<abstract xmlns="http://www.w3.org/1999/xhtml">

<p>Populations of beet cyst nematodes <italic>Heterodera schachtii</italic> vary in aggressiveness and virulence toward sugar beet varieties, but also in traits like host range, or decline rate in the field. Diversity of their essential pathogenicity gene <italic>vap1</italic> is shaped by diversifying selection and gene flow. The authors developed a technique to study inter-population variation and intra-population diversity and dynamics of <italic>H. schachtii</italic> based on the gene <italic>vap1</italic>. Degenerate primers were designed to amplify, clone, and sequence this gene from diverse species and populations of cyst nematodes. This resulted in a high diversity of sequences for <italic>H. schachtii</italic>, and allowed to design non-degenerated primers to amplify a fragment suitable for sequence dependent separation of gene variants in denaturing gradient gel electrophoresis (DGGE). The developed primers span a highly variable intron and part of a slightly variable exon. A marker comprised of the 14 mostly detected gene variants was established for gel-to-gel comparisons. For individual juveniles up to six gene variants were resolved and substantial variation within and among cysts was observed. A fast and easy DNA extraction procedure for 20 pooled cysts was established, which provided DGGE patterns with high similarity among replicate samples from field populations. Permutation tests on pairwise similarities within and among populations showed significant differences among <italic>vap1</italic> patterns of field populations of <italic>H. schachtii</italic>. Similarly, gene diversity as expressed by the Shannon index was statistically different among field populations. In conclusion, the DGGE technique is a fast and – compared to sequencing approaches – inexpensive tool to compare populations of <italic>H. schachtii</italic> and link observed biological characteristics to genetic pattern.</p>
</abstract>

Populations of beet cyst nematodes Heterodera schachtii vary in aggressiveness and virulence toward sugar beet varieties, but also in traits like host range, or decline rate in the field. Diversity of their essential pathogenicity gene vap1 is shaped by diversifying selection and gene flow. The authors developed a technique to study inter-population variation and intra-population diversity and dynamics of H. schachtii based on the gene vap1. Degenerate primers were designed to amplify, clone, and sequence this gene from diverse species and populations of cyst nematodes. This resulted in a high diversity of sequences for H. schachtii, and allowed to design non-degenerated primers to amplify a fragment suitable for sequence dependent separation of gene variants in denaturing gradient gel electrophoresis (DGGE). The developed primers span a highly variable intron and part of a slightly variable exon. A marker comprised of the 14 mostly detected gene variants was established for gel-to-gel comparisons. For individual juveniles up to six gene variants were resolved and substantial variation within and among cysts was observed. A fast and easy DNA extraction procedure for 20 pooled cysts was established, which provided DGGE patterns with high similarity among replicate samples from field populations. Permutation tests on pairwise similarities within and among populations showed significant differences among vap1 patterns of field populations of H. schachtii. Similarly, gene diversity as expressed by the Shannon index was statistically different among field populations. In conclusion, the DGGE technique is a fast and – compared to sequencing approaches – inexpensive tool to compare populations of H. schachtii and link observed biological characteristics to genetic pattern.

Effector gene <italic>vap1</italic> based DGGE fingerprinting to assess variation within and among <italic>Heterodera schachtii</italic> populations

Journal of Nematology

This work is licensed under the Creative Commons Attribution 4.0 International License.

Effector gene  based DGGE fingerprinting to assess variation within and among  populations

running-head

Population genetic variations of cyst nematodes:

Populations of beet cyst nematodes Heterodera schachtii vary in aggressiveness and virulence toward sugar beet varieties, but also in traits like host range,...

Effector gene vap1 based DGGE fingerprinting to assess variation within and among Heterodera schachtii populations

Published Online: Dec 03, 2018

Page range: 517 - 528

DOI: https://doi.org/10.21307/jofnem-2018-055

Keywords
Beet cyst nematode, Genetic fingerprinting technique, Method, Electrophoresis, gene, Venom allergen like protein

© 2018 Rasha Haj Nuaima et al., published by Sciendo

This work is licensed under the Creative Commons Attribution 4.0 International License.

Effector gene vap1 based DGGE fingerprinting to assess variation within and among Heterodera schachtii populations

Published Online: Dec 03, 2018

Page range: 517 - 528

DOI: https://doi.org/10.21307/jofnem-2018-055

KeywordsBeet cyst nematode, Genetic fingerprinting technique, Method, Electrophoresis, gene, Venom allergen like protein

© 2018 Rasha Haj Nuaima et al., published by Sciendo

This work is licensed under the Creative Commons Attribution 4.0 International License.

Keywords
Beet cyst nematode, Genetic fingerprinting technique, Method, Electrophoresis, gene, Venom allergen like protein