Population Differences in Transcript-Regulator Expression Quantitative Trait Loci

Gene expression quantitative trait loci (eQTL) are useful for identifying single nucleotide polymorphisms (SNPs) associated with diseases. At times, a genetic variant may be associated with a master regulator involved in the manifestation of a disease. The downstream target genes of the master regulator are typically co-expressed and share biological function. Therefore, it is practical to screen for eQTLs by identifying SNPs associated with the targets of a transcript-regulator (TR). We used a multivariate regression with the gene expression of known targets of TRs and SNPs to identify TReQTLs in European (CEU) and African (YRI) HapMap populations. A nominal p-value of <1×10−6 revealed 234 SNPs in CEU and 154 in YRI as TReQTLs. These represent 36 independent (tag) SNPs in CEU and 39 in YRI affecting the downstream targets of 25 and 36 TRs respectively. At a false discovery rate (FDR) = 45%, one cis-acting tag SNP (within 1 kb of a gene) in each population was identified as a TReQTL. In CEU, the SNP (rs16858621) in Pcnxl2 was found to be associated with the genes regulated by CREM whereas in YRI, the SNP (rs16909324) was linked to the targets of miRNA hsa-miR-125a. To infer the pathways that regulate expression, we ranked TReQTLs by connectivity within the structure of biological process subtrees. One TReQTL SNP (rs3790904) in CEU maps to Lphn2 and is associated (nominal p-value = 8.1×10−7) with the targets of the X-linked breast cancer suppressor Foxp3. The structure of the biological process subtree and a gene interaction network of the TReQTL revealed that tumor necrosis factor, NF-kappaB and variants in G-protein coupled receptors signaling may play a central role as communicators in Foxp3 functional regulation. The potential pleiotropic effect of the Foxp3 TReQTLs was gleaned from integrating mRNA-Seq data and SNP-set enrichment into the analysis

A major effect quantitative trait locus for whirling disease resistance identified in rainbow trout (Oncorhynchus mykiss)

Whirling disease, caused by the pathogen Myxobolus cerebralis, leads to skeletal deformation, neurological impairment and under certain conditions, mortality of juvenile salmonid fishes. The disease has impacted the propagation and survival of many salmonid species over six continents, with particularly negative consequences for rainbow trout. To assess the genetic basis of whirling disease resistance in rainbow trout, genome-wide mapping was initiated using a large outbred F2 rainbow trout family (n=480) and results were confirmed in three additional outbred F2 families (n=96 per family). A single quantitative trait locus (QTL) region on chromosome Omy9 was identified in the large mapping family and confirmed in all additional families. This region explains 50–86% of the phenotypic variance across families. Therefore, these data establish that a single QTL region is capable of explaining a large percentage of the phenotypic variance contributing to whirling disease resistance. This is the first genetic region discovered that contributes directly to the whirling disease phenotype and the finding moves the field closer to a mechanistic understanding of resistance to this important disease of salmonid fish

Biological control of cacao diseases

This chapter discusses the advances in biological control of cacao diseases over the last 15 years. Most attention has been focused on biological control of frosty pod rot (Moniliophthora roreri), witches' broom (Moniliophthora perniciosa) and black pod disease (Phytophthora spp.). Research on biocontrol of other diseases in the cacao phyllosphere or rhizosphere is scarce or in its infancy. There is, however, a steady increase in information regarding the factors influencing and the mechanisms underlying biological control of cacao diseases as well as practical aspects such as inoculum production, formulation and application. There has been a clear shift away from inundative approaches using epiphytic BCAs towards more classical biocontrol approaches using bacterial and fungal endophytes as well as vesicular arbuscular mycorrhiza. These have the advantage that they can permanently establish themselves in the cacao tree. Moreover, besides direct competition for space and nutrients, antibiosis and mycoparasitism, through induced resistance and growth promotion, endophytes have a larger arsenal of mechanisms through which they can help protect their host. Endophytic BCAs could thus provide more effective and sustainable disease control. Recent advances in our understanding of the mechanisms through which endophytic biocontrol agents can reduce pest and disease impact provide possibilities for innovative disease control strategies, including combination therapies together with natural or chemical products. Continued work on production, formulation and application is also necessary in order for biocontrol to become economically interesting. However, biological control will not become a stand-alone solution for disease control but should become part of integrated pest management strategies, with cultural management as a central and reinforcing pillar. (Résumé d'auteur

Host and Environmental Influences on Development of Disease

While many myxozoan parasites produce asymptomatic infections in fish hosts, several species cause diseases whose patterns of prevalence and pathogenicity are highly dependent on host and environmental factors. This chapter reviews how these factors influence pathogenicity and disease prevalence. Influential host factors include age, size and nutritional state. There is also strong evidence for host strains that vary in resistance to infection and that there is a genetic basis for resistance. A lack of co-evolutionary processes appears to generally underly the devastating impacts of diseases caused by myxozoans when introduced fish are exposed to novel parasites (e.g. PKD in rainbow trout in Europe) or when native fish are exposed to an introduced parasite (e.g. whirling disease in North America). Most available information on abiotic factors relates to water temperature, which has been shown to play a crucial role in several host parasite systems (e.g. whirling disease, PKD) and is therefore of concern in view of global warming, fish health and food sustainability. Eutrophication may also influence disease development. Abiotic factors may also drive fish disease via their impact on parasite development in invertebrate hosts