小偃麦渗入系是小麦与长穂偃麦草通过远缘杂交形成的异源隐形易位系，是开展外源基因功能研究和遗传育种的重要染色体工程材料。迄今为止，传统的基因组原位杂交技术难以清晰地鉴定小偃麦渗入系中偃麦草染色体片段，关于长穂偃麦草渗入片段的定位研究也鲜有报道。通过前期研究，申请者证明SLAF-seq技术能够高效地开发长穂偃麦草基因组特异标记和荧光探针，并可以应用于小偃麦渗入系的鉴定。在此基础上，本项目计划：通过规模化开发长穗偃麦草特异分子标记和荧光探针，研究小偃麦渗入系中长穂偃麦草染色体区段的定位及遗传规律，解析小偃麦衍生品种耐盐性状的遗传基础，分析外源基因组与耐盐特性的关系，为提高长穗偃麦草资源利用效率，加速小偃麦分子育种进程奠定理论和应用基础。

The wheat-Thinopyrum ponticum introgression lines are important chromosome engineering materials in wheat genetic analysis and breeding application, which carrying “invisible” alien chromosome fragments transferred from Thinopyrum ponticum into wheat by the distant hybridization. Up to now, it is difficult to identify the introgressed Thinopyrum ponticum genome in wheat background by GISH (genomic in situ hybridization), and the location of alien chromosome fragments in the introgression lines is not clear yet. Our previous study proved that the SLAF-seq (specific-locus amplified fragment sequencing) technique was efficient for developing alien-specific molecular markers in a wheat background and could be used to trace the alien chromosome segments in wheat-Thinopyrum ponticum introgression lines. Based on above research results, this project intends to: (i) develop a large number of Thinopyrum ponticum-specific molecular markers and FISH (fluorescence in situ hybridization) probes using SLAF-seq; (ii) locate the alien chromosome regions and analyze their genetic transmission in wheat-Thinopyrum ponticum introgression lines; (iii) study the genetic basis of salt tolerance in wheat-Thinopyrum ponticum derivative accessions, and analyze the effects of alien genome on the salt tolerance. These results will facilitate the utility of germplasm resource and provide theoretical and practical basis for wheat genetic improvement.