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. 2024 Dec 12:15:1501642.
doi: 10.3389/fpls.2024.1501642. eCollection 2024.

Frequent variations and phylogenetic relationships within the genus Secale identified by ND-FISH according to the genome-wide universal oligonucleotides chromosome probes

Zhi Li #  1   2   3 , Zixin Sun #  2   3 , Tianheng Ren  1   2   3
Affiliations

Frequent variations and phylogenetic relationships within the genus Secale identified by ND-FISH according to the genome-wide universal oligonucleotides chromosome probes

Zhi Li et al. Front Plant Sci. .

Abstract

Introduction: Rye (Secale cereale L.) played a very important role in wheat genetic improvement and forage production worldwide. However, since rye is a kind of cross-pollinated plant, high levels of genetic heterozygosity and heterogeneity existed in the genome. Genome-wide variation in repeat sequences is one of the most important reasons for chromosome evolution in rye. High-precision cytological identification can effectively identify the heterochromatin or repeat sequence variations in the rye genome, and the relationship between different rye varieties can be identified while obtaining the FISH-karyotype of different rye varieties. The evolution of rye chromosomes can be analyzed by the variation degree of different probes on rye chromosomes.

Methods: All materials were identified by non-denaturing fluorescence in situ hybridization (ND-FISH). Five probes, (AAC)6, Oligo-pSc119.2-1, Oligo-pTa71A-2, Oligo-pSc200, and Oligo-pSc250 were used to identify rye chromosomes.

Results: 15 rye varieties including S. cereale (cultivated rye and weedy rye), S. strictum (wild rye), S. sylvestre (wild rye), and S. vavilovii (wild rye) were examined by five oligonucleotides probes. 92 signal sites and 2074 signal patterns were observed, suggesting that high polymorphisms exist in the different rye genomes. The karyotypes of 15 rye varieties were obtained, the frequency of different signal types at each signal site was calculated and the model diagrams of probes (AAC)6, Oligo-pSc119.2-1, Oligo-pTa71A-2, Oligo-pSc200 + Oligo-pSc250 were drawn. The results showed that the rate of variation of different chromosomes of rye was not consistent. 1R, 6R, and 7R have higher variation and genetic diversity, while 2R and 3R have lower variation and are more conserved relative to other chromosomes. The results also indicated that S. sylvestre has a far genetic distance from other rye species, and S. vavilovii might be one of the ancestors of Chinese rye varieties.

Discussion: Results from this study confirmed rapid chromosome change and high levels of chromosome diversity in rye.

Keywords: FISH; evolution; genetic diversity; oligonucleotides; rye.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
The ND-FISH results of Oligo-pSc119.2-1 and (AAC)6 of 1R TO 7R chromosomes for 15 rye varieties. Red signal patterns: (AAC)6. Green signal patterns: Oligo-pSc119.2-1. The names of rye were showed on the right.
Figure 2
Figure 2
The model of the signal patterns of Oligo-pSc119.2-1. In the figure, the green spots on the chromosomes are the signal patterns at the signal sites of Oligo-pSc119.2-1 with the highest frequency. The distribution of the probe at each signal site on the chromosome and the frequency of signal intensity types were shown, the red were the types with the highest frequency at this spot.
Figure 3
Figure 3
The model of the signal patterns of (AAC)6. In the figure, the red spots on the chromosomes are the signal patterns at the signal sites of (AAC)6 with the highest frequency. The distribution of the probe at each signal site on the chromosome and the frequency of signal intensity types were shown, the red were the types with the highest frequency at this spot.
Figure 4
Figure 4
The ND-FISH results of Oligo-pSc200 + Oligo-pSc250 for 15 rye varieties. Green signal patterns: Oligo-pSc200 + Oligo-pSc250. The names of rye were showed on the right.
Figure 5
Figure 5
The model of the signal patterns of Oligo-pSc200 + Oligo-pSc250 and Oligo-pTa71A-2. In the figure, the red spots on the chromosomes are the signal patterns at the signal sites of Oligo-pTa71A-2 with the highest frequency. The green spots on the chromosomes are the signal patterns at the signal sites of Oligo-pSc200 + Oligo-pSc250 with the highest frequency. The distribution of the probe at each signal site on the chromosome and the frequency of signal intensity types were shown. The red were the types with the highest frequency at this spot.
Figure 6
Figure 6
The ND-FISH results of Oligo-pTa71A-2 for 15 rye varieties. The names of rye were showed on the top of the chromosomes. Green: Oligo-pTa71A-2.
Figure 7
Figure 7
Heatmap clustering analysis of 1R to 7R chromosomes of 15 rye varieties. (A) Heatmap clustering analysis of 1R chromosome. (B) Heatmap clustering analysis of 2R chromosome. (C) Heatmap clustering analysis of 3R chromosome. (D) Heatmap clustering analysis of 4R chromosome. (E) Heatmap clustering analysis of 5R chromosome. (F) Heatmap clustering analysis of 6R chromosome. (G) Heatmap clustering analysis of 7R chromosome. All signal patterns showed on the chromosomes were used for analysis.
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