DOP–PCR based painting of rye chromosomes in a wheat background

Abstract

To determine the appropriateness of chromosome painting for identifying genomic elements in rye, we microdissected the 1R and 1RS chromosomes from rye (Secale cereale L. var. King II) and wheat-rye addition line 1RS, respectively. Degenerate oligonucleotide primed - polymerase chain reaction (DOP-PCR) amplification of 1R and 1RS products from dissected chromosomes were used as probes to hybridize to metaphase chromosomes of rye, wheat-rye addition lines 1R and 1RS, translocation line 1RS.1BL, and allohexaploid triticale. The results showed that (i) the hybridization signal distribution patterns on rye chromosomes using 1R-derived DOP-PCR products as the probe were similar to those using 1RS-derived DOP-PCR products as the probe; (ii) 1R and (or) 1RS could not be distinguished from other rye chromosomes solely by the hybridization patterns using 1R- and (or) 1RS-derived DOP-PCR products as the probe; (iii) rye chromosomes and (or) rye chromosome fragments could be clearly identified in wheat-rye hybrids using either 1R- or 1RS-derived DOP-PCR products as the probe and could be more accurate in the nontelomeric region than using genomic in situ hybridization (GISH). Our results suggested that 1R- and (or) 1RS-derived DOP-PCR products contain many repetitive DNA sequences, are similar on different rye chromosomes, are R-genome specific, and can be used to identify rye chromosomes and chromosome fragments in wheat-rye hybrids. Our research widens the application range of chromosome painting in plants.

Degenerate Oligonucleotide Primed–Polymerase Chain Reaction‐Based Chromosome Painting of P Genome Chromosomes in Agropyron cristatum and Wheat–A. cristatum Addition Lines

“…The DOP–PCR products of the smallest St chromosome from Tai‐27 only distributed in the pericentromeric region of St genome chromosomes (Deng et al, 2013a). In addition, the DOP–PCR products of 1R and 1RS yielded weaker signals in the terminals of chromosomes than in the other regions (Deng et al, 2014). The similar phenomemon could also be found in the chromosome painting of spinach ( Spinacia oleracea L.) using DOP–PCR products of microdissected Y chromosome as a probe (Deng et al, 2013b).…”

“…Deng et al (2013a) utilized the DOP‐PCR products of St‐genome chromosome to analyze the genomic constitution of Thinopyrum intermedium . They obtained the DOP–PCR products of chromosome 1R and 1RS using the same methods, and applied them to the identification of R genome chromosome in a wheat background (Deng et al, 2014). In this study, we obtained DOP–PCR products of chromosomes 6PS and 6PL and clearly identified chromosomes 6P, 6PS and 6PL in wheat– A. cristatum addition lines using them as probes.…”

“…In mammalian species, chromosome painting can identify individual chromosome, so it is a powerful tool to study synteny and chromosomal evolution (Wienberg and Stanyon, 1997). In plant species, due to the presence of many repetitive DNA sequences in all chromosomes, this technique can only be used for identification of genome, and alien chromosomes in addition lines or translocation lines (Deng et al, 2014; Deng et al, 2013a). If the repetitive sequences were excluded from the painting probes, chromosome painting may identify individual chromosome of plant genome chromosomes (Jiang and Gill, 2006).…”

Chromosome Microdissection and Microcloning: Technique and Application in the Plant Sciences

“…The amplified products contain both high repetition and low copy sequences. Pich et al 1994, Hobza et al 2004, Deng et al 2014 Screening and identification of chromosomal microcloning Southern hybridization The genomic DNA labeled with certain markers hybridizes with the DNA library of the target chromosome/segment.…”

“…Nevertheless, the technique of chromosome microdissection and microcloning was successfully used in rye chromosomes by Saudery et al (1991), and the cloning of rye DNA was successfully achieved. Since then, the application of this technique in the field of plant research has rapidly developed (Casson et al 2005, Deng et al 2014, Cao et al 2017.…”