Construction of three linkage maps in bread wheat, Triticum aestivum

Genetic maps were compiled from the analysis of 160-180 doubled haploid lin es derived from 3 crosses: Cranbrook x Halberd, CD87 x Katepwa, and Sunco x Tasman. The parental wheat lines covered a wide range of the germplasm use d in Australian wheat breeding. The linkage maps were constructed with RFLP , AFLP, microsatellite markers, known genes, and proteins. The numbers of m arkers placed on each map were 902 for Cranbrook x Halberd, 505 for CD87 x Katepwa, and 355 for Sunco x Tasman. Most of the expected linkage groups co uld be determined, but 10-20% of markers could not be assigned to a specifi c linkage group. Homologous chromosomes could be aligned between the popula tions described here and linkage groups reported in the literature, based a round the RFLP, protein, and microsatellite markers. For most chromosomes, colinearity of markers was found for the maps reported here and those recor ded on published physical maps of wheat. AFLP markers proved to be effectiv e in filling gaps in the maps. In addition, it was found that many AFLP mar kers defined specific genetic loci in wheat across all 3 populations. The quality of the maps and the density of markers differs for each populat ion. Some chromosomes, particularly D genome chromosomes, are poorly covere d. There was also evidence of segregation distortion in some regions, and t he distribution of recombination events was uneven, with substantial number s of doubled haploid lines in each population displaying one or more parent al chromosomes. These features will affect the reliability of the maps in l ocalising loci controlling some traits, particularly complex quantitative t raits and traits of low heritability. The parents used to develop the mapping populations were selected based on their quality characteristics and the maps provide a basis for the analysis of the genetic control of components of processing quality. However, the p arents also differ in resistance to several important diseases, in a range of physiological traits, and in tolerance to some abiotic stresses.