Genetic diversity of the breeding collection of tomato varieties in Kazakhstan assessed using SSR, SCAR and CAPS markers

Pozharskiy A. Kostyukova V. Khusnitdinova M. Adilbayeva K. Nizamdinova G. Kapytina A. Kerimbek N. Taskuzhina A. Kolchenko M. Abdrakhmanova A. Kisselyova N. Kalendar R. Gritsenko D.
2023 PeerJ Inc.

PeerJ
2023 #11

Tomato is one of the most prominent crops in global horticulture and an important vegetable crop in Kazakhstan. The lack of data on the genetic background of local varieties limits the development of tomato breeding in the country. This study aimed to perform an initial evaluation of the breeding collection of tomato varieties from the point of view of their genetic structure and pathogen resistance using a set of PCR based molecular markers, including 13 SSR markers for genetic structure analysis, and 14 SCAR and CAPS markers associated with resistance to five pathogens: three viruses, fungus Fusarium oxysporum, and oomycete P hytophthora infestans. Nine SSR markers were with a PIC value varying from 0.0562 (low information content) to 0.629 (high information content). A weak genetic structure was revealed in the samples of varieties including local cultivars and, predominantly, varieties from Russia and other ex-USSR countries. The local varieties were closely related to several groups of cultivars of Russian origin. Screening for a set of resistance markers revealed the common occurrence of the resistance locus I against Fusarium oxysporum and only the occasional presence of resistance alleles of other markers. No markers of resistance to the three considered viruses were revealed in local tomato varieties. Only two local cultivars had markers of resistance to P. infestans, and only the ‘Meruert’ cultivar had a combination of resistance markers against P. infestans and F. oxysporum. The obtained results have demonstrated the need for further studies of local tomato varieties with a wider range of molecular markers and source germplasm to lay a foundation for the development of tomato breeding in Kazakhstan. Copyright 2023 Pozharskiy et al.

Disease resistance , Genetic markers , PCR , Solanum lycopersicum

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Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
Department of Molecular Biology and Genetics, Al Farabi Kazakh National University, Almaty, Kazakhstan
Fruit and Vegetable Research Institute, Almaty, Kazakhstan
Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan

Laboratory of Molecular Biology
Department of Molecular Biology and Genetics
Fruit and Vegetable Research Institute
Helsinki Institute of Life Science HiLIFE
National Laboratory Astana

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