Karyotype establishment and development of specific molecular markers of Aegilops geniculata Roth based on SLAF-seq

The constant evolution of pathogens poses a threat to wheat resistance against diseases, endangering food security. Developing resistant wheat varieties is the most practical approach to circumventing this problem. As a close relative of wheat, Aegilops geniculata, particularly accession SY159 has evolved numerous beneficial traits that could be applied to improve wheat. In this study, we established the karyotype of SY159 by fluorescence in situ hybridization (FISH) using oligonucleotide probes Oligo-pTa535 and Oligo-pSc119.2 and a complete set of wheat-Ae. geniculata accession TA2899 addition lines as a reference. Using specific-locus amplified fragment sequencing (SLAF-seq) technology, 400 specific markers were established for detecting the SY159 chromosomes with efficiencies reaching 81.5%. The SY159-specific markers were used for classification of different homologous groups of SY159 against wheat-Ae. geniculata addition lines. We used these specific markers on the 7Mg chromosome after classification, and we successfully confirmed their suitability for studying different chromosomes of SY159. This study provides a foundation for accelerating the application of SY159 for genetic breeding programs designed to improve wheat.