Sequencing of the 1RS chromosome arm of the Mv179 bread wheat line carrying the 1BL.1RS translocation and development of dna markers for the 1RS chromosome arm

The 1RS chromosome arm of rye (Secale cereale L.) is an important genetic source for improving disease resistance, yield, and stress tolerance in bread wheat (Triticum aestivum L.). The aim of this study was to sequence the 1RS chromosome arm of the bread wheat line Mv179, which carries a Kriszta rye-derived 1BL.1RS translocation, to compare this region with wheat and rye genomes, and to develop DNA markers specific to the 1RS arm. In this context, the Mv179 1BL.1RS chromosome was comprehensively characterized through an integrated approach including de novo sequence assembly, repeat analysis, homology comparison, variant calling, and functional annotation. The results revealed that the 1RS short arm retained its heterochromatic structure, rich in LTR retrotransposons, with the Ty3/Gypsy and Ty1/Copia superfamilies being predominant in this region. Homology and annotation analyses showed that the 1BL.1RS chromosome contained a wide repertoire of genes originating from both wheat 1B and rye 1R chromosomes, associated with metabolic processes, signal transduction, stress response, and defense mechanisms. Phylogenetic analysis of NLR genes indicated that many genes from the Mv179 1RS region of the 1BL.1RS chromosome were closely related to rye NLR genes and known resistance genes (e.g., Lr21, Pm2, Sr21, Lr34, Yr36, Pm21, Sr35, Sr50), suggesting the presence of novel resistance alleles within the 1RS arm. Based on Mv179-specific variants, 30 InDel primer pairs were developed, 24 of which were validated as reliable markers. Among them, 18 were effective in detecting genetic diversity, while 6 were specific for confirming the presence of the 1BL.1RS translocation. In conclusion, this study generated the sequence information of the 1RS chromosome, evaluated the potential use of this region in wheat breeding under abiotic and biotic stress factors, and demonstrated that this genetic resource should be rapidly and effectively utilized in bread wheat improvement programs.