Development of Thinopyrum ponticum-specific molecular markers and FISH probes based on SLAF-seq technology
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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.
KeywordsFISH 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).
- Jia QJ, Tan C, Wang JM, Zhang XQ, Zhu JH, Luo H, Yang JM, Westcott S, Broughton S, Moody D, Li CD (2016) Marker development using SLAF-seq and whole-genome shotgun strategy to fine-map the semi-dwarf gene ari-e in barley. BMC Genom 17(1):911. https://doi.org/10.1186/s12864-016-3247-4 CrossRefGoogle Scholar
- Kruppa K, Turkosi E, Mayer M, Toth V, Vida G, Szakacs E, Molnar-Lang M (2016) McGISH identification and phenotypic description of leaf rust and yellow rust resistant partial amphiploids originating from a wheat × Thinopyrum synthetic hybrid cross. J Appl Genet 57(4):427–437. https://doi.org/10.1007/s13353-016-0343-8 CrossRefPubMedCentralPubMedGoogle Scholar
- Santra DK, Watt C, Little L, Kidwell KK, Campbell KG (2006) Comparison of a modified assay method for the endopeptidase marker Ep-D1b with the sequence tag site marker XustSSR2001-7DL for strawbreaker foot rot resistance in wheat. Plant Breed 125(1):13–18. https://doi.org/10.1111/j.1439-0523.2006.01172.x CrossRefGoogle Scholar
- Schwarzacher T, Anamthawatjonsson K, Harrison GE, Islam AKMR, Jia JZ, King IP, Leitch AR, Miller TE, Reader SM, Rogers WJ, Shi M, Heslop-Harrison JS (1992) Genomic in situ hybridization to identify alien chromosomes and chromosome segments in wheat. Theor Appl Genet 84(7–8):778–786PubMedGoogle Scholar
- Shannon MC (1978) Testing salt tolerance variability among tall wheatgrass lines. Agron J 70:719–722. https://doi.org/10.2134/agronj1978.00021962007000050006x CrossRefGoogle Scholar
- Sibikeev SN, Badaeva ED, Gultyaeva EI, Druzhin AE, Shishkina AA, Dragovich AY, Kroupin PY, Karlov GI, Khuat TM, Divashuk MG (2017) Comparative analysis of Agropyron intermedium (Host) Beauv 6Agi and 6Agi2 chromosomes in bread wheat cultivars and lines with wheat-wheatgrass substitutions. Russ J Genet 53(3):314–324. https://doi.org/10.1134/s1022795417030115 CrossRefGoogle Scholar
- Sun X, Liu D, Zhang X, Li W, Liu H, Hong W, Jiang C, Guan N, Ma C, Zeng H, Xu C, Song J, Huang L, Wang C, Shi J, Wang R, Zheng X, Lu C, Wang X, Zheng H (2013) SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS One 8(3):e58700. https://doi.org/10.1371/journal.pone.0058700 CrossRefPubMedCentralPubMedGoogle Scholar
- Wang Y, Yu KF, Xie Q, Kang HY, Lin LJ, Fan X, Sha LN, Zhang HQ, Zhou YH (2011) Cytogenetic, genomic in situ hybridization (GISH) and agronomic characterization of alien addition lines derived from wheat-Psathyrostachys huashanica. Afr J Biotechnol 10(12):2201–2211Google Scholar
- Yang ZJ, Li GR, Chang ZJ, Zhou JP, Ren ZL (2006) Characterization of a partial amphiploid between Triticum aestivum cv. Chinese Spring and Thinopyrum intermedium ssp trichophorum. Euphytica 149(1–2):11–17Google Scholar
- Yao H, Tang CG, Zhao J, Zheng Q, Li B, Hao CY, Li ZS, Zhang XY (2016) Isolation of Thinopyrum ponticum genome specific repetitive sequences and their application for effective detection of alien segments in wheat. Sci Agri Sin 49(19):3683–3693. https://doi.org/10.3864/j.issn.0578-1752.2016.19.002 Google Scholar