Developing New Oligo Probes to Distinguish Specific Chromosomal Segments and the A, B, D Genomes of Wheat (Triticum aestivum L.) Using ND-FISH

Abstract

Non-denaturing FISH (ND-FISH) technology has been widely used to study the chromosomes of Triticeae species because of its convenience. The oligo probes for ND-FISH analysis of wheat (Triticum aestivum L.) chromosomes are still limited. In this study, the whole genome shotgun assembly sequences (IWGSC WGA v0.4) and the first version of the reference sequences (IWGSC RefSeq v1.0) of Chinese Spring (T. aestivum L.) were used to find new tandem repeats. One hundred and twenty oligo probes were designed according to the new tandem repeats and used for ND-FISH analysis of chromosomes of wheat Chinese Spring. Twenty nine of the 120 oligo probes produce clear or strong signals on wheat chromosomes. Two of the 29 oligo probes can be used to conveniently distinguish wheat A-, B-, and D-genome chromosomes. Sixteen of the 29 oligo probes only produce clear or strong signals on the subtelomeric regions of 1AS, 5AS, 7AL, 4BS, 5BS, and 3DS arms, on the telomeric regions of 1AL, 5AL, 2BS, 3BL, 6DS, and 7DL arms, on the intercalary regions of 4AL and 2DL arms, and on the pericentromeric regions of 3DL and 6DS arms. Eleven of the 29 oligo probes generate distinct signal bands on several chromosomes and they are different from those previously reported. In addition, the short and long arms of 6D chromosome have been confirmed. The new oligo probes developed in this study are useful and convenient for distinguishing wheat chromosomes or specific segments of wheat chromosomes.

Genome-Wide Distribution of Novel Ta-3A1 Mini-Satellite Repeats and Its Use for Chromosome Identification in Wheat and Related Species

“…However, these mini-satellite arrays in wheat represented moderately repeated families of less than 100 copies per array. Tang et al [47] reported five probes with mini-satellite sequences among ND-FISH probes as predicted by TRF, and we predicted 120 to 260 copy numbers across specific chromosome regions with total lengths of under 20 kb by B2DSC web server. The present study found that Ta-3A1 represented the highest copy number of a mini-satellite yet reported, and it covered a total length of over 2 Mb and was mainly located on five chromosomes of wheat (Figure 1).…”

Characterization of Chromosomal Rearrangement in New Wheat—Thinopyrum intermedium Addition Lines Carrying Thinopyrum—Specific Grain Hardness Genes

“…The ND-FISH based chromosome painting technique with the labelled oligonucleotide (oligo) is widely applied, due to obvious advantages over conventional FISH procedures, such as easy probes synthesis, flexible design, relatively low cost, and high-throughput [25,30,[36][37][38][39]. This technique has been successfully used for distinguishing different genomes, such as Oligo-1162 for Secale cereale [30] and Oligo-B and Oligo-D for wheat B-and D-chromosomes [39], respectively. GISH by using D. villosum genomic DNA as a probe [13,15], and FISH using Dasypyrum specific LTR pDb12H probe can distinguish the J S chromosomes of Th.…”

The Formation of Sex Chromosomes in Silene latifolia and S. dioica Was Accompanied by Multiple Chromosomal Rearrangements

“…Such probes, designed from conserved sequences of one species were used e.g. for developing karyotype among genetically related Solanum species , for differentiating of A, B, and D genomes in wheat (Tang et al, 2018), in comparative physical mapping of sex chromosomes in Populus (Xin et al, 2018) and in examination of meiotic pairing in polyploid Solanum species .…”