This chapter discusses the major potato diseases worldwide: late blight, early blight, wart, and powdery scab. Late blight, caused by the oomycete Phytophthora infestans, continues to be the main biotic constraint of potato production. Annual losses have been estimated to be about (sic)6.1 billion, with major consequences to food security, especially in developing countries. Symptoms of the disease can be seen in leaves (water-soaked light to dark brown spots), stems (brown spots), and tubers (slightly depressed areas with reddish-brown color). High humidity and mild temperatures are essential for disease development and, under optimal conditions, the disease can destroy a field in a few days. Phytophthora infestans evolves continuously, mainly through recombination and migration from other areas. Thus, monitoring of P. infestans populations is critical for the design of effective management strategies. Fungicides remain as the most common tactic for late blight management, but environmental considerations are increasing the pressure to use host resistance, sanitation, and other measures. New solutions being developed to manage late blight include, among others, smart phone-based decision support systems linked to portable molecular diagnostics kits that can disseminate disease information rapidly to a large number of farmers. Emerging research topics on P. infestans include the role of the pathogen-microbiota interaction in promotion or suppression of the disease, as well as the metabolism of P. infestans. The fungus Alternaria solani is the main pathogen causing early blight on potatoes. Early blight can be found in most potato-growing countries. Typical symptoms on the leaves are dark brown to black spots with concentric rings (target spot). In susceptible potato cultivars in particular, as well as in locations (especially in warmer areas) with increased occurrence of A. solani, the disease can cause considerable yield losses. Integrated pest management to control early blight requires the implementation of several approaches. The disease is primarily controlled by the use of cultural practices (to reduce the soil born inoculum), less susceptible cultivars and the use of pesticides. But there is a loss in sensitivity toward two groups of fungicides described. The loss in sensitivity towards succinate dehydrogenase inhibitor (SDHI) and Quinone outside inhibitor (QoI) fungicides are caused by different point mutations. In many countries the occurrence of SDHI and QoI mutants is reported. Therefore, the control of early blight will be a considerable challenge in the future. The increasing importance of early blight in potatoes is due to a number of factors. Synchytrium endobioticum is a soil-borne biotrophic fungus causing potato wart disease of cultivated potato. The fungus originates from the Andean zones of South America, from where it spread first to Europe in the late of the nineteenth century. Presently, the geographical distribution of this pathogen includes almost all European and Mediterranean Plant Protection Organization (EPPO) countries, Asia, North and South America as well as Oceania (New Zealand). The typical symptoms of cauliflower-like galls could develop on all meristematic tissues of potato except roots. S. endobioticum produces summer sporangia with mobile zoospores that can move in the soil. Winter (resting) sporangia are the dormant structures by which the fungus disperses to establish new infections. They can survive more than 40 years without plant hosts. The pathogen does not produce hyphae. Its long persistence in soil and the severe losses it inflicts to potato crops have prompted its inclusion into the A2 quarantine list of EPPO. Since the discovery of pathotype 2(G1) in Germany, more than 40 pathotypes were reported in Europe. In Europe, pathotypes 1(D1), 2(G1), 6(O1), and 18(T1) are the most relevant. Other pathotypes occur mainly in the rainy mountainous areas of central and eastern Europe. S. endobioticum is a still serious problem for crop production in countries with moderate climates. The strategies to confine the disease are strict quarantine and phytosanitary measures, and the cultivation of resistance cultivars of potato. Spongospora subterranea causes root galling and tuber powdery scab leading to quality and yield losses in seed and ware crops worldwide and is also important as the natural vector of potato mop-top virus (PMTV), an economically important tuber blemish disease of potato. S. subterranea spreads by movement of infected seed tubers and soil and can survive long periods in soils and some asymptomatic hosts. Powdery scab is particularly favored by cool, damp conditions and is an intractable disease. Avoidance is the best control for powdery scab, but once soil is infested with S. subterranea, cultural practices and chemical treatments are ineffective control methods, and host resistance appears to be the most promising mechanism for long-term management. Although sources of host resistance have been identified, they are not widely deployed in practice. S. subterranea is an unculturable biotroph, making research difficult. Recent progress in understanding the biology of S. subterranea as a result of the application of basic molecular techniques, and future opportunities to further advance knowledge of this understudied pathogen, and the virus that it vectors, are included.

The fungus Alternaria solani is the main pathogen causing early blight on potatoes (Solanum tuberosum L.). An increase in the development of resistance to the succinate dehydrogenase inhibitor (SDHI) boscalid, one of the main active ingredients for the control of early blight, has been reported. For this study, monitoring data from Germany were collected between 2013 and 2016 and an increase in the occurrence of A. solani succinate dehydrogenase (SDH) mutant isolates was observed. In addition to the known point mutations in sdh complex II, a new mutation in subunit C was found in German isolates (SdhC-H134Q). SDHI fungicide sensitivity testing was performed in the laboratory, greenhouse, and field. Reduced boscalid sensitivity was shown for mutant isolates (SdhB-H278Y and SdhC-H134R) both in vitro and in vivo. In addition, field trials with artificial inoculation were performed in 2016 and 2017. In both years, fungicide efficacy was significantly reduced after mutant inoculation compared with wild-type inoculation.

Early blight caused by Alternaria solani is a highly destructive disease of potatoes. Control of early blight mainly relies on the use of preventive fungicide treatments. Because of their high efficacy, azoxystrobin and other quinone outside inhibitors (QoIs) are commonly used to manage early blight. However, loss of sensitivity to QoIs has previously been reported for A. solani in the United States. Two hundred and three A. solani field isolates collected from 81 locations in Germany between 2005 and 2011 were screened for the presence of the F129L mutation in the cytochrome b gene; of these, 74 contained the F129L mutation. Sequence analysis revealed the occurrence of two structurally different cytb genes, which differed in the presence (genotype I) or absence (genotype II) of an intron, with genotype I being the most prevalent (63% of isolates). The F129L mutation was detected only in genotype II isolates, where it occurred in 97%. Sensitivity to azoxystrobin and pyraclostrobin was determined in conidial germination assays. All isolates possessing the F129L mutation had reduced sensitivity to azoxystrobin and, to a lesser extent, to pyraclostrobin. Early blight disease severity on plants treated with azoxystrobin was significantly higher for A. solani isolates with reduced fungicide sensitivity in the conidial germination assay compared with sensitive isolates. Data suggest an accumulation of F129L isolates in the German A. solani population over the years 2009–2011. It is assumed that the application of QoIs has selected for the occurrence of F129L mutations, which may contribute to loss of fungicide efficacy.

All subdivisions of the adult zebrafish brain maintain niches of constitutive neurogenesis, sustained by quiescent and multipotent progenitor populations. In the telencephalon, the latter potential neural stem cells take the shape of radial glia aligned along the ventricle and are controlled by Notch signalling. With the aim of identifying new markers of this cell type and of comparing the effectors of embryonic and adult neurogenesis, we focused on the family of hairy/enhancer of split [E(spl)] genes. We report the expression of seven hairy/E(spl) (her) genes and the new helt gene in three neurogenic areas of the adult zebrafish brain (telencephalon, hypothalamus, and midbrain) in relation to radial glia, proliferation, and neurogenesis. We show that the expression of most her genes in the adult brain characterizes quiescent radial glia, whereas only few are expressed in progenitor domains engaged in active proliferation or neurogenesis. The low proliferation status of most her-positive progenitors contrasts with the embryonic nervous system, in which her genes are expressed in actively dividing progenitors. Likewise, we demonstrate largely overlapping expression domains of a set of her genes in the adult brain, which is in striking contrast to their distinct embryonic expression profiles. Overall, our data provide a consolidated map of her expression, quiescent glia, proliferation, and neurogenesis in these various subdivisions of the adult brain and suggest distinct regulation and function of Her factors in the embryonic and adult contexts.

The maintenance of progenitor cells is a crucial aspect of central nervous system development and maturation, and bHLH transcription factors of the E(Spl) subfamily are involved in this process in all vertebrates studied to date. In the zebrafish embryonic neural plate, a large number of E(Spl) genes (her genes) are at play. We review recent data on this point, and propose a model where distinct subsets of these genes define different progenitor subtypes. Analysis of her genes expression in the adult zebrafish brain suggests that part of the embryonic her cascade might also be reused to define progenitors during adulthood. Further, available evidence on orthologous genes in the mouse (Hes genes) point to different modes of Hes regulation depending on cell location within the embryonic neural tube, perhaps associated with distinct progenitor types in this species as well. Out of these comparisons emerges a simple model of neural stem cell maintenance applicable from embryonic development until adulthood as well as across species. This working model suggests the directions for future experiments.

The zebrafish adult brain contains numerous neural progenitors and is a good model to approach the general mechanisms of adult neural stem cell maintenance and neurogenesis. Here we use this model to test for a correlation between Fgf signaling and cell proliferation in adult progenitor zones. We report expression of Fgf signals (fgf3,4,8a,8b,17b), receptors (fgfr1-4), and targets (erm, pea3, dusp6, spry1,2,4, and P-ERK) and document that genes of the embryonic fgf8 synexpression group acquire strikingly divergent patterns in the adult brain. We further document the specific expression of fgf3, fgfr1-3, dusp6, and P-ERK in ventricular zones, which contain neural progenitors. In these locations, however, a comparison at the single-cell level of fgfr/P-ERK expression with bromo-deoxy-uridine (BrdU) incorporation and the proliferation marker MCM5 indicates that Fgf signaling is not specifically associated with proliferating progenitors. Rather, it correlates with the ventricular radial glia state, some of which only are progenitors. Together these results stress the importance of Fgf signaling in the adult brain and establish the basis to study its function in zebrafish, in particular in relation to adult neurogenesis.

We report evidence for a mechanism for the maintenance of long-range conserved synteny across vertebrate genomes. We found the largest mammal-teleost conserved chromosomal segments to be spanned by highly conserved noncoding elements (HCNEs), their developmental regulatory target genes, and phylogenetically and functionally unrelated “bystander” genes. Bystander genes are not specifically under the control of the regulatory elements that drive the target genes and are expressed in patterns that are different from those of the target genes. Reporter insertions distal to zebrafish developmental regulatory genes pax6.1/2 , rx3 , id1 , and fgf8 and miRNA genes mirn9-1 and mirn9-5 recapitulate the expression patterns of these genes even if located inside or beyond bystander genes, suggesting that the regulatory domain of a developmental regulatory gene can extend into and beyond adjacent transcriptional units. We termed these chromosomal segments genomic regulatory blocks (GRBs). After whole genome duplication in teleosts, GRBs, including HCNEs and target genes, were often maintained in both copies, while bystander genes were typically lost from one GRB, strongly suggesting that evolutionary pressure acts to keep the single-copy GRBs of higher vertebrates intact. We show that loss of bystander genes and other mutational events suffered by duplicated GRBs in teleost genomes permits target gene identification and HCNE/target gene assignment. These findings explain the absence of evolutionary breakpoints from large vertebrate chromosomal segments and will aid in the recognition of position effect mutations within human GRBs.

Current models of vertebrate adult neural stem cells are largely restricted to the rodent forebrain. To extract the general mechanisms of neural stem cell biology, we sought to identify new adult stem cell populations, in other model systems and/or brain areas. The teleost zebrafish appears to be an ideal system, as cell proliferation in the adult zebrafish brain is found in many more niches than in the mammalian brain. As a starting point towards identifying stem cell populations in this system, we used an embryonic neural stem cell marker, the E(spl) bHLH transcription factor Her5. We demonstrate that her5 expression is not restricted to embryonic neural progenitors, but also defines in the adult zebrafish brain a new proliferation zone at the junction between the mid- and hindbrain. We show that adult her5-expressing cells proliferate slowly, self-renew and express neural stem cell markers. Finally, using in vivo lineage tracing in her5:gfp transgenic animals, we demonstrate that the her5-positive population is multipotent, giving rise in situ to differentiated neurons and glia that populate the basal midbrain. Our findings conclusively identify a new population of adult neural stem cells, as well as their fate and their endogenous environment, in the intact vertebrate brain. This cell population, located outside the forebrain, provides a powerful model to assess the general mechanisms of vertebrate neural stem cell biology. In addition, the first transcription factor characteristic of this cell population, Her5, points to the E(Spl) as a promising family of candidate adult neural stem cell regulators.

Our understanding of the cellular and molecular mechanisms underlying the adult neural stem cell state remains fragmentary. To provide new models on this issue, we searched for stem cells in the adult brain of the zebrafish. Using BrdU tracing and immunodetection of cell-type-specific markers, we demonstrate that the adult zebrafish telencephalon contains self-renewing progenitors, which show features of adult mammalian neural stem cells but distribute along the entire dorso-ventral extent of the telencephalic ventricular zone. These progenitors give rise to newborn neurons settling close to the ventricular zone within the telencephalon proper. They have no equivalent in mammals and therefore constitute a new model of adult telencephalic neural stem cells. In addition, progenitors from the ventral subpallium generate rapidly dividing progenitors and neuroblasts that reach the olfactory bulb (OB) via a rostral migratory stream and differentiate into GABAergic and TH-positive neurons. These ventral progenitors are comparable to the mammalian neural stem cells of the subependymal zone. Interestingly, dorsal and ventral progenitors in the adult telencephalon express a different combination of transcription factors than their embryonic counterparts. In the case of neurogenin1, this is due to the usage of different enhancer elements. Together, our results highlight the conserved and unique phylogenic and ontogenic features of adult neurogenesis in the zebrafish telencephalon and open the way to the identification of adult neural stem cell characters in cross-species comparative studies.

Transcription factors of the bHLH class play crucial roles in neurogenesis by controlling the location and timing of neuronal commitment and differentiation, as well as influencing neuronal identity. Proneural bHLH factors belong to the Olig, Neurogenin, NeuroD, Achaete-scute and Atonal subfamilies, and are expressed in partially overlapping or complementary patterns within the vertebrate embryonic neural tube. The combinatorial expression of these factors likely drives the generic and cell type-specific properties of neurogenesis throughout the nervous system. As an approach towards identifying a complete set of vertebrate proneural factors, we report here the isolation of two new zebrafish neural bHLH gene members, atoh1.2 and beta3.1. Among other sites, both are expressed in the late embryonic and early larval anterior hindbrain. In this territory we demonstrate that atoh1.2 and beta3.1 are transcribed in distinct precursors, further highlighting the subdivision of anterior zebrafish hindbrain into subdomains of bHLH expression.

Within the vertebrate embryonic neural plate, the first neuronal clusters often differentiate at the border of patterning identities. Whether the information inherent in the intersection of patterning identities alone controls all aspects of neuronal cluster development (location, identity, and size) is unknown. Here, we focus on the cluster of the medial longitudinal fascicle (nMLF) and posterior commissure (nPC), located at the forebrain/midbrain (fore/mid) boundary, to address this issue. We first identify expression of the transcription factor Six3 as a common and distinct molecular signature of nMLF and nPC neurons in zebrafish, and we use this marker to monitor mechanisms controlling the location and number of nMLF/nPC neurons. We demonstrate that six3 expression is induced at the fore/mid boundary in pax2.1/no‐isthmus and smoothened/slow muscle omitted mutants, where identities adjacent to the six3 cluster are altered; however, in these mutants, the subpopulation of six3‐positive cells located within the mispatterned territory is reduced. These results show that induction of the six3 cluster is triggered by the information derived from the intersection in patterning identities alone, whereas correct cluster size depends, in a modular manner, on the identities themselves. The size of the six3 cluster is also controlled independently of neural tube patterning: we demonstrate that the prechordal plate (PCP) is impaired in mixer/bonnie and clyde mutants and that this phenotype secondarily results in an increased production of six3‐positive cells at the fore/mid boundary, without correlatively affecting patterning in this area. Thus, a signaling process originating from the PCP distinguishes between neural patterning and the control of six3 cluster size at the fore/mid junction in vivo. Together, our results suggest that a combination of patterning‐related and ‐unrelated mechanisms specifically controls the size of individual early neuronal clusters within the anterior neural plate. Developmental Dynamics 227:524–535, 2003. © 2003 Wiley‐Liss, Inc.