, Volume 194, Issue 1, pp 67–78 | Cite as

Marker-assisted versus phenotypic selection for iron-deficiency chlorosis in soybean

  • C. M. Lamkey
  • T. C. Helms
  • R. J. Goos


Iron-deficiency chlorosis (IDC) is an important agronomic trait when soybean (Glycine max (L.) Merr.) is planted on calcareous soil. Breeders need confirmation that marker-QTL (quantitative trait loci) associations developed using association mapping, will be effective in a different set of genotypes than the ones used to identify those markers. Marker-QTL associations that had previously been identified in separate mapping experiments were evaluated. Marker-assisted selection (MAS) was compared to phenotypic selection (PS) to evaluate the association mapping approach to identifying markers. The PS or MAS criteria were used to select the 20 most IDC-tolerant and IDC-susceptible lines, based on three 2009 selection sites. Three sites in 2010 were used as validation to compare the effectiveness of the different selection criteria. A random sample (RS) was generated as a control. When validation was conducted averaged across three 2010 sites, PS was the best method to select for IDC with a mean of 1.78, compared to MAS with a mean of 2.05. Since PS was so effective the process of genotyping, which is required for MAS, was unnecessary. The additive effects of QTL that had been estimated from the original mapping experiments were biased upward when compared to QTL effects estimated from the 2009 data. Also, many markers in the target population of experimental lines did not have a gene frequency of 0.5, which greatly reduced the effectiveness of MAS.


Breeding Molecular markers Soybean 


  1. Beavis WD (1994) The power and deceit of QTL experiments: lessons from comparative QTL studies. Proceeding of the 49th annual corn and sorghum research Conference. Am Seed Trade Asso 49:250–265Google Scholar
  2. Charlson DV, Cianzio SR, Shoemaker RC (2003) Associating SSR markers with soybean resistance to iron deficiency chlorosis. J Plant Nutr 26:2267–2276CrossRefGoogle Scholar
  3. Charlson DV, Bailey TB, Cianzio SR, Shoemaker RC (2005) Molecular marker Satt481 is associated with iron-deficiency chlorosis resistance in a soybean breeding population. Crop Sci 45:2394–2399CrossRefGoogle Scholar
  4. Cockram J, White J, Leigh FJ, Lea VJ, Chiapparino E, Laurie DA, Mackay IJ, Powell W, O’Sullivan DM (2008) Association mapping of partitioning loci in barley. BMC Genet 9:16–29PubMedCrossRefGoogle Scholar
  5. Davies J, Berzonsky WA, Leach GD (2006) A comparison of marker-assisted and phenotypic selection for high grain protein content in spring wheat. Euphytica 152:117–134CrossRefGoogle Scholar
  6. Dudley JW (1993) Molecular markers in plant improvement: manipulation of genes affecting quantitative traits. Crop Sci 33:660–668CrossRefGoogle Scholar
  7. Falconer DS, Mackay TFC (1996) Introduction to quantitative genetics, 4th edn. The Longman Group Ltd, EssexGoogle Scholar
  8. Fazio G, Chung SM, Staub JE (2003) Comparative analysis of response to phenotypic and marker-assisted selection for multiple lateral branching in cucumber (Cucumis sativus L.). Theor Appl Genet 107:875–883PubMedCrossRefGoogle Scholar
  9. Fehr WR, and Caviness CE (1977) Stages of soybean development. Iowa State Univ. Spec. Rep. 80. Iowa State Univ., AmesGoogle Scholar
  10. Flint-Garcia SA, Darrah LL, McMullen MD, Hibbard BE (2003) Phenotypic versus marker-assisted selection for stalk strength and second generation European corn borer resistance in maize. Theor Appl Genet 107:1331–1336PubMedCrossRefGoogle Scholar
  11. Franzen DW, Richardson JL (2000) Soil factors affecting iron chlorosis of soybean in the Red River valley of North Dakota and Minnesota. J Plant Nutr 23:67–78CrossRefGoogle Scholar
  12. Froehlich DM, Fehr WR (1981) Agronomic performance of soybeans with differing levels of iron deficiency chlorosis on calcareous soil. Crop Sci 21:438–441CrossRefGoogle Scholar
  13. Goos RJ, Johnson B (2001) Seed treatment, seeding rate, and cultivar effects on iron deficiency chlorosis of soybean. J Plant Nutr 24:1255–1268CrossRefGoogle Scholar
  14. Helms TC, Scott RA, Schapaugh WT, Goos RJ, Franzen DW, Schlegel AJ (2010) Soybean iron-deficiency chlorosis tolerance and yield decrease on calcareous soils. Agron J 102:492–498CrossRefGoogle Scholar
  15. Inskeep WP, Bloom PR (1984) A comparative study of soil solution chemistry associated with chlorotic and nonchlorotic soybeans in western Minnesota. J Plant Nutr 7:513–531CrossRefGoogle Scholar
  16. Keim P, Shoemaker RC (1988) A rapid protocol for isolating soybean DNA. Soybean Genet Newslett 15:150–152Google Scholar
  17. Lamkey CM (2011) Phenotypic versus marker assisted selection for tolerance to iron deficiency chlorosis in soybean. M.S. Thesis, North Dakota State University Fargo, NDGoogle Scholar
  18. Lin S, Cianzio S, Shoemaker R (1997) Mapping genetic loci for iron deficiency chlorosis in soybean. Mol Breeding 3:219–229CrossRefGoogle Scholar
  19. Lin SF, Baumer J, Ivers D, Cianzio S, Shoemaker R (2000a) Nutrient solution screening of Fe chlorosis resistance in soybean evaluated by molecular characterization. J Plant Nutr 23:1915–1928CrossRefGoogle Scholar
  20. Lin SF, Grant D, Cianzio S, Shoemaker R (2000b) Molecular characterization of iron deficiency chlorosis in soybean. J Plant Nutr 23:1929–1939CrossRefGoogle Scholar
  21. Mamidi S, Chikara S, Goos RJ, Hyten DL, Annam D, Moghaddam SM, Lee RK, Cregan PB, McClean PE (2011) Genome-wide association analysis identifies candidate genes associated with iron deficiency chlorosis in soybean. The Plant Genome 4:154–164CrossRefGoogle Scholar
  22. Robbins MD, Staub JE (2009) Comparitive analysis of marker-assisted and phenotypic selection for yield components in cucumber. Theor Appl Genet 119:621–634PubMedCrossRefGoogle Scholar
  23. SAS Institute (2004) SAS STAT 9.1 User’s Guide, Volume 3. SAS Institute, Cary, N.CGoogle Scholar
  24. Stromberg LD, Dudley JW, Rufener GK (1994) Comparing conventional early generation selection with molecular marker-assisted selection in maize. Crop Sci 34:1221–1225CrossRefGoogle Scholar
  25. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielson D, Buckler ES IV (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289PubMedCrossRefGoogle Scholar
  26. Van Berloo R, Stam P (1999) Comparison between marker-assisted selection and phenotypical selection in a set of Arabidopsis thaliana recombinant inbred lines. Theor Appl Genet 98:113–118CrossRefGoogle Scholar
  27. Wang J, McClean PE, Lee R, Goos RJ, Helms T (2008) Association mapping of iron deficiency chlorosis loci in soybean (Glycine max L. Merr.) advanced breeding lines. Theor Appl Genet 116:777–787PubMedCrossRefGoogle Scholar
  28. Willcox MC, Khairallah MM, Bergvinson D, Crossa J, Deutsch JA, Edmeades GO, Gonzalez-de-Leon D, Jiang C, Jewell DC, Mihm JA, Williams WP, Hoisington D (2002) Selection for resistance to southwestern corn borer using marker-assisted and conventional backcrossing. Crop Sci 42:1516–1528CrossRefGoogle Scholar
  29. Yousef GG, Juvik JA (2001) Comparison of phenotypic and marker-assisted selection for quantitative traits in sweet corn. Crop Sci 41:645–655CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.Department of Agronomy and HorticultureUniversity of Nebraska, LincolnLincolnUSA
  2. 2.Department 7670NDSUFargoUSA
  3. 3.Department 7680NDSUFargoUSA

Personalised recommendations