Abstract
Chromosome painting is a useful technique for distinguishing specific chromosomes (fragments), elucidating the genetic relationships of different genomes or chromosomes, and identifying chromosomal rearrangements. The development of chromosome- or genome-specific probes is fundamental for chromosome painting. The possibility for developing such probes specifically painting homoeologous chromosomes in allopolyploid species has been questioned since that chromosomes belonging to the same homoeologous group share highly conserved sequences. In the present study, we attempted to construct a wheat chromosome 4D-specific oligo probe library by selecting 4D-specific sequences in reference genome of common wheat cv. Chinese Spring (CS, 2n = 6x = 42, AABBDD). The synthesized library contains 27,392 oligos. Oligo painting using the probe library confirmed its specificity, shown by that only chromosome 4D could be painted in three wheat genotypes and CS nulli-tetrasomic line N4AT4D. Oligo painting was successfully used to define the 4D breakpoints in CS deletion lines involving 4D and two wheat-Haynaldia villosa 4D–4V translocation lines. Thirteen wheat relatives and a Triticum durum-H. villosa amphiploid were used for oligo painting. Except the 4D in two Aegilops tauschii accessions, the 4M in Ae. comosa and 4U in Ae. umbellulata could be painted. In tetraploid Ae. ventricosa, both 4D and 4M could be painted; however, the signal intensity of 4M was less compared with 4D. No painted chromosome was observed for the other alien species. This indicated that the relationship among D/M/U was closer than that among D/A/B as well as D with genomes H/R/Ss/Sc/Y/P/N/J. Our successful development of 4D-specific oligo probe library may serve as a model for developing oligo probes specific for other homoeologous chromosomes.
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Abbreviations
- FISH:
-
Fluorescent in situ hybridization
- GISH:
-
Genomic in situ hybridization
- SSR:
-
Simple sequence repeat
- PCR:
-
Polymerase chain reaction
- BAC:
-
Bacterial artificial chromosome
- APM:
-
Amiprophos-methyl
- SSC:
-
2′ saline sodium citrate
- CCD:
-
Charge-coupled device
- DAP:
-
4′,6-diamidino-2-phenylindole
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Funding
This research was supported by the National Key Research and Development Program (2016YFD0102001), the National Natural Science Foundation of China (Grant No. 31771782, 31571653, 31201204), International Cooperation and Exchange of the National Natural Science Foundation of China (Grant No. 31661143005), ‘948’ Project of Ministry of Agriculture (2015-Z41), the special fund of Jiangsu Province for the transformation of scientific and technological achievements (BA2017138), the Program of Introducing Talents of Discipline to Universities (No. B08025), the Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), and the grants from the National Natural Science Foundation of China (Major Program) (No. 91935304), the National Natural Science Foundation of China (No.31971943), the Jiangsu Agricultural Technology System (JATS) (No. 2019429), and the Key Research and Development Plan of Ningxia (No. 2019BBF02022-04).
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XEW and HYW designed the project. XYS, RRS, JWZ, and HJS performed the experiments. TZ designed chromosome 4D-specific oligo probe probes. WKY and YFW analyzed data. JX processed the pictures. MLX and QFL contributed new experimental method. XYS wrote the manuscript. All authors read and approved the manuscript.
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Song, X., Song, R., Zhou, J. et al. Development and application of oligonucleotide-based chromosome painting for chromosome 4D of Triticum aestivum L.. Chromosome Res 28, 171–182 (2020). https://doi.org/10.1007/s10577-020-09627-0
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DOI: https://doi.org/10.1007/s10577-020-09627-0