No abstract

Drosophila melanogaster exhibits two expression-regulating systems that target whole, specific chromosomes: the dosage compensation system whereby the male-specific lethal complex doubles transcription of genes on the male X-chromosome and the chromosome 4-specific protein Painting of fourth, POF. POF is the first example of an autosome-specific protein and its presence raises the question of the universality of chromosome-specific regulation. Here we show that POF and heterochromatin protein 1 (HP1) are involved in the global regulation of the 4th chromosome. Contrary to previous conclusions, Pof is not essential for survival of diplo-4th karyotype flies. However, Pof is essential for survival of haplo-4th individuals and expression of chromosome 4 genes in diplo-4th individuals is decreased in the absence of Pof. Mapping of POF using chromatin immunoprecipitation suggested that it binds within genes. Furthermore, we show that POF binding is dependent on heterochromatin and that POF and HP1 bind interdependently to the 4th chromosome. We propose a balancing mechanism involving POF and HP1 that provides a feedback system for fine-tuning expression status of genes on the 4th chromosome.

Plant-herbivore interactions vary across the landscape and have been hypothesised to promote local adaption in plants to the prevailing herbivore regime. Herbivores that feed on European aspen (Populus tremula) change across regional scales and selection on host defence genes may thus change at comparable scales. We have previously observed strong population differentiation in a set of inducible defence genes in Swedish P. tremula. Here, we study the geographic patterns of abundance and diversity of herbivorous insects, the untargeted metabolome of the foliage and genetic variation in a set of wound-induced genes and show that the geographic structure co-occurs in all three data sets. In response to this structure, we observe local maladaptation of herbivores, with fewer herbivores on local trees than on trees originated from more distant localities. Finally, we also identify 28 significant associations between single nucleotide polymorphisms SNPs from defence genes and a number of the herbivore traits and metabolic profiles.

SummaryNorway spruce is a boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics underlying important wood quality traits in the species. We performed a functional genome‐wide association study (GWAS) of 17 wood traits in Norway spruce using 178 101 single nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood traits were defined using functional modelling of wood properties across annual growth rings. We applied a Least Absolute Shrinkage and Selection Operator (LASSO‐based) association mapping method using a functional multilocus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine a significant quantitative trait locus. The analysis provided 52 significant SNPs from 39 candidate genes, including genes previously implicated in wood formation and tree growth in spruce and other species. Our study represents a multilocus GWAS for complex wood traits in Norway spruce. The results advance our understanding of the genetics influencing wood traits and identifies candidate genes for future functional studies.

Future climate change has been predicted to disrupt local adaptation in many perennial plants, such as forest trees, but the magnitude and location of these effects are thus far poorly understood. Here, we assess local adaptation to current climate in European aspen (Populus tremula) by using environmental association analyses to identify genetic variants associated with two representative climate variables describing current day variation in temperature and precipitation. We also analysed patterns of genetic differentiation between southern and northern populations and observe that regions of high genetic differentiation are enriched for SNPs that are significantly associated with climate. Using variants associated with climate, we examined patterns of isolation by distance and environment and used spatial modelling to predict the geographic distribution of genomic variation in response to two scenarios of future climate change. We show that climate conditions at a northern reference site will correspond to climate conditions experienced by current day populations located 4–8 latitude degrees further south. By assessing the relationship between phenotypic traits and vegetative fitness, we also demonstrate that southern populations harbour genetic variation that likely would be adaptive further north under both climate change scenarios. Current day populations at the lagging edge of the distribution in Sweden can therefore serve as sources for introducing adaptive alleles onto northern populations, but the likelihood of this largely depends on naturally occurring levels of gene flow.

Community genetics aims to understand the effects of intraspecific genetic variation on community composition and diversity, thereby connecting community ecology with evolutionary biology. Thus far, research has shown that plant genetics can underlie variation in the composition of associated communities (e.g., insects, lichen and endophytes), and those communities can therefore be considered as extended phenotypes. This work, however, has been conducted primarily at the plant genotype level and has not identified the key underlying genes. To address this gap, we used genome‐wide association mapping with a population of 445 aspen (Populus tremuloides) genets to identify the genes governing variation in plant traits (defence chemistry, bud phenology, leaf morphology, growth) and insect community composition. We found 49 significant SNP associations in 13 Populus genes that are correlated with chemical defence compounds and insect community traits. Most notably, we identified an early nodulin‐like protein that was associated with insect community diversity and the abundance of interacting foundation species (ants and aphids). These findings support the concept that particular plant traits are the mechanistic link between plant genes and the composition of associated insect communities. In putting the “genes” into “genes to ecosystems ecology”, this work enhances understanding of the molecular genetic mechanisms that underlie plant–insect associations and the consequences thereof for the structure of ecological communities.

21Massively parallel sequencing has revolutionized the field of genetics by providing 22 comparatively high-resolution insights into whole genomes for large number of species so far. 23 However, whole-genome resequencing of many conspecific individuals remains cost-prohibitive for 24 most species. This is especially true for species with very large genomes with extensive genomic 25 redundancy, such as the genomes of coniferous trees. The genome assembly for the conifer Norway 26 spruce (Picea abies) was the first published draft genome assembly for any gymnosperm. Our goal was 27 to develop a dense set of genome-wide SNP markers for Norway spruce to be used for assembly 28 improvement and population studies. From 80,000 initial probe candidates, we developed two 29 partially-overlapping sets of sequence capture probes: one developed against 56 haploid 30 megagametophytes, to aid assembly improvement; and the other developed against 6 diploid needle 31 samples, to aid population studies. We focused probe development within genes, as delineated via the 32 annotation of ~67,000 gene models accompanying P. abies assembly version 1.0. The 31,277 probes 33 developed against megagametophytes covered 19,268 gene models (mean 1.62 probes/model). The 34 40,018 probes developed against diploid tissue covered 26,219 gene modules (mean 1.53 35 probes/model). Analysis of read coverage and variant quality around probe sites showed that initial 36 alignment of captured reads should be done against the whole genome sequence, rather than a subset of 37 probe-containing scaffolds, to overcome occasional capture of sequences outside of designed regions. 38 All three probe sets, anchored to the P. abies 1.0 genome assembly and annotation, are available for 39 download. 40 41 61 Depending on the hybridization technology, varying numbers of probes can be used. For humans, 62 multiple technologies are available which contain probes sufficient to capture whole exomes (Clark et 63 al., 2011; Shigemizu et al., 2015). Such comprehensive approaches can be used successfully in model 64 species with well-annotated genomes (Fu et al., 2013; Zhou et al. 2012; Zhou et al. 2014). However, 65 because sequence capture relies largely on the accuracy of genome annotations and the uniqueness of 66 probe targets, it may exhibit reduced efficiency when applied to non-model species with incomplete 67 annotations and/or species with complex genomes containing much repetitive content (Neves et al., 123 comprise the final probe set. 124 Plant material and DNA extraction. 125 Haploid genomic DNA was extracted from 52 megagametophytes. The megagametophytes 126 were excised from open pollinated seeds of Z4006 ramets (Z4006: the Norway spruce reference 127 sequence individual), under the microscope in order to avoid diploid tissue. DNA was extracted with 128 the NucleoSpin® Plant II kit, (Macherey-Nagel, http://www.mn-net.com). After several modifications 129 of the manufacture's recommended protocol, we achieved the highest concentration of DNA from 130 megagam...

Norway spruce ( Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (∼20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated ( www.congenie.org ), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.