Whole genome markers discovery for Thinopyrum bessarabicum and Secale anatolicum

Development of sequence-based markers has added a whole new scale and increased the speed in identification of alien introgressions in wheat. Expressed sequence tag (EST)-Sequence Tagged Sites (STS) markers have proved useful in tracing alien chromatin. In this study, we report the development of Thinopyrum bessarabicum and Secale specific EST-STS markers and their application in tracing the respective alien chromatin in the wheat background. The parental lines, Chinese Spring (CS), ISR991.1 (CS/Th. bessarabicum amphidiploid), and ISR1049.2 (CS/Secale anatolicum amphidiploid), were used as core experimental materials. Using comparative analysis of RNA-Seq data of these three lines, 10,555 and 6,992 candidate sequences specific to Th. bessarabicum and Secale, respectively, were assembled. To validate the genome specificity of these candidate sequences, 68 and 64 EST-STS markers were developed from a subset of randomly selected candidate sequences of Th. bessarabicum and Secale, respectively, and tested on sets of alien addition lines. A total of 55 and 53 markers of Th. bessarabicum and Secale were assigned to chromosomal location(s), respectively, using addition lines. The genome specific candidate sequences identified and the EST-STS markers developed will be a valuable resource for genetic and genomic studies involving Th. bessarabicum and Secale, thereby will facilitate the exploitation of alien gene(s) in wheat and triticale breeding.