Polymorphism of Russian Populations of Rhopalosiphum padi L. Based on DNA Markers

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Abstract

Using the next-generation sequencing (NGS) technology, the nucleotide polymorphism in a fragment of the ND4 gene encoding NADH dehydrogenase subunit 4 was studied in 14 samples from three populations of the bird cherry-oat aphid (Rhopalosiphum padi L.) and the range of nucleotide polymorphism was determined. The insects were collected in 2021 and 2022 in the North-West of Russia (in the vicinity of St. Petersburg) and in the northern Caucasus (Krasnodar Territory and Dagestan). Mitochondrial DNA haplotypes were identified, which have 97.95–99.80% sequence identity with the reference GenBank accession number KT447631.1. The level of intraspecific polymorphism of a 438 bp ND4 gene fragment in Rh. padi varied from 0.2 to 4.3%. In the two-year experiments, 33 polymorphic sites (17 transitions and 16 transversions) were found in the ND4 sequences, which made it possible to identify 30 mitochondrial DNA haplotypes. The Rh. padi populations collected simultaneously on different host plants or at different times on bird cherry (spring) and cereals (summer) differed in the proportion of the main haplotype, as well as in the composition of unique minor haplotypes. Analysis of the ratio of mitochondrial DNA haplotypes suggests the important role of the host plant genotype in the formation of the structure of Rh. padi populations.

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About the authors

E. E. Radchenko

Vavilov All-Russian Institute of Plant Genetic Resources

Author for correspondence.
Email: eugene_radchenko@rambler.ru
Russian Federation, St. Petersburg, 190000

I. N. Anisimova

Vavilov All-Russian Institute of Plant Genetic Resources

Email: eugene_radchenko@rambler.ru
Russian Federation, St. Petersburg, 190000

N. V. Alpatieva

Vavilov All-Russian Institute of Plant Genetic Resources

Email: eugene_radchenko@rambler.ru
Russian Federation, St. Petersburg, 190000

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Supplementary files

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2. Fig. 1. Diversity of the 438 bp fragment of the mitochondrial ND4 gene in Rh. padi samples. Analysis of 34 nucleotide sequences was performed in the MEGA7 program [13] using the UPGMA algorithm (unweighted pairwise grouping with averaging) [17].

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3. Fig. 2. Alignment of selected nucleotide sequences found in Rh. padi samples. Unique substitutions found in the insect sample collected in 2021 on wheat are highlighted.

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4. Fig. 3. Frequency of mtDNA haplotypes in Rh. padi samples collected in St. Petersburg on bird cherry, wheat and barley in 2021.

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5. Fig. 4. Occurrence of mtDNA haplotypes in Rh. padi samples collected in St. Petersburg on bird cherry, barley, oats and two wheat varieties in 2022.

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6. Fig. 5. Multivariate diagram of genetic similarity by mtDNA haplotypes between Rh. padi samples (1–14) according to Fst fixation index. 1 – Dagestan, wild sorghum, 04.2021; 2 – St. Petersburg, bird cherry, 05.2021; 3 – St. Petersburg, wheat collection, 06.2021; 4 – St. Petersburg, barley collection, 06.2021; 5 – Krasnodar Krai, barley collection, 07.2021; 6 – Krasnodar Krai, sorghum (variety SLV-2), 07.2021; 7 – Krasnodar Krai, sorghum (Efremovskoye white), 07.2021; 8 – Dagestan, wheat (Bezostaya 1), 05.2022; 9 – St. Petersburg, wheat (Leningradka), 07.2022; 10 – St. Petersburg, barley (Belogorsky), 08.2022; 11 – St. Petersburg, wheat (Leningradka), 08.2022; 12 – St. Petersburg, wheat (Delfi 400), 08.2022; 13 – St. Petersburg, oats (Borrus), 08.2022; 14 – St. Petersburg, bird cherry, 05.2022.

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7. Fig. 6. Multivariate diagram of genetic similarity by mtDNA haplotypes between Rh. padi populations according to the Fₛₜ fixation index.

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