References for Markers-Assisted Selection

(Note: not all of these references are cited in the lesson)

Beavis, W.D. 1998. QTL analysis: Power, precision, and accuracy. pp. 145-161. In A.H. Paterson (ed.) Molecular dissection of complex traits. CRC Press, Boca Raton, FL.

Bonnett, D.G., G.J. Rebetzke, and W. Spielmeyer. 2005. Strategies for efficient implementation of molecular markers in wheat breeding. Mol. Breeding 15:75-85.

Castro, A.J., F. Capettini, A.E. Corey, T. Filichkina, P.M. Hayes, A. Kleinhofs, D. Kudrna, K. Richardson, S. Sandoval-Islas, C. Rossi, and H. Vivar. 2003. Mapping and pyramiding of qualitative and quantitative resistance to stripe rust in barley. Theor. Appl. Genet. 107:922-930.

Concibido, V.C., B. La Vallee, P. Mclaird, N. Pineda, J. Meyer, L. Hummel, J. Yang, K. Wu, and X. Delannay. 2003. Introgression of a quantitative trait locus for yield from Glycine soja into commercial soybean cultivars. Theor. Appl. Genet. 106:575-582.

Concibido, V.C., R.L. Denny, D.A. Lange, J.H. Orf, and N.D. Young. 1996. RFLP mapping and marker-assisted selection of soybean cyst nematode resistance in PI 209332. Crop Sci. 36:1643-1650.

Dreher, K., M. Khairallah, J.M. Ribaut, and M. Morris. 2003. Money matters (I): Costs of field and laboratory procedures associated with conventional and marker-assisted maize breeding at CIMMYT. Molecular Breeding 11:221-234.

Ellis, M.H., W. Spielmeyer, K.R. Gale, G.J. Rebetzke, and R.A. Richards. 2002. 'Perfect' markers for the Rht-B1b and Rht-D1b dwarfing genes in wheat. Theor. Appl. Genet. 105:1038-1042.

Flint-Garcia, S.A., L.L. Darrah, M.D. McMullen, and B.E. Hibbard. 2003. Phenotypic versus marker-assisted selection for stalk strength and second-generation European corn borer resistance in maize. Theor. Appl. Genet. 107:1331-1336.

Frisch, M., and A.E. Melchinger. 2001. Marker-assisted backcrossing for introgression of a recessive gene. Crop Sci. 41:1485-1494.

Frisch, M., M. Bohn, and A.E. Melchinger. 1999a. Minimum sample size and optimal positioning of flanking markers in marker-assisted backcrossing for transfer of a target gene. Crop Sci. 39:967-975.

Frisch, M., M. Bohn, and A.E. Melchinger. 1999b. Comparison of selection strategies for marker-assisted backcrossing of a gene. Crop Sci. 39:1295-1301. (See also Errata, Frisch et al., 1999. Crop Sci. 39:1903.)

Hernandez, P., A. Martin, and G. Dorado. 1999. Development of SCARs by direct sequencing of RAPD products: a practical tool for the introgression and marker-assisted selection of wheat. Molecular Breeding 5:245-253.

Hospital, F. 2003. Marker-assisted breeding. pp. 30-59. In H.J. Newbury (ed.) Plant molecular breeding. Blackwell Publishing and CRC Press, Oxford and Boca Raton.

Jefferies, S.P., B.J. King, A.R. Barr, P. Warner, S.J. Logue, and P. Langridge. 2003. Marker-assisted backcross introgression of the Yd2 gene conferring resistance to barley yellow dwarf virus in barley. Plant Breeding 122:52-56.

Kearsey, M.J., and A.G.L. Farquhar. 1998. QTL analysis in plants; where are we now? Heredity 80:137-142.

Knapp, S. 1998. Marker-assisted selection as a strategy for increasing the probability of selecting superior genotypes. Crop Science 38:1164-1174.

Knight, J. 2003. Crop improvement: A dying breed. Nature 421:568-570.

Michelmore, R.W., I. Paran, and R.V. Kesseli. 1991. Identification of markers linked to disease-resistance genes by bulked segregant analysis: A rapid method to detect markers in specific genomic regions by using segregating populations. Proc. Natl. Acad. Sci. USA. 88:9828-9832.

Morgante, M., and F. Salamini. 2003. From plant genomics to breeding practice. Current Opinion in Biotechnology 14:214-219.

Morris, M., K. Dreher, J.M. Ribaut, and M. Khairallah. 2003. Money matters (II): Costs of maize inbred line conversion schemes at CIMMYT using conventional and marker-assisted selection. Molecular Breeding 11:235-247.

Peleman, J.D., and J. R. van der Voort. 2003. Breeding by design. Trends in Plant Science 8:330-334.

Peng, J.H., T. Fahima, M. S. Röder, Y. C. Li, A. Grama, and E. Nevo. 2000. Microsatellite high-density mapping of the stripe-rust resistance gene YrH52 region on chromosome 1B and evaluation of its marker-assisted selection in the F2 generation in wild emmer wheat. New Phytologist 146:141-154.

Podlich, D.W., C.R. Winkler, M. Cooper. 2004. Mapping as you go: An effective approach for marker-assisted selection of complex traits. Crop Sci. 44:1560-1571.

Ribaut, J. M., and D. Hoisington. 1998. Marker-assisted selection: new tools and strategies. Trends in Plant Science 3:236-238.

Ribaut, J.M., X.Y. Hu, D. Hoisington, D. Gonzalez-de-Leon. 1997. Use of STSs and SSRs as rapid and reliable preselection tools in a marker-assisted selection-backcross scheme. Plant Molecular Biology Reporter15:154-162.

Robert, V.J.M., M.A.L. West, S. Inai, A. Caines, L. Arntzen, J.K. Smith, and D.A. St Clair. 2001. Marker-assisted introgression of blackmold resistance QTL alleles from wild Lycopersicon cheesmanii to cultivated tomato (L. esculentum) and evaluation of QTL phenotypic effects. Molecular Breeding 8:217-233.

Smith, S., and W. Beavis. 1996. Molecular marker assisted breeding in a company environment. pp. 259-272. In B.W.S. Sobral (ed.) The impact of plant molecular genetics. Birkhauser, Boston.

Thomas, W.T.B. 2003. Prospects for molecular breeding of barley. Ann. Appl. Biol. 142:1-12.

Toojinda, T., E. Baird, A. Booth, L. Broers, P. Hayes, W. Powell, W. Thomas, H. Vivar, and G. Young. 1998. Introgression of quantitative trait loci (QTLs) determining stripe rust resistance in barley: an example of marker-assisted line development. Theor. Appl. Genet. 96:123-131.

Xu, Y. 2003. Developing marker-assisted selection strategies for breeding hybrid rice. Plant Breeding Reviews 23:73-174.

Young, N. 1999. A cautiously optimistic vision for marker-assisted breeding. Molecular Breeding 5:505-510.

Yousef, G.G., and Juvik, J.A. 2001. Comparison of phenotypic and marker-assisted selection for quantitative traits in sweet corn. Crop Science 41: 645-655.

Marker-assisted selection resources on the Web

Grafgen: Design of Precision Graphical Genotypes (, a computer program developed by Frederic Hospital’s group at INRA, France. Using marker data for a population, the program displays each individual’s allelic composition in a graphical format as an aid to selecting desirable genotypes.

MAS Wheat: Bringing Genomics to the Wheat Fields ( This is the web site for a USDA-funded project that seeks to translate genomic discoveries into practical protocols for MAS in wheat. Contains protocols for over 20 genes or markers associated with disease resistance, insect resistance, and grain quality.

Molecular Plant Breeding (, an Australian-based initiative to incorporate marker-assisted strategies into plant breeding programs.

PLABSIM, MAS simulation software available from Matthias Frisch’s web site at the University of Hohenheim, Germany--Link updated 10-25-2013. ( The program is described in Frisch et al. 2000. PLABSIM: Software for simulation of marker-assisted backcrossing. Journal of Heredity 91:86-87.

Popmin (, another computer program from Frederic Hospital’s group at INRA, France. This program calculates optimum population sizes for marker-assisted backcrossing programs.

Molecular marker assisted selection as a potential tool for genetic improvement of crops, forest trees, livestock and fish in developing countries ( This site reports results of a conference sponsored by FAO’s Electronic Forum on Biotechnology in Food and Agriculture.