Abstract
Oligonucleotide probes and the non-denaturing fluorescence in situ hybridization (ND-FISH) technique are widely used to analyze plant chromosomes because they are convenient tools. New oligonucleotide probes, Oligo-Ku, Oligo-3B117.1, Oligo-3B117.2, Oligo-3B117.2.1, Oligo-3B117.3, Oligo-3B117.4, Oligo-3B117.5, Oligo-3B117.6, Oligo-pTa71A-1, Oligo-pTa71A-2, Oligo-pTa71B-1, Oligo-pTa71B-2, Oligo-pTa71C-1, Oligo-pTa71C-2, Oligo-pTa71C-3 and Oligo-pTa71D were designed based on the repetitive sequences KU.D15.15, pSc119.2-like sequence 3B117 and pTa71. Oligonucleotide probe (GT)7 was also used. Oligo-Ku and (GT)7 can be together used to identify Dasypyrum villosum from wheat chromosomes and to distinguish individual D. villosum chromosomes. The oligonucleotide probes that were derived from the same repeat sequence displayed different signal intensity and hybridization sites on the same chromosomes. Both the length and the nucleotide composition of oligonucleotide probes determined their signal intensity. For example, Oligo-3B117.2 (25 bp) and Oligo-pTa71A-2 (46 bp) produced the strongest signals on chromosomes of wheat (Triticum aestivum L.), rye (Secale cereale L.), barley (Hordeum vulgare ssp. vulgare) or D. villosum, the signal of Oligo-3B117.4 (18 bp) on the short arm of 7B chromosome was weaker than that of Oligo-3B117.2.1 (15 bp) and Oligo-3B117.3 (16 bp), and Oligo-pTa71A-1 (38 bp) produced the same strong signals as Oligo-pTa71A-2 did on 1B and 6B chromosomes, but its signals on 1R and 1V chromosomes were weaker than the ones of Oligo-pTa71A-2. Oligonucleotide probes and ND-FISH analysis can reflect the distribution and structural statues of different segments of tandem repeats on chromosomes. The possible reasons why different segments derived from the same repeat sequence produced different signal patterns are discussed.
Highlights
Since the non-denaturing fluorescence in situ hybridization (ND-FISH) technique was used to detect plant telomeres [1], it is often used to analyze plant chromosomes [2,3,4]
No signals of the seven oligonucleotide probes were observed on the oligonucleotide probes (Figure 1; Table 1)
Depends on the length of probes and on the nucleotide composition. All these results indicate that the signal strength of oligonucleotide probes depends on the length of probes butProbes on nucleotide composition
Summary
Since the non-denaturing fluorescence in situ hybridization (ND-FISH) technique was used to detect plant telomeres [1], it is often used to analyze plant chromosomes [2,3,4]. ND-FISH has been widely used to study the chromosomes of wheat and its relatives [5,6,7,8,9,10,11,12,13]. Two main types of oligonucleotide probes are often used for ND-FISH analysis of chromosomes of wheat and its relatives. They are simple sequence repeats (SSRs) [2,3,5,6,7] and non-SSR oligonucleotides [8,9,10,11,12,13].
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