Representation of visual scenes by local neuronal populations in layer 2/3 of mouse visual cortex

How are visual scenes encoded in local neural networks of visual cortex? In rodents, visual cortex lacks a columnar organization so that processing of diverse features from a spot in visual space could be performed locally by populations of neighboring neurons. To examine how complex visual scenes are represented by local microcircuits in mouse visual cortex we measured visually evoked responses of layer 2/3 neuronal populations using 3D two-photon calcium imaging. Both natural and artificial movie scenes (10 seconds duration) evoked distributed and sparsely organized responses in local populations of 70–150 neurons within the sampled volumes. About 50% of neurons showed calcium transients during visual scene presentation, of which about half displayed reliable temporal activation patterns. The majority of the reliably responding neurons were activated primarily by one of the four visual scenes applied. Consequently, single-neurons performed poorly in decoding, which visual scene had been presented. In contrast, high levels of decoding performance (>80%) were reached when considering population responses, requiring about 80 randomly picked cells or 20 reliable responders. Furthermore, reliable responding neurons tended to have neighbors sharing the same stimulus preference. Because of this local redundancy, it was beneficial for efficient scene decoding to read out activity from spatially distributed rather than locally clustered neurons. Our results suggest a population code in layer 2/3 of visual cortex, where the visual environment is dynamically represented in the activation of distinct functional sub-networks

Endosperm and seed transcriptomes reveal possible roles for small RNA pathways in wild tomato hybrid seed failure

Crosses between the wild tomato species Solanum peruvianum and S. chilense result in hybrid seed failure (HSF), characterized by endosperm misdevelopment and embryo arrest. We previously showed that genomic imprinting, the parent-of-origin–dependent expression of alleles, is perturbed in hybrid endosperm, with many of the normally paternally expressed genes losing their imprinted status. Here, we report transcriptome-based analyses of gene and small RNA expression levels. We identified 2,295 genes and 468 small RNAs (sRNAs) as differentially expressed (DE) when comparing reciprocal hybrid seed to seeds and endosperms from the two within-species crosses. Our analyses uncovered a pattern of overdominance in endosperm gene expression in both cross directions, in marked contrast to the patterns of sRNA expression in whole seeds. Intriguingly, patterns of increased gene expression resembled the previously reported increased maternal expression proportions in hybrid endosperms. We identified physical clusters of sRNAs; DE sRNAs exhibited reduced levels of expression in hybrid seeds from both cross directions. Moreover, sRNAs mapped to genes coding for key proteins involved in epigenetic regulation of gene expression, suggesting a regulatory feedback mechanism. We describe examples of genes that are targets of sRNA-mediated gene silencing; in these cases, reduced sRNA expression was concomitant with increased gene expression in hybrid seeds. Our analyses also show that S. peruvianum dominance impacts gene and sRNA expression in hybrid seeds. Overall, our study indicates roles for sRNA-mediated epigenetic regulation in HSF between closely related wild tomato species

Incidence and developmental timing of endosperm failure in post-zygotic isolation between wild tomato lineages

Background and AimsDefective hybrid seed development in angiosperms might mediate the rapid establishment of intrinsic post-zygotic isolation between closely related species. Extensive crosses within and among three lineages of wild tomatoes (Solanum section Lycopersicon) were performed to address the incidence, developmental timing and histological manifestations of hybrid seed failure. These lineages encompass different, yet fairly recent, divergence times and both allopatric and partially sympatric pairs.MethodsMature seeds were scored visually 2 months after hand pollinations, and viable-looking seeds were assessed for germination success. Using histological sections from early-developing seeds from a sub-set of crosses, the growth of three major seed compartments (endosperm, embryo and seed coat) was measured at critical developmental stages up to 21 d after pollination, with a focus on the timing and histological manifestations of endosperm misdevelopment in abortive hybrid seeds.Key ResultsFor two of three interspecific combinations including the most closely related pair that was also studied histologically, almost all mature seeds appeared ‘flat’ and proved inviable; histological analyses revealed impaired endosperm proliferation at early globular embryo stages, concomitant with embryo arrest and seed abortion in both cross directions. The third interspecific combination yielded a mixture of flat, inviable and plump, viable seeds; many of the latter germinated and exhibited near-normal juvenile phenotypes or, in some instances, hybrid necrosis and impaired growth.ConclusionsThe overall results suggest that near-complete hybrid seed failure can evolve fairly rapidly and without apparent divergence in reproductive phenology/biology. While the evidence accrued here is largely circumstantial, early-acting disruptions of normal endosperm development are most probably the common cause of seed failure regardless of the type of endosperm (nuclear or cellular)

The apple REFPOP - a reference population for genomics-assisted breeding in apple

Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates. Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs, and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic conditions. Here we present an apple reference population: the apple REFPOP, a large collection formed of 534 genotypes planted in six European countries, as a unique tool to accelerate apple breeding. The population consisted of 269 accessions and 265 progeny from 27 parental combinations, representing the diversity in cultivated apple and current European breeding material, respectively. A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of 0.95. Based on the genotypic data, linkage disequilibrium was low and population structure was weak. Two well-studied phenological traits of horticultural importance were measured. We found marker-trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date, respectively. With decreasing SNP density, the detection of significant marker-trait associations varied depending on trait architecture. Regardless of the trait, 10,000 SNPs sufficed to maximize genomic prediction ability. We confirm the suitability of the apple REFPOP design for genomics-assisted breeding, especially for breeding programs using related germplasm, and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era

Diversity in olfactory bulb size in birds reflects allometry, ecology, and phylogeny

The relative size of olfactory bulbs (OBs) is correlated with olfactory capabilities across vertebrates and is widely used to assess the relative importance of olfaction to a species’ ecology. In birds, variations in the relative size of OBs are correlated with some behaviors; however, the factors that have led to the high level of diversity seen in OB sizes across birds are still not well understood. In this study, we use the relative size of OBs as a neuroanatomical proxy for olfactory capabilities in 135 species of birds, representing 21 orders. We examine the scaling of OBs with brain size across avian orders, determine likely ancestral states and test for correlations between OB sizes and habitat, ecology, and behavior. The size of avian OBs varied with the size of the brain and this allometric relationship was for the most part isometric, although species did deviate from this trend. Large OBs were characteristic of more basal species and in more recently derived species the OBs were small. Living and foraging in a semiaquatic environment was the strongest variable driving the evolution of large OBs in birds; olfaction may provide cues for navigation and foraging in this otherwise featureless environment. Some of the diversity in OB sizes was also undoubtedly due to differences in migratory behavior, foraging strategies and social structure. In summary, relative OB size in birds reflect allometry, phylogeny and behavior in ways that parallel that of other vertebrate classes. This provides comparative evidence that supports recent experimental studies into avian olfaction and suggests that olfaction is an important sensory modality for all avian species

Association between maternal nutritional status in pregnancy and offspring cognitive function in childhood and adolescence; a systematic review

Background The mother is the only source of nutrition for fetal growth including brain development. Maternal nutritional status (anthropometry, macro- and micro-nutrients) before and/or during pregnancy is therefore a potential predictor of offspring cognitive function. The relationship of maternal nutrition to offspring cognitive function is unclear. This review aims to assess existing evidence linking maternal nutritional status with offspring cognitive function. Methods Exposures considered were maternal BMI, height and weight, micronutrient status (vitamins D, B12, folate and iron) and macronutrient intakes (carbohydrate, protein and fat). The outcome was any measure of cognitive function in children aged <18 years. We considered observational studies and trials with allocation groups that differed by single nutrients. We searched Medline/PubMed and the Cochrane Library databases and reference lists of retrieved literature. Two reviewers independently extracted data from relevant articles. We used methods recommended by the Centre for Reviews and Dissemination, University of York and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. Results Of 16,143 articles identified, 38 met inclusion criteria. Most studies were observational, and from high-income settings. There were few randomized controlled trials. There was consistent evidence linking maternal obesity with lower cognitive function in children; low maternal BMI has been inadequately studied. Among three studies of maternal vitamin D status, two showed lower cognitive function in children of deficient mothers. One trial of folic acid supplementation showed no effects on the children’s cognitive function and evidence from 13 observational studies was mixed. Among seven studies of maternal vitamin B12 status, most showed no association, though two studies in highly deficient populations suggested a possible effect. Four out of six observational studies and two trials (including one in an Iron deficient population) found no association of maternal iron status with offspring cognitive function. One trial of maternal carbohydrate/protein supplementation showed no effects on offspring cognitive function. Conclusions Current evidence that maternal nutritional status during pregnancy as defined by BMI, single micronutrient studies, or macronutrient intakes influences offspring cognitive function is inconclusive. There is a need for more trials especially in populations with high rates of maternal undernutrition. Systematic review registration Registered in PROSPERO CRD42013005702

Variability of Hybrid Seed Failure in Wild Tomatoes (Solanum sect. Lycopersicon): Phenotypic and Molecular Signatures in the Developing Endosperm

Seed development represents a critical stage for plant reproductive success. This dissertation focuses on phenotypic and molecular correlates of hybrid seed failure between closely-related species. Three main compartments comprise the angiosperm seed, each with different genomic make-up: the seed coat (maternal), the endosperm (2m:1p), and the embryo (1m:1p). The endosperm plays a central role in early seed development because it regulates embryo nutrient acquisition while synchronizing growth between seed compartments. Importantly, hybrid seed abortion is generally associated with an altered endosperm development. Moreover, genomic imprinting, i.e. parent-of-origin–dependent expression, is exceedingly rare in other plant tissues but widespread in the endosperm. Potential functional links between imprinting perturbation or -mismatch and seed abortion are predicted by evolutionary theory based on parental conflict, but have only begun to be elucidated at the molecular level. Wild tomatoes (Solanum sect. Lycopersicon) were chosen to compare seed development and gene expression in the endosperm of seeds from intraspecific and hybrid crosses, and to address the role of genomic imprinting in lineage divergence and hybrid seed failure. To this end, I used three tomato lineages with interesting hybrid seed phenotypes and patterns of genetic divergence: S. arcanum var marañón (A), S. chilense (C), and S. peruvianum (P). A large part of my study was based on laser-microdissected developing endosperm obtained from seeds of intra- and interspecific crosses and subsequent transcriptome sequencing. In Chapter 1, I hypothesized that seed abortion in wild tomatoes is triggered by endosperm failure and that viable hybrid progenies, after seed germination, may reveal additional symptoms of hybrid incompatibility. Jointly with my collaborators, I provided a comprehensive morphological description of seed development in intra- and interspecific crosses. I found that the incidence of hybrid seed failure was variable among species combinations, with marked phenotypic asymmetries between reciprocal crosses with near- complete seed inviability. For the latter, circumstantial evidence pointed to endosperm proliferation defects being responsible for embryo arrest at early globular stages. The reciprocal C×A and A×C hybrid crosses yielded intermediate levels of viable seeds, from which we grew an F1 hybrid cohort showing some developmental abnormalities, interpreted as reflecting post-germination genetic incompatibilities. Chapter 2 focuses on seeds from intraspecific crosses, i.e. those with normal seed development. My hypothesis was that genomic imprinting in the endosperm of normally developing seeds serves specific functions and is nonrandomly shared between recently diverged species. I found that the degree of overlap among imprinted genes across the three wild tomato lineages was significant, and higher for Paternally Expressed Genes (PEGs) than for Maternally Expressed Genes (MEGs). However, variation in imprinting status for many genes is suggestive of an evolutionarily fast turnover of imprinted expression. MEGs and PEGs appear to be associated with distinct functions, but I found evidence that they interact in functional and physical networks. In particular, I inferred that interactions between imprinted genes contribute to cell-cycle control. Candidate imprinted genes identified in this chapter should be representative of the typical imprinting landscape of wild tomato viable endosperm; they were used as a reference to compare parent-specific gene expression in within-lineage- and hybrid endosperms in Chapter 3. Chapter 3 aimed at testing the hypothesis that hybrid seed failure involves imprinting perturbation and/or large gene expression changes in wild tomato hybrid endosperms. When compared to intraspecific endosperms, those from strongly abortive crosses were characterized by extensive gene expression perturbation together with increased maternal expression proportions. Two homogeneous groups of hybrid endosperms were separated by the largest expression differences in the whole dataset, congruent with either maternal-excess-like (P×A and P×C) or paternal-excess-like (A×P and C×P) endosperms at the phenotypic level. I found strong evidence for perturbations of parental dosage mechanisms in these abortive endosperms, particularly the widespread loss of imprinting status of candidate PEGs. Crosses yielding only partial seed abortion (A×C and C×A) had far fewer expression changes than strongly abortive endosperms and also retained the imprinted status of most candidate PEGs. I discuss the potential roles of parental conflict and coadaptation in driving expression perturbation in abortive endosperm. Finally, I hypothesize that different ‘genetic strengths’ evolved since lineage divergence and identify candidate genes, such as AGAMOUS-LIKE transcriptions factors, that may underlie this dosage-related phenomenon. Such genes may significantly contribute to postzygotic reproductive isolation between wild tomato lineages. By revealing the widespread perturbation of imprinted expression in abortive hybrid endosperms, my project accrued molecular evidence for the fundamental role of parental dosage in successful seed development. As a collateral resource, it also provides a large number of candidate genes that are potentially useful for developmental and evolutionary biology and for plant breeding

Endosperm and Seed Transcriptomes Reveal Possible Roles for Small RNA Pathways in Wild Tomato Hybrid Seed Failure

Crosses between the wild tomato species Solanum peruvianum and Solanum chilense result in hybrid seed failure (HSF), characterized by endosperm misdevelopment and embryo arrest. We previously showed that genomic imprinting, the parent-of-origin–dependent expression of alleles, is perturbed in the hybrid endosperm, with many of the normally paternally expressed genes losing their imprinted status. Here, we report transcriptome-based analyses of gene and small RNA (sRNA) expression levels. We identified 2,295 genes and 387 sRNA clusters as differentially expressed when comparing reciprocal hybrid seed to seeds and endosperms from the two within-species crosses. Our analyses uncovered a pattern of overdominance in endosperm gene expression in both hybrid cross directions, in marked contrast to the patterns of sRNA expression in whole seeds. Intriguingly, patterns of increased gene expression resemble the previously reported increased maternal expression proportions in hybrid endosperms. We identified physical clusters of sRNAs; differentially expressed sRNAs exhibit reduced transcript abundance in hybrid seeds of both cross directions. Moreover, sRNAs map to genes coding for key proteins involved in epigenetic regulation of gene expression, suggesting a regulatory feedback mechanism. We describe examples of genes that appear to be targets of sRNA-mediated gene silencing; in these cases, reduced sRNA abundance is concomitant with increased gene expression in hybrid seeds. Our analyses also show that S. peruvianum dominance impacts gene and sRNA expression in hybrid seeds. Overall, our study indicates roles for sRNA-mediated epigenetic regulation in HSF between closely related wild tomato species