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Next-generation sequencing (NGS) was used to study polymorphism in a fragment of the
ND4
gene encoding NADH dehydrogenase subunit 4. The point substitution range was evaluated in populations of the cowpea aphid
Aphis craccivora
C.L. Koch, the English grain aphid
Sitobion avenae
Fabricius, the bird cherry-oat aphid
Rhopalosiphum padi
L., and the greenbug
Schizaphis graminum
Rondani collected in Krasnodar Territory and in Northwestern Russia. The detected mitochondrial haplotypes matched the reference sequences by 96–100%. The level of intraspecific polymorphism of the
ND4
gene was 0.2–4.0% in
A. craccivora
, 0.2–1.9% in
S. avenae
, 0.9–3.3% in
Rh.
padi
, and 0.2–0.9% in
Sch.
graminum
. The proportion of polymorphic sites in the
ND4
gene sequences among different aphid species was higher than within one species. Analysis of the mitochondrial haplotype ratio can be used to assess the influence of various factors, such as host plant resistance, on the structure of insect populations. A significant difference in the ratio of Sg1–Sg3 haplotypes was observed between
Sch.
graminum
samples collected simultaneously on sorghum varieties differing in resistance to this aphid, and a unique Sg4 haplotype was found in the sample from the moderately resistant Efremovskoe Beloe variety.