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qPCR as a Selective Tool for Cytogenetics.

Mikhail G Divashuk¹, Ekaterina A Nikitina¹, Victoria M Sokolova¹

¹All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia.

Plants (Basel, Switzerland)

|January 8, 2023

Summary

Quantitative PCR (qPCR) aids in selecting markers for Fluorescence In Situ Hybridization (FISH) analysis in plant genomics. This study demonstrates qPCR

Keywords:

DNA repeats copy number fluorescent in situ hybridization sea buckthorn tandem satellite repeats wheat wheatgrass whole genome sequencing

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Area of Science:

Plant Genomics
Cytogenetics
Molecular Biology

Background:

Quantitative PCR (qPCR) is a standard technique for plant genome and transcriptome studies.
qPCR can serve as a crucial auxiliary step for marker selection in Fluorescence In Situ Hybridization (FISH) analysis.

Purpose of the Study:

To evaluate the utility of qPCR in identifying and selecting satellite tandem repeats (TRs) for FISH analysis.
To compare TR abundance and transferability across related plant species using qPCR data.

Main Methods:

Utilized quantitative qPCR to analyze satellite tandem repeat (TR) abundance in *Dasypyrum*, *Thinopyrum*, and *Aegilops* species.
Assessed TR transferability between wheat and related species.
Investigated intraspecific copy number variation of TRs in *Thinopyrum ponticum* and wheat-wheatgrass partial amphidiploids.

Main Results:

Identified TRs with contrasting abundance and demonstrated TR transfer between wheat and related species.
Revealed intraspecific copy number variation in TRs and identified a TR specific to the sea buckthorn Y chromosome.
Highlighted challenges in qPCR, including the absence of reference genes and primer inefficiencies.

Conclusions:

qPCR data strongly correlate with subsequent FISH analysis results, validating its role in cytogenetic studies.
qPCR is a valuable tool for preparing and selecting markers for FISH, aiding in plant genome research.