qPCR as a Selective Tool for Cytogenetics

Abstract

qPCR is widely used in quantitative studies of plant genomes and transcriptomes. In this article, this method is considered as an auxiliary step in the preparation and selection of markers for FISH analysis. Several cases from the authors’ research on populations of the same species were reviewed, and a comparison of the closely related species, as well as the adaptation of the markers, based on satellite tandem repeats (TRs) using quantitative qPCR data was conducted. In the selected cases, TRs with contrast abundance were identified in the cases of the Dasypyrum, Thinopyrum and Aegilops species, and the transfer of TRs between the wheat and related species was demonstrated. TRs with intraspecific copy number variation were revealed in Thinopyrum ponticum and wheat-wheatgrass partial amphidiploids, and the TR showing predominant hybridization to the sea buckthorn Y chromosome was identified. Additionally, problems such as the absence of a reference gene for qPCR, and low-efficiency and self-complementary primers, were illustrated. In the cases considered here, the qPCR results clearly show high correlation with the subsequent results of the FISH analysis, which confirms the value of this method for cytogenetic studies.

Comparative assessment of the copy number of satellite repeats in the genome of Triticeae species

“…A wellestablished method for quantifying the number of copies of repetitive DNA, including satellite repeats, is quantitative realtime PCR (qPCR) (Harpke, Peterson, 2007;NavajasPérez et al, 2009;Baruch, Kashkush, 2012;Feliciello et al, 2015;Divashuk et al, 2016Divashuk et al, , 2019Divashuk et al, , 2022Pereiera et al, 2018;Shams, Raskina, 2018). Compared to Southern blot or dot-blot hybridization on a membrane, or fluorescent in situ hybridization on chromosomes, qPCR has proven to be an easier-to-use, accurate, and effective method for assessing the copy number of the target sequence.…”