and their use in plant improvement. Theor Appl Genet 110:167–174CrossRefGoogle Scholar
  6. Mendel G (1865) Experiments in plant hybridization. Read at the meetings of February 8th, and March 8th, 1865, Brünn Natural History SocietyGoogle Scholar
  7. NASS (2007) Crop values 2006 summary.
  8. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Humana Press, Totowa, NJGoogle Scholar
  9. SALG (2008) Student assessment of their learning gains [Online]. Verified 02 October
  10. Shoemaker RC, Polzin K, Labate J, Specht J, Brummer EC, Olson T, Young N, Concibido V, Wilcox J, Tamulonis JP, Kochert G, Boerma HR (1996) Genome duplication in soybean (Glycine subgenus soja). Genetics 144:329–338Google Scholar
  11. Shultz JL, Ray JD, Lightfoot DA (2007a) A sequence based synteny map between soybean and Arabidopsis thaliana. BMC Genomics 8:8. doi: 10.1186/1471-2164-8-8 CrossRefGoogle Scholar
  12. Shultz JL, Kazi S, Bashir R, Afzal JA, Lightfoot DA (2007b) The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. Theor Appl Genet 114:1081–1090. doi: 10.1007/s00122-007-0501-9 CrossRefGoogle Scholar
  13. Shultz JL, Ray JD, Smith JR (2008) Mapping two genes in the purine metabolism pathway of soybean. DNA Seq 19:264–269. doi: 10.1080/10425170701607522 CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  1. 1.School of Biological SciencesLouisiana Tech UniversityRustonUSA

Personalised recommendations