Cytogenetic Characterization and Molecular Marker Development for a Wheat- 4A (4B) Disomic Substitution Line with Stripe Rust Resistance.

(2n = 2x = 14, AA) is an important relative of wheat. This species tolerates many different types of environmental stresses, including drought, salt, and pathogenic infection, and is lower in dietary fiber and higher in antioxidants, protein (15 to 18%), lipids, and trace elements than common wheat. However, the gene transfer rate from this species to common wheat is low, and few species-specific molecular markers are available. In this study, the wheat- substitution line Z1889, derived from a cross between the common wheat cultivar Crocus and line G52, was identified using multicolor fluorescence in situ hybridization, multicolor genomic in situ hybridization, and a 55K single-nucleotide polymorphism array. Z1889 was revealed to be a 4A (4B) substitution line with a high degree of resistance to stripe rust pathogen strains prevalent in China. In addition, 22 4A chromosome-specific molecular markers and 11 genome-specific molecular markers were developed from 1,145 4A chromosome-specific fragments by comparing the sequences generated by specific-length amplified fragment sequencing, with an efficiency of up to 55.0%. Furthermore, the specificity of these markers was verified in four species containing the A genome. These markers not only can be used for the detection of the 4A chromosome but also provide a basis for molecular marker-assisted, selection-based breeding in wheat.