Phenotyping mediterranean durum wheat landraces for resistance to Zymoseptoria tritici in Tunisia

Durum wheat landraces have huge potential for the identification of genetic factors valuable for improving resistance to biotic stresses. Tunisia is known as a hot spot for Septoria tritici blotch disease (STB), caused by the fungus Zymoseptoria tritici (Z. tritici). In this context, a collection of 3166 Mediterranean durum wheat landraces were evaluated at the seedling and adult stages for STB resistance in the 2016–2017 cropping season under field conditions in Kodia (Tunisia). Unadapted/susceptible accessions were eliminated to reach the final set of 1059 accessions; this was termed the Med-collection, which comprised accessions from 13 countries and was also screened in the 2018–2019 cropping season. The Med-collection showed high frequency of resistance reactions, among which over 50% showed an immune reaction (HR) at both seedling and adult growth stages. Interestingly, 92% of HR and R accessions maintained their resistance levels across the two years, confirming the highly significant correlation found between seedling-and adult-stage reactions. Plant Height was found to have a negative significant effect on adult-stage resistance, suggesting that either this trait can influence disease severity, or that it can be due to environmental/epidemiological factors. Accessions from Italy showed the highest variability, while those from Portugal, Spain and Tunisia showed the highest levels of resistance at both growth stages, suggesting that the latter accessions may harbor novel QTLs effective for STB resistance

Characterization of Major Histocompatibility Complex (MHC) DRB Exon 2 and DRA Exon 3 Fragments in a Primary Terrestrial Rabies Vector (Procyon lotor)

The major histocompatibility complex (MHC) presents a unique system to explore links between genetic diversity and pathogens, as diversity within MHC is maintained in part by pathogen driven selection. While the majority of wildlife MHC studies have investigated species that are of conservation concern, here we characterize MHC variation in a common and broadly distributed species, the North American raccoon (Procyon lotor). Raccoons host an array of broadly distributed wildlife diseases (e.g., canine distemper, parvovirus and raccoon rabies virus) and present important human health risks as they persist in high densities and in close proximity to humans and livestock. To further explore how genetic variation influences the spread and maintenance of disease in raccoons we characterized a fragment of MHC class II DRA exon 3 (250bp) and DRB exon 2 (228 bp). MHC DRA was found to be functionally monomorphic in the 32 individuals screened; whereas DRB exon 2 revealed 66 unique alleles among the 246 individuals screened. Between two and four alleles were observed in each individual suggesting we were amplifying a duplicated DRB locus. Nucleotide differences between DRB alleles ranged from 1 to 36 bp (0.4–15.8% divergence) and translated into 1 to 21 (1.3–27.6% divergence) amino acid differences. We detected a significant excess of nonsynonymous substitutions at the peptide binding region (P = 0.005), indicating that DRB exon 2 in raccoons has been influenced by positive selection. These data will form the basis of continued analyses into the spatial and temporal relationship of the raccoon rabies virus and the immunogenetic response in its primary host

Amino acid sequences of MHC DRB exon 2 alleles in raccoons.

<p>Dots indicate identity to the reference sequences. The putative peptide binding regions (PBR; Brown et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012066#pone.0012066-Brown1" target="_blank">[38]</a>; Stern et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012066#pone.0012066-Stern1" target="_blank">[39]</a>) are marked with asterisks.</p

Average rates of nonsynonymous substitutions per nonsynonymous site (d_N) and synonymous substitutions per synonymous site (d_S).

<p>Results are given as percentages (stander errors obtained through 1000 bootstrap replicates in parentheses) and results of the Z-test for positive selection.</p

Bayesian phylogenetic relationship of raccoon MHC DRB exon 2.

<p>This tree was constructed using the best fit model from the JModel test <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012066#pone.0012066-Guindon1" target="_blank">[42]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012066#pone.0012066-Posada1" target="_blank">[43]</a>. In addition to the 66 raccoon alleles, three MHC alleles belonging to other mammals were included as outgroups: <i>Zalophus californianus</i> (GenBank Accession AY491456), <i>Ailuropoda melanoleuca</i> (GenBank Accession EF125965), and <i>Mustela lutreola</i> (GenBank Accession EU263550).</p

Number of individuals and geographic locations of MHC DRB exon 2 alleles.

<p>Number of individuals and geographic locations of MHC DRB exon 2 alleles.</p

Average nucleotide and amino acid distances among raccoon MHC DRB exon 2 alleles.

<p>Standard errors (in parentheses) were obtained through 1000 bootstrap replicates. Distances were corrected for multiple substitutions using K2P model for nucleotide distances and Poisson distribution for amino acid differences. Putative peptide binding region (PBR) sites were those determined by Brown et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012066#pone.0012066-Brown1" target="_blank">[38]</a> and Stern et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012066#pone.0012066-Stern1" target="_blank">[39]</a> Distances are given as a percentage per site.</p

Data from: Spatial patterns of neutral and functional genetic variation reveal patterns of local adaptation in raccoon (Procyon lotor) populations exposed to raccoon rabies

Local adaptation is necessary for population survival and depends on the interplay between responses to selective forces and demographic processes that introduce or retain adaptive and maladaptive attributes. Host-parasite systems are dynamic, varying in space and time, where both host and parasites must adapt to their ever-changing environment in order to survive. We investigated patterns of local adaptation in raccoon populations with varying temporal exposure to the raccoon rabies virus (RRV). RRV infects approximately 85% of the population when epizootic and has been presumed to be completely lethal once contracted; however, disease challenge experiments and varying spatial patterns of RRV spread suggest some level of immunity may exist. We first assessed patterns of local adaptation in raccoon populations along the eastern seaboard of North America by contrasting spatial patterns of neutral (microsatellite loci) and functional, major histocompatibility complex (MHC) genetic diversity and structure. We explored variation of MHC allele frequencies in light of temporal population exposure to RRV (0-60 years) and specific RRV strains in infected raccoons. Our results revealed high levels of MHC variation (66 DRB exon 2 alleles) and pronounced genetic structure relative to neutral microsatellite loci, indicative of local adaptation. We found a positive association linking MHC genetic diversity and temporal RRV exposure, but no association with susceptibility and resistance to RRV strains. These results have implications for landscape epidemiology studies seeking to predict the spread of RRV and present an example of how population demographics influence the degree to which populations adapt to local selective pressures

Microsatellite and MHC genetic data

First sheet: Neutral microsatellite data for 10 loci in 203 raccoon samples analyzed from four regions (Ontario, New York, Alabama and Florida). Second sheet: MHC alleles identified in 203 raccoon samples including information of animals positive or negative to rabies virus, years of exposure per region, and alleles identified as resistance or susceptible to rabies and within their corresponding lineage 1 (L1) or lineage 3 (L3). Third sheet: number of alleles associated to lineage 1 and 3 per individual and regio