Exploring the assumptions underlying genetic variation in host nematode resistance (Open Access publication)

The wide range of genetic parameter estimates for production traits and nematode resistance in sheep obtained from field studies gives rise to much speculation. Using a mathematical model describing host – parasite interactions in a genetically heterogeneous lamb population, we investigated the consequence of: (i) genetic relationships between underlying growth and immunological traits on estimated genetic parameters for performance and nematode resistance, and (ii) alterations in resource allocation on these parameter estimates. Altering genetic correlations between underlying growth and immunological traits had large impacts on estimated genetic parameters for production and resistance traits. Extreme parameter values observed from field studies could only be reproduced by assuming genetic relationships between the underlying input traits. Altering preferences in the resource allocation had less pronounced effects on the genetic parameters for the same traits. Effects were stronger when allocation shifted towards growth, in which case worm burden and faecal egg counts increased and genetic correlations between these resistance traits and body weight became stronger. Our study has implications for the biological interpretation of field data, and for the prediction of selection response from breeding for nematode resistance. It demonstrates the profound impact that moderate levels of pleiotropy and linkage may have on observed genetic parameters, and hence on outcomes of selection for nematode resistance.     

First evidence of cryptic species diversity and significant population structure in a widespread freshwater nematode morphospecies (Tobrilus gracilis)

Free‐living nematodes are ubiquitous and highly abundant in terrestrial and aquatic environments, where they sustain ecosystem functioning by mineralization processes and nutrient cycling. Nevertheless, very little is known about their true diversity and intraspecific population structure. Recent molecular studies on marine nematodes indicated cryptic diversity and strong genetic differentiation of distinct populations, but for freshwater nematode species, analogous studies are lacking. Here, we present the first extensive molecular study exploring cryptic species diversity and genetic population structure of a widespread freshwater nematode morphospecies, Tobrilus gracilis, from nine postglacially formed European lakes. Taxonomic species status of individuals, analysed for fragments of the mitochondrial COI gene and for the large (LSU) and small (SSU) ribosomal subunits, were determined by morphological characteristics. Mitochondrial and nuclear markers strongly supported the existence of three distinct genetic lineages (Tg I–III) within Tobrilus gracilis, suggesting that this morphospecies indeed represents a complex of highly differentiated biological species. High genetic diversity was also observed at the population level. Across the nine lakes, 19 mitochondrial, and seven (LSU) and four (SSU) nuclear haplotypes were determined. A phylogeographical analysis revealed remarkable genetic differentiation even among neighbouring lake populations for one cryptic lineage. Priority and persistent founder effects are possible explanations for the observed population structure in the postglacially colonized lakes, but ask for future studies providing direct estimates of freshwater nematode dispersal rates. Our study suggests therefore that overall diversity of limnetic nematodes has been so far drastically underestimated and challenges the assumed ubiquitous distribution of other, single freshwater nematode morphospecies.     

Reflections on Plant and Soil Nematode Ecology: Past,Present and Future

The purpose of this review is to highlight key developments in nematode ecology from its beginnings to where it stands today as a discipline within nematology. Emerging areas of research appear to be driven by crop production constraints, environmental health concerns, and advances in technology. In contrast to past ecological studies which mainly focused on management of plant-parasitic nematodes, current studies reflect differential sensitivity of nematode faunae. These differences, identified in both aquatic and terrestrial environments include response to stressors, environmental conditions, and management practices. Methodological advances will continue to influence the role nematodes have in addressing the nature of interactions between organisms, and of organisms with their environments. In particular, the C. elegans genetic model, nematode faunal analysis and nematode metagenetic analysis can be used by ecologists generally and not restricted to nematologists.     

Microsatellites reveal genetic diversity in Rotylenchulus reniformis populations

Rotylenchulus reniformis is the predominant parasitic nematode of cotton in the Mid South area of the United States. Although variable levels of infection and morphological differences have been reported for this nematode, genetic variability has been more elusive. We developed microsatellite-enriched libraries for R. reniformis, produced 1152 clones, assembled 694 contigs, detected 783 simple sequence repeats (SSR) and designed 192 SSR-markers. The markers were tested on six R. reniformis cultures from four states, Texas, Louisiana, Mississippi and Georgia, in the USA. Based on performance we selected 156 SSR markers for R. reniformis from which 88 were polymorphic across the six reniform nematode populations, showing as the most frequent motif the dinucleotide AG. The polymorphic information content of the markers ranged from 0.00 to 0.82, and the percentage of multiallelic loci of the isolates was between 40.9 and 45.1%. An interesting finding in this study was the genetic variability detected among the three Mississippi isolates, for which 22 SSR markers were polymorphic. We also tested the level of infection of these isolates on six cotton genotypes, where significant differences were found between the Texas and Georgia isolates. Coincidentally, 62 polymorphic markers were able to distinguish these two populations. Further studies will be necessary to establish possible connections, if any, between markers and level of pathogenicity of the nematode. The SSR markers developed here will be useful in the assessment of the genetic diversity of this nematode, could assist in management practices for control of reniform nematode, be used in breeding programs for crop resistance, and help in detecting the origin and spread of this nematode in the United States.     

One perfect worm

Recent studies show that local populations of the nematode Caenorhabditis elegans possess nearly as much genetic variation as that seen in existing worldwide collections. This suggests either wide-ranging migration and intense natural selection or recent dispersal, perhaps by human association. Either way, the effective population size of this ubiquitous model organism is unexpectedly small.     

甜菜胞囊线虫抗性基因及遗传工程改良策略

甜菜胞囊线虫(Heterodera schachtii)是甜菜的重要病害之一,给甜菜生产造成了极大的损失。随着分子生物学和遗传工程技术的发展,采用遗传工程改良策略进行甜菜抗性品种选育是甜菜胞囊线虫防治中最经济、有效的方法。介绍了甜菜胞囊线虫的生育史及抗性机制,综述了甜菜胞囊线虫抗性基因的克隆和鉴定研究进展及甜菜胞囊线虫抗性育种的遗传工程改良策略,并提出今后甜菜胞囊线虫抗性育种的展望。     

Genetic variation in the invasive process of Bursaphelenchus xylophilus (Aphelenchida: Aphelenchoididae) and its possible spread routes in China

Pinewood nematode (Bursaphelenchus xylophilus) is an invasive species that causes a destructive forest disease-pine wilt disease. This disease has been prevalent in some countries in Asia since the 1970s. An amplified fragment length polymorphism survey was used to compare the genetic variation of native and invasive nematode populations in China and to examine the changes in genetic diversity during the invasion process. The genetic diversity of Chinese populations was slightly higher than that of American populations. Analysis of groups sampled from different invasive stages in China, showed that no obvious change in genetic diversity. Hence, genetic drift and founder effects are not obvious in the invasion process. Phylogenetic analysis showed that Chinese pinewood nematode populations were closer to Japanese populations than to American populations. On the basis of the genetic relationships among samples, two major invasion pathways in China are suggested. One is from Guangdong to Anhui and Zhejiang, and the other is from Guangdong to Jiangsu and then from Jiangsu to Hubei, Guizhong and Congqing. The results imply that it is important to reinforce both domestic and international quarantine to control the spread of pinewood nematode.     

The free-living generation of the nematode Strongyloides papillosus undergoes sexual reproduction

The nematode genus Strongyloides consists of parasites that live as parthenogenetic females in the small intestines of their hosts. They can also form a facultative free-living generation with males and females. Recently, research on Strongyloides cellular and molecular biology has concentrated on Strongyloides ratti and Strongyloides stercoralis. We propose that the related nematode Strongyloides papillosus, a common parasite of ruminants, is well suited for comparative and evolutionary studies and we show that it is phylogentically basal to S. ratti and S. stercoralis. Based on cytological observations several reports have proposed that Strongyloides males do not contribute genetically to the next generation, leaving open the question of why males still exist. In contrast, the only study employing molecular markers showed that S. ratti males do pass on genetic material. Here, we demonstrate that in S. papillosus males also contribute molecular genetic markers to the next generation. This is interesting for two reasons. First, it shows that S. papillosus is amenable to genetic analysis and second, it indicates that sexual reproduction is more common in Strongyloides than previously assumed.     

Cloning, sequencing, and mapping of an alpha-actinin gene from the nematode Caenorhabditis elegans.

The dense-bodies in the body wall muscle of the nematode Caenorhabditis elegans function to anchor the actin thin filaments to the adjacent sarcolemma. One of the major components of the dense-bodies is the actin-binding protein alpha-actinin. To facilitate a genetic analysis of alpha-actinin, we have cloned a cDNA encoding the nematode protein, identified its position on the nematode physical map, and developed a unique PCR based approach to test the position of the cloned gene relative to known genetic deletions. The peptide sequence deduced from the cDNA shows that, apart from a few exceptional regions, the nematode protein shows strong similarity to other known alpha-actinins. Its position on the genetic map shows that none of the known muscle affecting mutations identified in C. elegans are in this alpha-actinin gene. This gene has been given the name atn-1 (alpha-actinin-1).     

Comparative genetics: a third model nematode species

Recent studies have introduced Oscheius sp. CEW1 as a third nematode species accessible to genetic analysis, joining the better known Caenorhabditis elegans and Pristionchus pacificus. A group of vulva-defective mutants in Oscheius has been identified, with defects not seen in C. elegans.     

Tropical nematode diversity: vertical stratification of nematode communities in a Costa Rican humid lowland rainforest

Comparisons of nematode communities among ecosystems have indicated that, unlike many organisms, nematode communities have less diversity in the tropics than in temperate ecosystems. There are, however, few studies of tropical nematode diversity on which to base conclusions of global patterns of diversity. This study reports an attempt to estimate nematode diversity in the lowland tropical rainforest of La Selva Biological Research Station in Costa Rica. We suggest one reason that previous estimates of tropical nematode diversity were low is because habitats above the mineral soil are seldom sampled. As much as 62% of the overall genetic diversity, measured by an 18S ribosomal barcode, existed in litter and understorey habitats and not in soil. A maximum-likelihood tree of barcodes from 360 individual nematodes indicated most major terrestrial nematode lineages were represented in the samples. Estimated 'species' richness ranged from 464 to 502 within the four 40 × 40 m plots. Directed sampling of insects and their associated nematodes produced a second set of barcodes that were not recovered by habitat sampling, yet may constitute a major class of tropical nematode diversity. While the generation of novel nematode barcodes proved relatively easy, their identity remains obscure due to deficiencies in existing taxonomic databases. Specimens of Criconematina, a monophyletic group of soil-dwelling plant-parasitic nematodes were examined in detail to assess the steps necessary for associating barcodes with nominal species. Our results highlight the difficulties associated with studying poorly understood organisms in an understudied ecosystem using a destructive (i.e. barcode) sampling method.     

A recessive soybean cyst nematode allele for incompatibility with soybean PI 88287

The objective of this research was to characterise the degree of dominance of a soybean cyst nematode (Heterodera glycines) allele for incompatibility which interacts with a recessive soybean (Glycine max) allele for incompatibility to prevent the formation of cysts. Crosses of inbred nematode populations were made and the F, and F, populations evaluated for the numbers of cysts they could produce on several soybean lines. The nematode gene for avirulence interacts with the one recessive gene for resistance in soybean line PI 88287 and also appears to be recessive. This is the first example of a recessive-recessive gene-for-gene interaction; genes for avirulence and resistance are usually dominant. The difficulties of doing definitive genetic studies with cyst nematodes are discussed.     

The nematode Caenorhabditis elegans as a model to study the roles of proteoglycans

The nematode Caenorhabditis elegans is a powerful animal model for exploring the genetic basis of metazoan development. Recent genetic and biochemical studies have revealed that the molecular machinery of glycosaminoglycan (GAG) biosynthesis and modification is highly conserved between C. elegans and mammals. In addition, genetic studies have implicated GAGs in vulval morphogenesis and zygotic cytokinesis. The extensive knowledge of C. elegans biology, including its elucidated cell lineage, together with the completed and well annotated DNA sequence and availability of reverse genetic tools, provide a platform for studying the functions of proteoglycans and their GAG modification. Published in 2003.     

Increasing the resistance of rape plants to the parasitic nematode Heterodera schachtii using RNAi technology

A vector for the constitutive expression of antisense to the conservative region of the 8H07 gene of the nematode H.schachtii dsRNA is constructed and a genetic transformation of rape plants is conducted by means of A. tumefaciens. Using molecular genetic methods, the presence of the vector expression of antinematode dsRNA in the genome of transgenic rape plants is shown, as well as the high level of their silencing activity is confirmed both in nematodes and in infected plants. In laboratory studies, a considerable increase in the tolerance of transgenic rape plants to the root parasitic nematode H. schachtii was shown for physiological signs.     

Transport proteins of the ABC systems superfamily and their role in drug action and resistance in nematodes

The completion of a number of nematode genomes has provided significant information on ABC systems in these organisms. Nematodes have more ABC systems genes and greater diversity than do mammalian species. Class 1 and class 2 ABC systems, more commonly known as ABC transporters, are present. As in other organisms, nematode ABC systems are characterized by a highly conserved ATP-binding domain (ABC_2) and a less conserved transmembrane domain (ABC_TM1/TM1F). Studies of drug resistance in nematodes have suggested that ABC transporters are part of the resistance mechanism. Evidence in support of this has been obtained from genetic studies where an association between anthelmintic selection and ABC transporters was shown by comparisons between unselected and drug selected, or resistant, populations of parasitic nematodes. In drug resistant populations, genetic polymorphism and diversity, genotype patterns, and linkage disequilibrium were disrupted. Multidrug resistance (MDR) reversing agents that inhibit ABC function improve efficacy in sensitive nematode populations and restore sensitivity in resistant populations. Similar to the situation in clinical oncology, overexpression of ABC systems occurs in drug resistant and sensitive populations following drug exposure, particularly those in the P-glycoprotein (PGP) subfamily. Deletion or disruption of ABC genes, particularly PGP and the multidrug resistance associated protein (MRP), increases sensitivity to some drugs, particularly ivermectin. These studies provide evidence that ABC transporters play a role in drug action and resistance in nematodes.     

Evolution of nematode development

Multiple evolutionary variations occur in the cellular and genetic programming of nematode development. Many changes involve alterations of inductive interactions. Surprisingly, inductive processes vary during evolution, irrespective of changes in the final cell lineages and morphological structures. Genetic studies in some nematodes also shed light on the underlying mechanisms of evolutionary change.     

Cell proliferation and growth in C. elegans.

The cell division and differentiation events that occur during the development of the nematode Caenorhabditis elegans are nearly identical between different individuals, a feature that distinguishes this organism from larger and more complex metazoans, such as humans and Drosophila. In view of this discrepancy, it might be expected that the regulation of cell growth, division and differentiation in C. elegans would involve mechanisms separate from those utilized in larger animals. However, the results of recent genetic, molecular and cellular studies indicate that C. elegans employs an arsenal of developmental regulatory mechanisms quite similar to those wielded by its arthropod and vertebrate relatives. Thus, the nematode system is providing both novel and complementary insights into the general problem of how growth and patterning events are integrated in development. This review offers a general perspective on the regulation of cell division and growth in C. elegans, emphasizing recent studies of these crucial aspects of development.     

Linking DNA sequences to morphology: cryptic diversity and population genetic structure in the marine nematode Thoracostoma trachygaster (Nematoda,Leptosomatidae)

Derycke, S., De Ley, P., De Ley, I.T., Holovachov, O., Rigaux, A. & Moens, T. (2010). Linking DNA sequences to morphology: cryptic diversity and population genetic structure in the marine nematode Thoracostoma trachygaster (Nematoda, Leptosomatidae).—Zoologica Scripta, 39, 276–289. Recent taxonomic and population genetic studies have revealed the presence of substantial cryptic diversity through sequence analysis of nematode morphospecies classified in different major clades. Correct interpretations of intra‐ and interspecific genetic variation require certainty about the conspecificity of the sequenced specimens, which in turn must depend on appropriate protocols with built‐in verifiability procedures. In this study, we performed a population genetic study in the free‐living marine nematode Thoracostoma trachygaster, a member of one of the earliest major clades to diverge in nematode phylogeny. We collected 367 nematodes from 11 populations located in the Californian Bight, all of which were video captured before DNA extraction to document and verify their individual morphology. Sequences for the cytochrome c oxidase subunit 1 (COI), D2D3 and 18S genes showed eight deeply divergent clades, and using a reverse taxonomy approach, six of these clades proved to be other morphospecies than T. trachygaster. Phylogenetic analyses of COI, internal transcribed spacer and D2D3 showed evidence for two sympatrically distributed cryptic species within the morphospecies T. trachygaster. Population genetic analyses of the most widespread cryptic species showed a moderate genetic structuring (Φ_ST = 0.28), and 18% of this genetic variation was caused by differences between populations north and south of Point Conception. Within the southern Californian Bight, some genetic differentiation could be attributed to differences between populations north and south of Malibu, supporting the idea of a barrier to gene flow near Los Angeles region. The results for T. trachygaster support the contention that species diversity within free‐living nematodes is underestimated, and that dispersal of marine nematodes from tidal environments associated with kelp holdfasts is substantial at scales of a few 100 km.     

Beyond induced mutants: using worms to study natural variation in genetic pathways

Induced mutants in the nematode Caenorhabditis elegans are used to study genetic pathways of processes ranging from aging to behavior. The effects of such mutations are usually analyzed in a single wildtype background: N2. However, studies in other species demonstrate that the phenotype(s) of induced mutations can vary widely depending on the genetic background. Moreover, induced mutations in one genetic background do not reveal the allelic effects that segregate in natural populations and contribute to phenotypic variation. Because other wildtype Caenorhabditis spp., including C. elegans, are now available, we review how current mapping resources and methodologies within and between species support the use of Caenorhabditis spp. for studying genetic variation, with a focus on pathways associated with human disease.     

RNAi As a tool for understanding germline development in Caenorhabditis elegans: uses and cautions.

RNA-mediated genetic interference (RNAi) has become a very useful tool for analyzing gene function in development and other processes. RNAi can be used as a complement to traditional genetic studies or as a primary means of determining biological function. However, the efficacy of RNAi depends on a variety of factors that the researcher must take into consideration. This review focuses on germline development in the nematode, Caenorhabditis elegans, and discusses the uses and limitations of RNAi in providing new information about gene function as well as the possible endogenous role RNAi plays in germline physiology.