In a study of polymorphism and stability in rye chromosomes, three rye vari
eties and the sets of wheat-rye addition and substitution lines were compar
ed using two non-homologous highly repetitive DNA families, pSc200 and pSc2
50. The rye varieties, Petkus, Imperial and Onohoiskaya, showed polymorphis
m for the presence and the size of the pSc200 in-situ hybridization signals
on chromosome pairs, 2R, 4R and 7R, and the pSc250 signals on chromosomes,
5R, 6R and 7R. Chromosome 1R was heteromorphic within the Onohoiskaya vari
ety. Differences in the distribution of chromosome polymorphisms imply that
intervarietal changes to these highly repetitive DNA families occurred ind
ependently, despite their juxtaposition or even overlapping locations in su
btelomeric heterochromatic regions. In the set of Saratovskaya 29 wheat/Ono
hoiskaya substitution lines, only chromosome 2R was altered relative to its
counterpart in the parental rye variety due to amplification of the pSc250
signal on the long arm, although this did not exceed intervarietal polymor
phism. In the set of Chinese Spring wheat/ Imperial addition lines, only tw
o Imperial chromosomes, 4R and 6R, were unchanged. We detected the loss of
one or both rye homologous chromosomes, the loss of one arm, and the deleti
on of subtelomeric heterochromatin accompanied by the loss of the pSc200 si
gnal. The results show that Saratovskaya 29/Onohoiskaya chromosome substitu
tion lines possess increased chromosome stability compared with Chinese Spr
ing/Imperial addition lines.