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The 1AL.1RS wheat-rye chromosomal translocation originally found in ‘Amigo’ wheat possesses resistance genes for stem rust, powdery mildew and greenbug biotypes B and C, but also has a negative effect on wheat processing quality. Recently, a second 1AL.1RS translocation carrying Gb6 a gene conferring resistance to greenbug biotypes B, C, E, G and I, was identified in the wheat germplasm line ‘GRS1290’. Protein analytical methods, and the DNA polymerase chain reaction were used to identify markers capable of differentiating the 1RS chromosome arms derived from ‘Amigo’ and ‘GRS1201’. The secalin proteins encoded by genes on 1RS chromosome arms differed in ‘Amigo’ and ‘GRS1201’. A 70 kDa secalin was found in the ‘Amigo’ 1AL.1RS, but did not occur in the ‘GRS1201’ 1AL.1RS. Polymorphisms detected by PCR primers derived from a family of moderately repetitive rye DNA sequences also differentiated the two translocations. When ‘GRS1201’ was mated with a non-1RS wheat, no recombinants between 1RS markers were observed. In crosses between 1RS and non-1 RS parents, both DNA markers and secalins would be useful as selectable markers for 1RS-derived greenbug resistance. Recombination between 1RS markers did occur when 1RS from ‘Amigo’ and 1RS from ‘GRS1201’ were combined\ but in such intermatings, the molecular markers described herein could still be used to develop a population enriched in lines carrying Gb6. No differences in grain yield or grain and flour quality characteristics were observed when lines carrying 1RS from ‘Amigo’ were compared with lines with 1RS from ‘GRS1201’. Hence, differences in secalin composition did not result in differential quality effects. When compared with sister lines with 1AL.1AS derived from the wheat cultivar ‘Redland’, lines with ‘GRS1201’ had equal grain yield, but produced flours with significantly shorter mix times, weaker doughs, and lower sodium dodecyl sulphate sedimentation volumes.