FISH landmarks reflecting meiotic recombination and structural alterations of chromosomes in wheat (Triticum aestivum L.)

BACKGROUND: DNA sequence composition affects meiotic recombination. However, the correlation between tandem repeat composition and meiotic recombination in common wheat (Triticum aestivum L.) is unclear. RESULTS: Non-denaturing fluorescent in situ hybridization (ND-FISH) with oligonucleotide (oligo) probes derived from tandem repeats and single-copy FISH were used to investigate recombination in three kinds of the long arm of wheat 5A chromosome (5AL). 5AL(535–18/275) arm carries the tandem repeats pTa-535, Oligo-18, and pTa-275, 5AL(119.2–18/275) arm carries the tandem repeats pSc119.2, Oligo-18 and pTa-275, and 5AL(119.2) arm carries the tandem repeats pSc119.2. In the progeny of 5AL(535–18/275) × 5AL(119.2), double recombination occurred between pSc119.2 and pTa-535 clusters (119–535 interval), and between pTa-535 and Oligo-18/pTa-275 clusters (535–18 interval). The recombination rate in the 119–535 interval in the progeny of 5AL(535–18/275) × 5AL(119.2–18/275) was higher than that in the progeny of 5AL(535–18/275) × 5AL(119.2). Recombination in the 119–535 interval produced 5AL(119 + 535) segments with pTa-535 and pSc119.2 tandem repeats and 5AL(No) segments without these repeats. The 5AL(119 + 535) and 5AL(No) segments were localized between the signal sites of the single-copy probes SC5A-479 and SC5A-527. The segment between SC5A-479 and SC5A-527 in the metaphase 5AL(No) was significantly longer than that in the metaphase 5AL(119 + 535). CONCLUSION: The structural variations caused by tandem repeats might be one of the factors affecting meiotic recombination in wheat. Meiotic recombination aggregated two kinds of tandemly repeated clusters into the same chromosome, making the metaphase chromosome more condensed. To conclude, our study provides a robust tool to measure meiotic recombination and select parents for wheat breeding programs. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-021-02947-1.