, Volume 247, Issue 5, pp 1099–1108 | Cite as

Development of Thinopyrum ponticum-specific molecular markers and FISH probes based on SLAF-seq technology

  • Liqin Liu
  • Qiaoling Luo
  • Wan Teng
  • Bin Li
  • Hongwei Li
  • Yiwen Li
  • Zhensheng Li
  • Qi Zheng
Original Article


Main conclusion

Based on SLAF-seq, 67 Thinopyrum ponticum-specific markers and eight Th. ponticum-specific FISH probes were developed, and these markers and probes could be used for detection of alien chromatin in a wheat background.


Decaploid Thinopyrum ponticum (2n = 10x = 70) is a valuable gene reservoir for wheat improvement. Identification of Th. ponticum introgression would facilitate its transfer into diverse wheat genetic backgrounds and its practical utilization in wheat improvement. Based on specific-locus-amplified fragment sequencing (SLAF-seq) technology, 67 new Th. ponticum-specific molecular markers and eight Th. ponticum-specific fluorescence in situ hybridization (FISH) probes have been developed from a tiny wheat—Th. ponticum translocation line. These newly developed molecular markers allowed the detection of Th. ponticum DNA in a variety of materials specifically and steadily at high throughput. According to the hybridization signal pattern, the eight Th. ponticum-specific probes could be divided into two groups. The first group including five dispersed repetitive sequence probes could identify Th. ponticum chromatin more sensitively and accurately than genomic in situ hybridization (GISH). Whereas the second group having three tandem repetitive sequence probes enabled the discrimination of Th. ponticum chromosomes together with another clone pAs1 in wheat–Th. ponticum partial amphiploid Xiaoyan 68.


FISH GISH Molecular markers SLAF-seq Thinopyrum ponticum  Triticum aestivum 



Genome in situ hybridization


Fluorescence in situ hybridization


Wheat cv. Chinese spring


Specific-locus-amplified fragment sequencing



We would like to thank Prof. Yonghong Zhou from Sichuan Agricultural University, Prof. Diaoguo An from Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Dr. Jinpeng Zhang from Chinese Academy of Agricultural Sciences, for kindly providing seeds of some of the accessions used in this study. This project was supported by the National Key Research and Development Program of China (2016YFD0102000) and the Strategic Priority Research Program of the Chinese Academy of Sciences (No. XDA08030105).

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Institute of Genetics and Developmental BiologyChinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome EngineeringBeijingChina
  2. 2.University of Chinese Academy of SciencesBeijingChina

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