Molecular Breeding

, Volume 34, Issue 3, pp 1281-1300

First online:

Construction of dense linkage maps “on the fly” using early generation wheat breeding populations

  • J. T. EckardAffiliated withDepartment of Plant Science, South Dakota State University
  • , J. L. Gonzalez-HernandezAffiliated withDepartment of Plant Science, South Dakota State University Email author 
  • , S. ChaoAffiliated withUSDA, Agricultural Research Service
  • , P. St AmandAffiliated withUSDA, Agricultural Research Service
  • , G. BaiAffiliated withUSDA, Agricultural Research Service

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In plant species, construction of framework linkage maps to facilitate quantitative trait loci mapping and molecular breeding has been confined to experimental mapping populations. However, development and evaluation of these populations is detached from breeding efforts for cultivar development. In this study, we demonstrate that dense and reliable linkage maps can be constructed using extant breeding populations derived from a large number of crosses, thus eliminating the need for extraneous population development. Using 565 segregating F1 progeny from 28 four-way cross breeding populations, a linkage map of the hexaploid wheat genome consisting of 3,785 single nucleotide polymorphism (SNP) loci and 22 simple sequence repeat loci was developed. Map estimation was facilitated by application of mapping algorithms for general pedigrees implemented in the software package CRI-MAP. The developed linkage maps showed high rank-order concordance with a SNP consensus map developed from seven mapping studies. Therefore, the linkage mapping methodology presented here represents a resource efficient approach for plant breeding programs that enables development of dense linkage maps “on the fly” to support molecular breeding efforts.


Linkage mapping Consensus map Pedigree analysis Wheat breeding High-throughput genotyping