Genome Scans Reveal Homogenization and Local Adaptations in Populations of the Soybean Cyst Nematode

Abstract

Determining the adaptive potential of alien invasive species in a new environment is a key concern for risk assessment. As climate change is affecting local climatic conditions, widespread modifications in species distribution are expected. Therefore, the genetic mechanisms underlying local adaptations must be understood in order to predict future species distribution. The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is a major pathogen of soybean that was accidentally introduced in most soybean-producing countries. In this study, we explored patterns of genetic exchange between North American populations of SCN and the effect of isolation by geographical distance. Genotyping-by-sequencing was used to sequence and compare 64 SCN populations from the United States and Canada. At large scale, only a weak correlation was found between genetic distance (Wright's fixation index, FST) and geographic distance, but local effects were strong in recently infested states. Our results also showed a high level of genetic differentiation within some populations, allowing them to adapt to new environments and become established in new soybean-producing areas. Bayesian genome scan methods identified 15 loci under selection for climatic or geographic co-variables. Among these loci, two non-synonymous mutations were detected in SMAD-4 (mothers against decapentaplegic homolog 4) and DOP-3 (dopamine receptor 3). High-impact variants linked to these loci by genetic hitchhiking were also highlighted as putatively involved in local adaptation of SCN populations to new environments. Overall, it appears that strong selective pressure by resistant cultivars is causing a large scale homogenization with virulent populations.

Microsatellite markers reveal two genetic groups in European populations of the carrot cyst nematode Heterodera carotae

“…The genetic structure and the evolutionary history of several cyst nematodes have been previously studied at different spatial scales, e.g. the potato cyst nematodes Globodera pallida (Eves-van den Akker et al, 2015;Picard et al, 2004;Picard et al, 2007;Plantard et al, 2008) and G. rostochiensis (Boucher et al, 2013;Mimee et al, 2015), the tobacco cyst nematode G. tabacum (Alenda et al, 2014;Marché et al, 2001), the beet cyst nematode Heterodera schachtii (Kim et al, 2018;Plantard and Porte, 2004), the cereal cyst nematode H. avenae 6 (Wang et al, 2018) or the soybean cyst nematode H. glycines (St-Marseille et al, 2018;Wang et al, 2015). However, to our knowledge, no study has been conducted to describe the genetic structure of the carrot cyst nematode Heterodera carotae, except two recent studies using genic markers with a diagnostic purpose (Escobar-Avila et al, 2018;Madani et al, 2017).…”

The population genetics of parasitic nematodes of wild animals

“…Hence, there is now a need for studies on a comparatively larger scale that examine the distribution of polymorphisms within genomes as well as among them. In an intriguing recent study, whole-genome sequencing was used to interrogate the population genetics of the plant-parasitic nematode Heterodera glycines without the use of a reference genome [ 170 ]. This study, which made use of the UNEAK bioinformatics pipeline [ 171 ], was able to not only elucidate the population genetic structure of H. glycines , but also to identify genetic variants showing signatures of selection.…”

Single Nematode Transcriptomic Analysis, Using Long-Read Technology, Reveals Two Novel Virulence Gene Candidates in the Soybean Cyst Nematode, Heterodera glycines

“…Nevertheless, our approach did prove crucial in the discovery of novel transcripts and novel genes of potential significance in the acquisition of pathogenicity and virulence. Other approaches, such as pool-seq based on short reads, allow the capturing of the full genetic diversity in a population, without having to amplify single nematode transcriptomes but do not allow specific alleles to be associated with traits such as virulence nor to precisely reconstruct the repertoire of splice variants [62].…”