Identification of a wheat–Thinopyrum intermedium substitution line as revealed by GISH, FISH, SSR and EST-SSR markers

The development of alien substitution lines is important for transferring useful genes of exotic species into bread wheat. In situ hybridization, SSR and EST-SSR marker analysis were used to identify a wheat–Thinopyrum intermedium substitution line designated as Zhong 199. Zhong 199 was detected with the chromosome number 2n=42 and stable agronomic traits were evaluated during the 2012 field harvest season. Genomic in situ hybridization analysis with the genomic Th. intermedium DNA as a probe showed that Zhong 199 contained a pair of Th. intermedium chromosomes. Fluorescence in situ hybridization, using a repetitive sequence, pAs1, derived from Aegilops squarrosa L., indicated the replacement of chromosome 2D of wheat in the wheat–Th. intermedium substitution line. Seven SSR markers specific for chromosome 2D of wheat further confirmed that the substituted wheat chromosome was 2D in the substitution line. Such result was also confirmed by using EST-SSR marker analysis. This study provided some useful information for effective exploitation of the source of genetic variability for the improvement of wheat.