New Oligonucleotide Probes for ND-FISH Analysis to Identify Barley Chromosomes and to Investigate Polymorphisms of Wheat Chromosomes

Abstract

Oligonucleotide probes that can be used for non-denaturing fluorescence in situ hybridization (ND-FISH) analysis are convenient tools for identifying chromosomes of wheat (Triticum aestivum L.) and its relatives. New oligonucleotide probes, Oligo-HvT01, Oligo-pTa71-1, Oligo-s120.1, Oligo-s120.2, Oligo-s120.3, Oligo-275.1, Oligo-275.2, Oligo-k566 and Oligo-713, were designed based on the repetitive sequences HVT01, pTa71, pTa-s120, pTa-275, pTa-k566 and pTa-713. All these probes can be used for ND-FISH analysis and some of them can be used to detect polymorphisms of wheat chromosomes. Probes Oligo-HvT01, Oligo-pTa71-1, Oligo-s120.3, Oligo-275.1, Oligo-k566 and Oligo-713 can, respectively, replace the roles of their original sequences to identify chromosomes of some barley (Hordeum vulgare ssp. vulgare) and the common wheat variety Chinese Spring. Oligo-s120.1, Oligo-s120.2 and Oligo-275.2 produced different hybridization patterns from the ones generated by their original sequences. In addition, Oligo-s120.1, Oligo-s120.2 and Oligo-s120.3, which were derived from pTa-s120, revealed different signal patterns. Likewise, Oligo-275.1 and Oligo-275.2, which were derived from pTa-275, also displayed different hybridization patterns. These results imply that differently arranged or altered structural statuses of tandem repeats might exist on different chromosome regions. These new oligonucleotide probes provide extra convenience for identifying some wheat and barley chromosomes, and they can display polymorphisms of wheat chromosomes.

Identification and comparison of individual chromosomes of three accessions ofHordeum chilense,Hordeum vulgare, andTriticum aestivumby FISH

“…The chromosome spread is critical for obtaining good hybridization patterns when individual chromosomes, chromosome arms, or smaller chromosome regions are identified. Some of the hybridization patterns described in this work have already been described previously using different methods for chromosomes spread preparations such as the use of colchicine, ice cold water, or nitrous oxide gas (N 2 O) (Cabrera et al 1995;Taketa et al 1999Taketa et al , 2000Komuro et al 2013;Tang et al 2016). These three treatments are extensively used in cytogenetic analysis.…”

Identification and comparison of individual chromosomes of threeHordeum chilenseaccessions,Hordeum vulgareandTriticum aestivumby FISH

“…The chromosome spread is critical for obtaining good hybridization patterns when individual chromosomes, chromosome arms or smaller chromosome regions are identified. Some of the hybridization patterns described in this work have already been described previously using different methods for chromosomes spread preparations such as the use of colchicine, ice cold water or nitrous oxide gas (N 2 O) (Cabrera et al 1995; Taketa et al 1999, 2000; Komuro et al 2013; Tang et al 2016). These three treatments are extensively used in cytogenetic analysis.…”

Development of a karyotype associated with the genome map and its applications in identification and characterization of chromosomes in peanut

“…The whole genome assembly sequences of Tifrunner and A. ipaensis were downloaded from Peanutbase (https://peanutbase.org/home). The sequences of both Tifrunner and A. ipaensis genomes were analyzed to obtain tandem repeat sequences using the Tandem Repeats Finder (TRF, version 4.09) [38] based on the methods of Tang et al [27]. Brie y, the TRF algorithm used the following alignment parameters: Match = 2; Mismatch = 7; Indel = 7; Probability of match = 80; Probability of indel = 10; Min score = 50; and Max period = 2000.…”

“…Repetitive single-stranded oligo probe uorescence in situ hybridization (SSON FISH), based on genomic sequences provides a new solution for cost-effective chromosome identi cation [24][25][26][27]. Development of genome-wide repetitive oligo probes to establish high-resolution chromosome-painting karyotypes can accurately identify both naturally occurred and arti cially-induced chromosomal structural variants [20,[28][29][30].…”