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Open AccessArticle

Development of Specific Thinopyrum Cytogenetic Markers for Wheat-Wheatgrass Hybrids Using Sequencing and qPCR Data

1
Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia
2
Kurchatov Genomics Center—ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(12), 4495; https://doi.org/10.3390/ijms21124495
Received: 14 May 2020 / Revised: 15 June 2020 / Accepted: 21 June 2020 / Published: 24 June 2020
(This article belongs to the Collection Genetics and Molecular Breeding in Plants)
The cytogenetic study of wide hybrids of wheat has both practical and fundamental values. Partial wheat-wheatgrass hybrids (WWGHs) are interesting as a breeding bridge to confer valuable genes to wheat genome, as well as a model object that contains related genomes of Triticeae. The development of cytogenetic markers is a process that requires long and laborious fluorescence in situ hybridization (FISH) testing of various probes before a suitable probe is found. In this study, we aimed to find an approach that allows to facilitate this process. Based on the data sequencing of Thinopyrum ponticum, we selected six tandem repeat (TR) clusters using RepeatExplorer2 pipeline and designed primers for each of them. We estimated the found TRs’ abundance in the genomes of Triticum aestivum, Thinopyrum ponticum, Thinopyrum intermedium and four different WWGH accessions using real-time qPCR, and localized them on the chromosomes of the studied WWGHs using fluorescence in situ hybridization. As a result, we obtained three tandem repeat cytogenetic markers that specifically labeled wheatgrass chromosomes in the presence of bread wheat chromosomes. Moreover, we designed and tested primers for these repeats, and demonstrated that they can be used as qPCR markers for quick and cheap monitoring of the presence of certain chromosomes of wheatgrass in breeding programs. View Full-Text
Keywords: DNA repeats; fluorescence in situ hybridization; real-time quantitative PCR; wheat-wheatgrass hybrids DNA repeats; fluorescence in situ hybridization; real-time quantitative PCR; wheat-wheatgrass hybrids
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Nikitina, E.; Kuznetsova, V.; Kroupin, P.; Karlov, G.I.; Divashuk, M.G. Development of Specific Thinopyrum Cytogenetic Markers for Wheat-Wheatgrass Hybrids Using Sequencing and qPCR Data. Int. J. Mol. Sci. 2020, 21, 4495.

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