Dataset Information

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

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.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.

SUBMITTER: Nuaima RH

PROVIDER: S-EPMC6909312 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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

Nuaima Rasha Haj RH Roeb Johannes J Hallmann Johannes J Daub Matthias M Otte Sandra S Heuer Holger H

Journal of nematology 20180101 4

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 de ...[more]

PMID: 31094153

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Project description:Productivity of sugar beet and brassica vegetable crops is constrained by the nematode Heterodera schachtii worldwide. In sugar beet cropping areas of Central Europe and North America, H. schachtii is managed by crop rotation, and cultivation of resistant brassica cover crops. The recently released nematode-tolerant sugar beet cultivars suffer less damage than susceptible cultivars at high initial population densities of H. schachtii. Many tolerant cultivars allow for less nematode reproduction than susceptible cultivars. Monoculture of susceptible hosts can facilitate the evolution of suppressive soil. Objectives of this study were to determine if susceptible hosts are required for this process, and if monoculture with sugar beet genotypes of different host status (susceptible, resistant, tolerant) impact this capacity. Additionally, we tested if amending soil with the cyst nematode pathogens Pasteuria nishizawae or Hyalorbilia sp. strain DoUCR50 favored the establishment of soil suppressiveness. In 4-year microplot studies with H. schachtii Schach0 or Schach1, one susceptible, one Schach0-resistant, and one tolerant sugar beet genotype were monocultured. In 2010, plots were amended with P. nishizawae or DoUCR50, the last being introduced into non-treated soil for Schach0, and into previously biocide-treated soil for Schach1. In 2011, respective Schach0 plots received a second amendment with DoUCR50. Nematode population densities and growth and yield parameters were determined annually. Effects of P. nishizawae and DoUCR50 on populations of H. schachtii were limited and not consistent. Starting in the second year of the monoculture, eggs of both H. schachtii pathotypes became diseased. Up to 90% of the total eggs were encumbered by the third cropping cycle, under the susceptible, resistant, and tolerant cultivar. In all years, the tolerant genotype produced the highest and most stable white sugar yields while yields of the other cultivars slowly improved during the monoculture. Results of this study suggested the presence of egg-infecting factors in this sugar beet monoculture that dramatically increased the proportions of diseased eggs. The tolerant cultivar allowed establishment of soil suppressiveness without the initial yield decline observed when susceptible sugar beet genotypes are grown in monoculture.

Dataset Information

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

Publications

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

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