HR matching - molecular pathotyping of parasitic nematodes to maximize agronomic life span of non-hosts and host plant resistances

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Netherlands

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Abstract

Fertile arable soils are among the most precious and basic commodities on our planet as they are indispensible for the production of food, feed and fiber. Soil is teeming with life, and the soil living community provides essential functions such as carbon and nutrient cycling, and water retention. The condition of the soil living community is gradually declining at a global scale, mainly due to large-scale, single crop production systems in combination with non-durable agricultural practices. For food production at an affordable price, large scale mono-crop production systems are unavoidable, but pathogens thrive is such systems. For decades wide-spectrum pesticides have been used especially for below-ground pathogen control. Because of their highly negative impact on the environment, most of these wide-spectrum pesticides have been or will be phased out(not just in the European Union but worldwide. With an estimated damage of $US 125 billion per year [1], plant-parasitic nematodes are probably the most harmful category of soil pathogens. Mainly because of their limited mobility in soil and their low number of generations per year, host plant resistances are a remarkably durable means to manage of this category of pathogens. The fundament of host plant resistances is the recognition of the pathogen by the plant. Knowledge about the virulence determinants of individual plant-parasitic nematode species is essential to predict the effectiveness of host plant resistances. Fast and affordable diagnostic assays for the determination of virulence characteristics of plant-parasitic nematodes are required to fully exploit the control potential of resistant varieties and non-hosts. Currently, diagnostics for virulence characteristics compatible with practical applications are non-existent. To manipulate their hosts, plant-parasitic nematodes secrete a diverse repertoire of proteins, so-called effectors. To evade being recognized by highly specific resistance proteins in host plants, parasitic nematodes constantly modify their effectors and this process has resulted in enormous expansion of effector gene families. Hence, virulence determinants of plant-parasitic nematodes should be sought among (a) expanded gene families, showing (b) diversifying selection, and encoding proteins (c) harboring secretion signals. In this project, we will use a field pathogenomics approach to identify members of effector families that trigger three, commercially highly relevant resistances in potato: the H1 gene against two pathotypes of the potato cyst nematode (PCN) Globodera rostochiensis, Grp1 conferring resistance against a G. rostochiensis and a G. pallida pathotype, and Rmc1, a major R gene against the Columbian root-knot nematode Meloidogyne chitwoodi. By exploiting the same principles, we will pinpoint effectors that determine host plant specificities of races of the stem nematode Ditylenchus dipsaci, a major pathogen in horticulture (including flower bulbs). Based on our preliminary data with a tropical root knot nematode, we foresee that criteria a, b and c will result about 15 candidate virulence-determining gene families per nematode species. Targeted PCR amplification of these families followed by next generation sequencing in a range of well-characterized populations will provide insight in environment-exposed, variable protein domains that tightly correlate with resistance protein activation and, in case of the stem nematode, host preference. Effector domain variations that determine recognition by selected resistance proteins, or - in case of races of stem nematodes - host preferences, will serve as the very basis for affordable and specific quantitative PCR assays that will allow full exploitation of the control potential of resistant and non-host plant genotypes.