Genetic heterogeneity of residual variance in broiler chickens

Aims were to estimate the extent of genetic heterogeneity in environmental variance. Data comprised 99 535 records of 35-day body weights from broiler chickens reared in a controlled environment. Residual variance within dam families was estimated using ASREML, after fitting fixed effects such as genetic groups and hatches, for each of 377 genetically contemporary sires with a large number of progeny (> 100 males or females each). Residual variance was computed separately for male and female offspring, and after correction for sampling, strong evidence for heterogeneity was found, the standard deviation between sires in within variance amounting to 15–18% of its mean. Reanalysis using log-transformed data gave similar results, and elimination of 2–3% of outlier data reduced the heterogeneity but it was still over 10%. The correlation between estimates for males and females was low, however. The correlation between sire effects on progeny mean and residual variance for body weight was small and negative (-0.1). Using a data set bigger than any yet presented and on a trait measurable in both sexes, this study has shown evidence for heterogeneity in the residual variance, which could not be explained by segregation of major genes unless very few determined the trait.     

Natural quantitative genetic variance in plant growth differs in response to ecologically relevant temperature heterogeneity

Adaptation to large‐scale spatial heterogeneity in the environment accounts for a major proportion of genetic diversity within species. Theory predicts the erosion of adaptive genetic variation on a within‐population level, but considerable genetic diversity is often found locally. Genetic diversity could be expected to be maintained within populations in temporally or spatially variable conditions if genotypic rank orders vary across contrasting microenvironmental settings. Taking advantage of fine‐resolution environmental data, we tested the hypothesis that temperature heterogeneity among years could be one factor maintaining quantitative genetic diversity within a natural and genetically diverse plant population. We sampled maternal families of Boechera stricta, an Arabidopsis thaliana relative, at one location in the central Rocky Mountains and grew them in three treatments that, based on records from an adjacent weather station, simulated hourly temperature changes at the native site during three summers with differing mean temperatures. Treatment had a significant effect on all traits, with 2–3‐fold increase in above‐ and belowground biomass and the highest allocation to roots observed in the treatment simulating the warmest summer on record at the site. Treatment affected bivariate associations between traits, with the weakest correlation between above‐ and belowground biomass in the warmest treatment. The magnitude of quantitative genetic variation for all traits differed across treatments: Genetic variance of biomass was 0 in the warmest treatment, while highly significant diversity was found in average conditions, resulting in broad‐sense heritability of 0.31. Significant genotype × environment interactions across all treatments were found only in root‐to‐shoot ratio. Therefore, temperature variation among summers appears unlikely to account for the observed levels of local genetic variation in size in this perennial species, but may influence family rank order in growth allocation. Our results indicate that natural environmental fluctuations can have a large impact on the magnitude of within‐population quantitative genetic variance.     

The sugar,biomass and biofuel potential of temperate by tropical maize hybrids

The demand for biofuels has created a market for feedstocks to meet future energy requirements. Temperate × tropical maize (Zea mays L.) hybrids, which combine high biomass and fermentable stalk sugars, have yet to be considered as a biomass feedstock. Our objective was to evaluate biological potential, genetic variability and impact of nitrogen (N) on biomass, stalk sugar, and biofuel potential of temperate × tropical maize (TTM) hybrids. Twelve TTM hybrids, two grain and silage hybrids were grown in 2008, followed in 2009 by seven earshoot‐bagged TTM hybrids. In both years, they were grown with and without supplemental N (202 kg ha^?1) in Champaign, IL. Plants were sampled for total and partitioned biomass, and analyzed for concentration and content of sugar. The TTM hybrids were 40% taller, exhibited later reproductive maturity, greater flowering asynchrony, and remained green longer. All hybrids responded to supplemental N by producing more biomass and grain, a lower percent of biomass partitioned to stalk and leaf, whereas TTM also had a decreased concentration of sugar. Total average biomass yields were 24 Mg ha^?1 for both the TTM and grain hybrids. However, TTM partitioned 50% more biomass to the stalk and produced 50% more sugar, and had less than half the grain of the commercial hybrids, indicating grain production and sugar accumulation are inversely related. When grain formation was prevented by earshoot bagging, TTM hybrids produced, without supplemental N fertilizer, an average of 4024 kg ha^?1 of sugar, which was three‐ to four‐fold greater than the non earshoot‐bagged TTM and ear removed hybrid. Calculated estimates for ethanol production, considering the potential from sugar, stover and grain, indicate TTM can yield nearly the amount of ethanol per hectare as modern grain hybrids, but with a decreased requirement for supplemental fertilizer N.     

Heritability of male attractiveness persists despite evidence for unreliable sexual signals in Drosophila simulans

Sexual signals can be used to attract mates, but to be honest indicators of signaller quality they need to convey information reliably. However, environmental variation and genotype‐by‐environment (G × E) interactions have the potential to compromise the reliability of sexual signals. Here, we test the reliability of cuticular hydrocarbons (CHCs) as signals of heritable aspects of male attractiveness in Drosophila simulans. We examined the heritability of male attractiveness and a measure of the difference between fathers' and sons' CHC profiles across dietary and temperature environments. Our results show that environmental heterogeneity disrupts the similarity of some components of father and son CHC profile. However, overall male attractiveness is heritable within and across environments, so that sire attractiveness is a good predictor of son attractiveness even with environmental heterogeneity. This suggests that although some male CHC signals are unreliable, attractive genotypes retain their attractiveness across environments on average.     

Development and validation of the Axiom®Apple480K SNP genotyping array

Cultivated apple (Malus × domestica Borkh.) is one of the most important fruit crops in temperate regions, and has great economic and cultural value. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid linkage disequilibrium decay, makes it difficult to perform genome‐wide association (GWA) studies. Single nucleotide polymorphism arrays offer highly multiplexed assays at a relatively low cost per data point and can be a valid tool for the identification of the markers associated with traits of interest. Here, we describe the development and validation of a 487K SNP Affymetrix Axiom^® genotyping array for apple and discuss its potential applications. The array has been built from the high‐depth resequencing of 63 different cultivars covering most of the genetic diversity in cultivated apple. The SNPs were chosen by applying a focal points approach to enrich genic regions, but also to reach a uniform coverage of non‐genic regions. A total of 1324 apple accessions, including the 92 progenies of two mapping populations, have been genotyped with the Axiom^®Apple480K to assess the effectiveness of the array. A large majority of SNPs (359 994 or 74%) fell in the stringent class of poly high resolution polymorphisms. We also devised a filtering procedure to identify a subset of 275K very robust markers that can be safely used for germplasm surveys in apple. The Axiom^®Apple480K has now been commercially released both for public and proprietary use and will likely be a reference tool for GWA studies in apple.     

Inferring the potentially complex genetic architectures of adaptation,sexual dimorphism and genotype by environment interactions by partitioning of mean phenotypes

Genetic architecture fundamentally affects the way that traits evolve. However, the mapping of genotype to phenotype includes complex interactions with the environment or even the sex of an organism that can modulate the expressed phenotype. Line‐cross analysis is a powerful quantitative genetics method to infer genetic architecture by analysing the mean phenotype value of two diverged strains and a series of subsequent crosses and backcrosses. However, it has been difficult to account for complex interactions with the environment or sex within this framework. We have developed extensions to line‐cross analysis that allow for gene by environment and gene by sex interactions. Using extensive simulation studies and reanalysis of empirical data, we show that our approach can account for both unintended environmental variation when crosses cannot be reared in a common garden and can be used to test for the presence of gene by environment or gene by sex interactions. In analyses that fail to account for environmental variation between crosses, we find that line‐cross analysis has low power and high false‐positive rates. However, we illustrate that accounting for environmental variation allows for the inference of adaptive divergence, and that accounting for sex differences in phenotypes allows practitioners to infer the genetic architecture of sexual dimorphism.     

Genetic by environment interactions affect plant–soil linkages

The role of plant intraspecific variation in plant–soil linkages is poorly understood, especially in the context of natural environmental variation, but has important implications in evolutionary ecology. We utilized three 18‐ to 21‐year‐old common gardens across an elevational gradient, planted with replicates of five Populus angustifolia genotypes each, to address the hypothesis that tree genotype (G), environment (E), and G × E interactions would affect soil carbon and nitrogen dynamics beneath individual trees. We found that soil nitrogen and carbon varied by over 50% and 62%, respectively, across all common garden environments. We found that plant leaf litter (but not root) traits vary by genotype and environment while soil nutrient pools demonstrated genotype, environment, and sometimes G × E interactions, while process rates (net N mineralization and net nitrification) demonstrated G × E interactions. Plasticity in tree growth and litter chemistry was significantly related to the variation in soil nutrient pools and processes across environments, reflecting tight plant–soil linkages. These data overall suggest that plant genetic variation can have differential affects on carbon storage and nitrogen cycling, with implications for understanding the role of genetic variation in plant–soil feedback as well as management plans for conservation and restoration of forest habitats with a changing climate.     

Thermal adaptation and phenotypic plasticity in a warming world: Insights from common garden experiments on Alaskan sockeye salmon

An important unresolved question is how populations of coldwater‐dependent fishes will respond to rapidly warming water temperatures. For example, the culturally and economically important group, Pacific salmon (Oncorhynchus spp.), experience site‐specific thermal regimes during early development that could be disrupted by warming. To test for thermal local adaptation and heritable phenotypic plasticity in Pacific salmon embryos, we measured the developmental rate, survival, and body size at hatching in two populations of sockeye salmon (Oncorhynchus nerka) that overlap in timing of spawning but incubate in contrasting natural thermal regimes. Using a split half‐sibling design, we exposed embryos of 10 families from each of two populations to variable and constant thermal regimes. These represented both experienced temperatures by each population, and predicted temperatures under plausible future conditions based on a warming scenario from the downscaled global climate model (MIROC A1B scenario). We did not find evidence of thermal local adaptation during the embryonic stage for developmental rate or survival. Within treatments, populations hatched within 1 day of each other, on average, and among treatments, did not differ in survival in response to temperature. We did detect plasticity to temperature; embryos developed 2.5 times longer (189 days) in the coolest regime compared to the warmest regime (74 days). We also detected variation in developmental rates among families within and among temperature regimes, indicating heritable plasticity. Families exhibited a strong positive relationship between thermal variability and phenotypic variability in developmental rate but body length and mass at hatching were largely insensitive to temperature. Overall, our results indicated a lack of thermal local adaptation, but a presence of plasticity in populations experiencing contrasting conditions, as well as family‐specific heritable plasticity that could facilitate adaptive change.     

Diet,Obesity, and Hyperglycemia in LG/J and SM/J Mice

Objective: To examine the differential response of obesity‐ and diabetes‐related traits to a high‐ or low‐fat diet in LG/J and SM/J mice. We also examined food consumption in these strains. Research Methods and Procedures: Mice were placed on a high‐ or low‐fat diet after weaning. Animals were weighed once per week and subjected to glucose tolerance tests at 20 weeks. At sacrifice, fat pads and internal organs were removed along with serum samples. For food consumption, LG/J and SM/J mice of each sex were assigned to a high‐fat or low‐fat diet after reaching maturity. Mice were weighed three times per week, and food consumed was determined by subtraction. Results: LG/J animals consume more total food, but SM/J animals consume more food per gram of body weight. LG/J mice grow faster to 10 weeks but slower from 10 to 20 weeks, have higher cholesterol and free fatty acid levels, and have lower basal glucose levels and better response to a glucose challenge than SM/J mice. For most traits, SM/J mice respond more strongly to a high‐fat diet than LG/J mice, including body weight and growth, basal glucose levels, organ weights, fat distribution, and circulating triglycerides and cholesterol levels. Discussion: Obesity‐related phenotypes, as well as response to increased dietary fat, differ genetically between LG/J and SM/J and can, therefore, be mapped. This study indicates that the cross of SM/J and LG/J mice would be an excellent model system for the study of gene‐by‐diet interaction in obesity.     

Quantitative trait loci and candidate genes underlying genotype by environment interaction in the response of Arabidopsis thaliana to drought

Drought stress was imposed on two sets of Arabidopsis thaliana genotypes grown in sand under short‐day conditions and analysed for several shoot and root growth traits. The response to drought was assessed for quantitative trait locus (QTL) mapping in a genetically diverse set of Arabidopsis accessions using genome‐wide association (GWA) mapping, and conventional linkage analysis of a recombinant inbred line (RIL) population. Results showed significant genotype by environment interaction (G×E) for all traits in response to different watering regimes. For the RIL population, the observed G×E was reflected in 17 QTL by environment interactions (Q×E), while 17 additional QTLs were mapped not showing Q×E. GWA mapping identified 58 single nucleotide polymorphism (SNPs) associated with loci displaying Q×E and an additional 16 SNPs associated with loci not showing Q×E. Many candidate genes potentially underlying these loci were suggested. The genes for RPS3C and YLS7 were found to contain conserved amino acid differences when comparing Arabidopsis accessions with strongly contrasting drought response phenotypes, further supporting their candidacy. One of these candidate genes co‐located with a QTL mapped in the RIL population.     

Transcriptomics and in vivo tests reveal novel mechanisms underlying endocrine disruption in an ecological sentinel,Nucella lapillus

Anthropogenic endocrine disruptors now contaminate all environments globally, with concomitant deleterious effects across diverse taxa. While most studies on endocrine disruption (ED) have focused on vertebrates, the superimposition of male sexual characteristics in the female dogwhelk, Nucella lapillus (imposex), caused by organotins, provides one of the most clearcut ecological examples of anthropogenically induced ED in aquatic ecosystems. To identify the underpinning mechanisms of imposex for this ‘nonmodel’ species, we combined Roche 454 pyrosequencing with custom oligoarray fabrication inexpensively to both generate gene models and identify those responding to chronic tributyltin (TBT) treatment. The results supported the involvement of steroid, neuroendocrine peptide hormone dysfunction and retinoid mechanisms, but suggested additionally the involvement of putative peroxisome proliferator–activated receptor (PPAR) pathways. Application of rosiglitazone, a well‐known vertebrate PPARγ ligand, to dogwhelks induced imposex in the absence of TBT. Thus, while TBT‐induced imposex is linked to the induction of many genes and has a complex phenotype, it is likely also to be driven by PPAR‐responsive pathways, hitherto not described in invertebrates. Our findings provide further evidence for a common signalling pathway between invertebrate and vertebrate species that has previously been overlooked in the study of endocrine disruption.     

Cyclooxygenase‐1 inhibition reduces amyloid pathology and improves memory deficits in a mouse model of Alzheimer's disease

Several epidemiological and preclinical studies suggest that non‐steroidal anti‐inflammatory drugs (NSAIDs), which inhibit cyclooxygenase (COX), reduce the risk of Alzheimer's disease (AD) and can lower β‐amyloid (Aβ) production and inhibit neuroinflammation. However, follow‐up clinical trials, mostly using selective cyclooxygenase (COX)‐2 inhibitors, failed to show any beneficial effect in AD patients with mild to severe cognitive deficits. Recent data indicated that COX‐1, classically viewed as the homeostatic isoform, is localized in microglia and is actively involved in brain injury induced by pro‐inflammatory stimuli including Aβ, lipopolysaccharide, and interleukins. We hypothesized that neuroinflammation is critical for disease progression and selective COX‐1 inhibition, rather than COX‐2 inhibition, can reduce neuroinflammation and AD pathology. Here, we show that treatment of 20‐month‐old triple transgenic AD (3 × Tg‐AD) mice with the COX‐1 selective inhibitor SC‐560 improved spatial learning and memory, and reduced amyloid deposits and tau hyperphosphorylation. SC‐560 also reduced glial activation and brain expression of inflammatory markers in 3 × Tg‐AD mice, and switched the activated microglia phenotype promoting their phagocytic ability. The present findings are the first to demonstrate that selective COX‐1 inhibition reduces neuroinflammation, neuropathology, and improves cognitive function in 3 × Tg‐AD mice. Thus, selective COX‐1 inhibition should be further investigated as a potential therapeutic approach for AD.     

Reduced fire blight susceptibility in apple cultivars using a high‐efficiency CRISPR/Cas9‐FLP/FRT‐based gene editing system

The bacterium Erwinia amylovora, the causal agent of fire blight disease in apple, triggers its infection through the DspA/E effector which interacts with the apple susceptibility protein MdDIPM4. In this work, MdDIPM4 knockout has been produced in two Malus × domestica susceptible cultivars using the CRISPR/Cas9 system delivered via Agrobacterium tumefaciens. Fifty‐seven transgenic lines were screened to identify CRISPR/Cas9‐induced mutations. An editing efficiency of 75% was obtained. Seven edited lines with a loss‐of‐function mutation were inoculated with the pathogen. Highly significant reduction in susceptibility was observed compared to control plants. Sequencing of five potential off‐target sites revealed no mutation event. Moreover, our construct contained a heat‐shock inducible FLP/FRT recombination system designed specifically to remove the T‐DNA harbouring the expression cassettes for CRISPR/Cas9, the marker gene and the FLP itself. Six plant lines with reduced susceptibility to the pathogen were heat‐treated and screened by real‐time PCR to quantify the exogenous DNA elimination. The T‐DNA removal was further validated by sequencing in one plant line. To our knowledge, this work demonstrates for the first time the development and application of a CRISPR/Cas9‐FLP/FRT gene editing system for the production of edited apple plants carrying a minimal trace of exogenous DNA.     

1H‐NMR screening for the high‐throughput determination of genotype and environmental effects on the content of asparagine in wheat grain

Free asparagine in cereals is known to be the precursor of acrylamide, a neurotoxic and carcinogenic product formed during cooking processes. Thus, the development of crops with lower asparagine is of considerable interest to growers and the food industry. In this study, we describe the development and application of a rapid ¹H‐NMR‐based analysis of cereal flour, that is, suitable for quantifying asparagine levels, and hence acrylamide‐forming potential, across large numbers of samples. The screen was applied to flour samples from 150 bread wheats grown at a single site in 2005, providing the largest sample set to date. Additionally, screening of 26 selected cultivars grown for two further years in the same location and in three additional European locations in the third year (2007) provided six widely different environments to allow estimation of the environmental (E) and G x E effects on asparagine levels. Asparagine concentrations in the 150 genotypes ranged from 0.32 to 1.56 mg/g dry matter in wholemeal wheat flours. Asparagine levels were correlated with plant height and therefore, due to recent breeding activities to produce semi‐dwarf varieties, a negative relationship with the year of registration of the cultivar was also observed. The multisite study indicated that only 13% of the observed variation in asparagine levels was heritable, whilst the environmental contribution was 36% and the GxE component was 43%. Thus, compared to some other phenotypic traits, breeding for low asparagine wheats presents a difficult challenge.     

The morphology and activity of the extrafloral nectaries in Reynoutria × bohemica (Polygonaceae)

• Reynoutria × bohemica is an invasive species causing significant damage to native ecosystems in North America and Europe.
• In this work, we performed an in‐depth micromorphological characterisation of the extrafloral nectaries (EFN), during their secretory and post‐secretory phases, in combination with field monitoring of nectary activity over time and the qualitative pool of insect visitors.
• EFN consist of secretory trichomes and vascularised parenchyma. Polysaccharides, lipids and proteins were histochemically detected in all trichome cells; phenolic substances were detected in parenchyma cells. Our data indicate that all nectary regions are involved in nectar production and release, constituting a functional unit. Moreover, the main compound classes of nectar and their transfer change over time: first, granulocrine secretion for sugars prevails, then eccrine secretion of the lipophilic fraction takes place. Active nectaries are mainly located in the apical portion of the stem during the growth phase (April–May), when we detected the highest number of individuals visited by ants; from mid‐August onwards, during flowering, the number of active nectaries declined then ceased production (September), with a concomitant decrease in visits by the ants. The spectrum of nectar‐foraging ants mainly included representatives of the genera Formica, Lasius and Camponotus.
• Reynoutria × bohemica produces an attractive secretion able to recruit local ants that may potentially act as ‘bodyguards’ for protecting young shoots, reducing secretions during the blooming stage. This defence mechanism against herbivores is the same as that displayed by the parental species in its native areas.

     

玉米农田土壤呼吸作用的空间异质性及其根系呼吸作用的贡献

基于4月底到9月底东北地区玉米农田土壤呼吸作用全生长季的观测,阐明了土壤呼吸作用的空间异质性特征,综合分析了水热因子、土壤性质、根系生物量及其测定位置对土壤呼吸作用空间异质性的影响,并对生长季中根系呼吸作用占土壤呼吸作用的比例进行了估算。结果表明,在植株尺度上,土壤呼吸作用存在着明显的空间异质性,较高的土壤呼吸速率通常出现在靠近玉米植株的地方。根系生物量的分布格局是影响土壤呼吸作用空间异质性的关键因素。在空间尺度上,土壤呼吸作用与根系生物量呈显著的线性关系,而土壤湿度、土壤有机质、全氮和碳氮比对土壤呼吸作用空间异质性的影响并不显著。通过建立土壤呼吸作用与玉米根系生物量的回归方程,对根系呼吸作用占土壤呼吸作用的比例进行了间接估算。玉米生长季中,根系呼吸作用占土壤呼吸作用的比例在43．1％～63．6％之间波动,均值为54．5％。     

RNAi‐mediated endogene silencing in strawberry fruit: detection of primary and secondary siRNAs by deep sequencing

RNA interference (RNAi) has been exploited as a reverse genetic tool for functional genomics in the nonmodel species strawberry (Fragaria × ananassa) since 2006. Here, we analysed for the first time different but overlapping nucleotide sections (>200 nt) of two endogenous genes, FaCHS (chalcone synthase) and FaOMT (O‐methyltransferase), as inducer sequences and a transitive vector system to compare their gene silencing efficiencies. In total, ten vectors were assembled each containing the nucleotide sequence of one fragment in sense and corresponding antisense orientation separated by an intron (inverted hairpin construct, ihp). All sequence fragments along the full lengths of both target genes resulted in a significant down‐regulation of the respective gene expression and related metabolite levels. Quantitative PCR data and successful application of a transitive vector system coinciding with a phenotypic change suggested propagation of the silencing signal. The spreading of the signal in strawberry fruit in the 3′ direction was shown for the first time by the detection of secondary small interfering RNAs (siRNAs) outside of the primary targets by deep sequencing. Down‐regulation of endogenes by the transitive method was less effective than silencing by ihp constructs probably because the numbers of primary siRNAs exceeded the quantity of secondary siRNAs by three orders of magnitude. Besides, we observed consistent hotspots of primary and secondary siRNA formation along the target sequence which fall within a distance of less than 200 nt. Thus, ihp vectors seem to be superior over the transitive vector system for functional genomics in strawberry fruit.     

Genotype‐by‐genotype interactions between an insect and its pathogen

Genotype‐by‐genotype (G×G) interactions are an essential requirement for the coevolution of hosts and parasites, but have only been documented in a small number of animal model systems. G×G effects arise from interactions between host and pathogen genotypes, such that some pathogen strains are more infectious in certain hosts and some hosts are more susceptible to certain pathogen strains. We tested for G×G interactions in the gypsy moth (Lymantria dispar) and its baculovirus. We infected 21 full‐sib families of gypsy moths with each of 16 isolates of baculovirus and measured the between‐isolate correlations of infection rate across host families for all pairwise combinations of isolates. Mean infectiousness varied among isolates and disease susceptibility varied among host families. Between‐isolate correlations of infection rate were generally less than one, indicating nonadditive effects of host and pathogen type consistent with G×G interactions. Our results support the presence of G×G effects in the gypsy moth–baculovirus interaction and provide empirical evidence that correlations in infection rates between field‐collected isolates are consistent with values that mathematical models have previously shown to increase the likelihood of pathogen polymorphism.