Efficient Anchoring of Erianthus   arundinaceus Chromatin Introgressed into Sugarcane by Specific Molecular Markers.

Erianthus   arundinaceus is a valuable gene reservoir for sugarcane improvement. However, insufficient molecular markers for high-accuracy identification and tracking of the introgression status of E.   arundinaceus chromatin impede sugarcane breeding. Fortunately, suppression subtractive hybridization (SSH) technology provides an excellent opportunity for the development of high-throughput E.   arundinaceus -specific molecular markers at a reasonable cost. In this study, we constructed a SSH library of E.   arundinaceus . In total, 288 clones of E.   arundinaceus -specific repetitive sequences were screened out and their distribution patterns on chromosomes were characterized by fluorescence in situ hybridization (FISH). A subtelomeric repetitive sequence Ea086 and a diffusive repetitive sequence Ea009, plus 45S rDNA-bearing E.   arundinaceus chromosome repetitive sequence EaITS were developed as E.   arundinaceus -specific molecular markers, namely, Ea086-128, Ea009-257, and EaITS-278, covering all the E.   arundinaceus chromosomes for high-accuracy identification of putative progeny. Both Ea086-128 and Ea009-257 were successfully applied to identify the authenticity of F 1 , BC 1 , BC 2 , BC 3 , and BC 4 progeny between sugarcane and E.   arundinaceus . In addition, EaITS-278 was a 45S rDNA-bearing E.   arundinaceus chromosome-specific molecular marker for rapid tracking of the inherited status of this chromosome in a sugarcane background. Three BC 3 progeny had apparently lost the 45S rDNA-bearing E.   arundinaceus chromosome. We reported herein a highly effective and reliable SSH-based technology for discovery of high-throughput E.   arundinaceus -specific sequences bearing high potential as molecular markers. Given its reliability and savings in time and efforts, the method is also suitable for development of species-specific molecular markers for other important wild relatives to accelerate introgression of wild relatives into sugarcane.