The Effects of Founding Events and Agricultural Practices on the Genetic Structure of Three Metapopulations of Globodera pallida

[Quarantine nematode species and pathotypes potentially dangerous for domestic potato production: populations diversity and the genetics of potato resistance]

Обзор посвящен проблеме потенциально опасных для отечественного картофелеводства каран- тинных видов и патотипов нематод. Картофель поражают более 30 видов паразитических нематод, однако в статье основное внимание уделено самым вредоносным, приносящим большой ущерб картофелеводству пред- ставителям родов Globodera, Ditylenchus, Nacobbus и Meloidogyne. Проанализированы фитопатологические и молекулярные методы идентификации видов и патотипов и основные достижения в изучении изменчивости популяций паразитических нематод картофеля. Показано, что, благодаря особенностям жизненного цикла не- матод и лабильности их геномов, генетическая изменчивость этих организмов очень велика, что создает угрозу образования новых патогенных генотипов паразита. Сведения о внутри- и межпопуляционной изменчивости нематод важны для изучения путей интродукции и распространения отдельных видов, а также поиска корреля- ций молекулярных маркеров с определенным патотипом. Филогенетические исследования, основанные на со- временных данных по генетической изменчивости популяций, позволили выявить комплексы видов у Globodera pallida (Stone) Behrens и Nacobbus aberrans (Thorne) Thorne & Allen (sensu lato), включающие криптические виды. К основным составляющим успешной защиты, предотвращающей массовое распространение паразитических нематод, относятся карантинные мероприятия, агротехнические приемы, биологические способы защиты и возделывание устойчивых сортов. Особое внимание в обзоре уделено вопросам селекции сортов картофеля с длительной устойчивостью к различным видам нематод, поскольку возделывание таких сортов – экологически наиболее безопасный и экономически выгодный способ предотвращения эпифитотий. В настоящее время до- стигнуты значительные успехи в генетической защите сортов картофеля, особенно в отношении цистообразую- щих нематод. Приведены сведения об источниках устойчивости картофеля к паразитическим нематодам, выде- ленных в коллекциях диких и культурных видов. Проанализированы данные об идентифицированных R-генах и QTL устойчивости, которые были интрогрессированы в селекционный материал с помощью различных методов и подходов. Представлены результаты изучения структурной и функциональной организации генов устойчиво- сти к цистообразующим нематодам картофеля. Рассмотрены результаты исследований по использованию моле- кулярных маркеров определенных генов в маркер-опосредованной селекции для создания новых устойчивых сортов, в том числе с групповой устойчивостью.

A Spatiotemporal Analysis and Dispersal Patterns of the Potato Cyst Nematode Globodera pallida in Idaho

The potato cyst nematode Globodera pallida is a globally regulated potato pest. It was detected for the first time in the United States in the state of Idaho in 2006, and as of February 2019, the infestation is limited to 1,326 hectares. G. pallida is a specialized obligate sedentary endoparasite that can survive in the soil for up to 30 years in the absence of its potato host. In highly infested fields, the nematode can reduce tuber yields up to 80% and is spread mainly through the movement of soil, tubers, or farm equipment. The objectives of this study were to describe the spatiotemporal pattern of G. pallida in infested fields and model its dispersal patterns in southeastern Idaho. We used geostatistical tools and simulation models for precise mapping and to describe the relationships between G. pallida incidence and the spatial configurations. We found that the nematode is spatially clustered and prevalent around edges of fields, and its dispersal pattern followed the direction of cultivation. We found that the absence of potato in an infested field significantly reduced the number of cysts sampled each year subsequent to the initial delimitation sampling in 2007. Phytosanitary measures prohibiting the growth of potato contributed to stopping nematode reproduction, and the use of chemical fumigants and biofumigant cover crops contributed to a significant reduction in egg viability. We observed a process of a nonlinear decline in the prevalence of cysts as the distance separation from the primary infestation focus increased. A power law model was used to fit G. pallida dispersal capabilities. This study contributed to describing G. pallida infestation for Idaho. The goal of this study is to provide information on the spatial pattern and landscape ecology of G. pallida in Idaho for policy makers, industry, and researchers as well as facilitate common understandings on the challenges and opportunities for controlling this pest in Idaho.

A new method for studying population genetics of cyst nematodes based on Pool-Seq and genomewide allele frequency analysis

Cyst nematodes are important agricultural pests responsible for billions of dollars of losses each year. Plant resistance is the most effective management tool, but it requires a close monitoring of population genetics. Current technologies for pathotyping and genotyping cyst nematodes are time-consuming, expensive and imprecise. In this study, we capitalized on the reproduction mode of cyst nematodes to develop a simple population genetic analysis pipeline based on genotyping-by-sequencing and Pool-Seq. This method yielded thousands of SNPs and allowed us to study the relationships between populations of different origins or pathotypes. Validation of the method on well-characterized populations also demonstrated that it was a powerful and accurate tool for population genetics. The genomewide allele frequencies of 23 populations of golden nematode, from nine countries and representing the five known pathotypes, were compared. A clear separation of the pathotypes and fine genetic relationships between and among global populations were obtained using this method. In addition to being powerful, this tool has proven to be very time- and cost-efficient and could be applied to other cyst nematode species.

Resistance genes against plant-parasitic nematodes: a durable control strategy?

Plant-parasitic nematodes are a major pest of all agricultural systems, causing extensive economic losses. Natural resistance (R) genes offer an alternative to chemical control and have been shown effectively to limit nematode damage to crops in the field. Whilst a number of resistant cultivars have conferred resistance against root-knot and cyst nematodes for many decades, an increasing number of reports of resistance-breaking nematode pathotypes are beginning to emerge. The forces affecting the emergence of virulent nematodes are complex, multifactorial and involve both the host and parasite of the plant-nematode interaction. This review provides an overview of the root-knot and cyst nematodeRgenes characterised to date, in addition to examining the evolutionary forces influencing nematode populations and the emergence of virulence. Finally, potential strategies to improveRgene durability in the field are outlined, and areas that would benefit from further research efforts are highlighted.

Origin and genetic diversity of Western European populations of the potato cyst nematode (Globodera pallida) inferred from mitochondrial sequences and microsatellite loci

Native to South America, the potato cyst nematode Globodera pallida is one of the principal pests of Andean potato crops and is also an important global pest following its introduction to Europe, Africa, North America, Asia and Oceania. Building on earlier work showing a clear south to north phylogeographic pattern in Peruvian populations, we have been able to identify the origin of Western European populations with high accuracy. They are all derived from a single restricted area in the extreme south of Peru, located between the north shore of the Lake Titicaca and Cusco. Only four cytochrome b haplotypes are found in Western Europe, one of them being also found in some populations of this area of southern Peru. The allelic richness at seven microsatellite loci observed in the Western European populations, although only one-third of that observed in this part of southern Peru, is comparable to the allelic richness observed in the northern region of Peru. This result could be explained by the fact that most of the genetic variability observed at the scale of a field or even of a region is already observed at the scale of a single plant within a field. Thus, even introduction via a single infected potato plant could result in the relatively high genetic variability observed in Western Europe. This finding has important consequences for the control of this pest and the development of quarantine measures.

Inbreeding and population structure of the potato cyst nematode (Globodera pallida) in its native area (Peru)

The dispersal abilities and the population genetic structure of nematodes living in the soil are poorly known. In the present study, we have pursued these issues in the potato cyst nematode Globodera pallida, which parasitizes potato roots and is indigenous to South America. A hierarchical sampling regime was conducted in Peru to investigate gene flow on regional, field and plant scales. Multilocus genotypes of single individuals were obtained using eight polymorphic microsatellites markers. Large heterozygote deficiencies were observed at most loci. The limited active dispersal of larvae from their cyst, which favours mating between (half) siblings, could be responsible for this pattern. Within fields, as well as among fields within regions (even 35 km apart), low F(ST) values suggest extensive gene flow. Among fields within regions, only 1.5-4.4% genetic variability was observed. Passive dispersal of cysts by natural means (wind, running water, or wild animals) or by anthropogenic means (tillage, movement of infected seed tubers) is probably responsible for the results observed. Among regions, high F(ST) values were observed. Thus long-range dispersal (more than 320 km apart) is probably limited by major biogeographical barriers such as the mountains found in the Andean Cordillera. These results provide useful information for the management of resistant varieties, to slow down the emergence and spread of resistance-breaking pathotypes.

Population genetic structure of the sugar beet cyst nematode Heterodera schachtii: a gonochoristic and amphimictic species with highly inbred but weakly differentiated populations

The sugar beet cyst nematode Heterodera schachtii is a soil-dwelling phytoparasitic nematode that feeds on beet roots. It is an important pest in most sugar beet growing areas, and better knowledge of its genetic variability is an important step to preserve the durability of resistant sugar beet varieties. The population genetic structure of this species in northern France was studied using five microsatellite markers. A hierarchical sampling design was used to investigate spatial structuring at the scale of the region, the field and the plant. Multilocus genotypes were obtained for single individual second-stage larvae, using only one individual per cyst in order to avoid the analysis of closely allied individuals (larvae from the same cyst share at least the same mother). A consistent trend of heterozygote deficit at all loci was observed at all spatial scales. Heterozygote deficit at the level of individual plants argues against its generation through a Wahlund effect. Inbreeding could be due to very limited active dispersal of larvae in the soil, favouring mating between siblings, such as larvae emerging from the same cyst. Such behaviour could have important consequences for the evolution of virulence in increasing the production of homozygous virulent individuals. Moreover, an analysis of molecular variance (amova) reveals that only 1.6% of the genetic variability is observed among regions, 3.7% among fields of the same region and 94.6% within fields. The very low level of genetic differentiation among fields is also indicated by low values of FST (</= 0.105) even for fields 150 km apart. We suggest that long-distance gene flows occur due to passive transport of cysts by human activities, water or wind. As such mechanisms of gene flow would involve cysts and not larvae, the strong signals of inbreeding observed at the local scale should not be disrupted. To our knowledge, this study constitutes the first investigation of the genetic structure of a phytoparasitic nematode based on neutral codominant genetic markers scored in single individuals.