REINTERPRETATION OF A CONULARIID-LIKE FOSSIL FROM THE VENDIAN OF RUSSIA

Abstract:  Vendoconularia triradiata Ivantsov and Fedonkin, recently described from Vendian (latest Proterozoic) strata of Russia, has been interpreted as a six-sided conulariid cnidarian. However, comparison of published illustrations of V .  triradiata with Palaeozoic conulariids suggests that certain key features of the anatomy of V .  triradiata should be reinterpreted. Specifically, features previously homologized with the corners of conulariid thecae may actually be homologous to the conulariid midlines. Under this new interpretation, the corners of the Vendoconularia theca were sulcate, and the midline of each face was non-sulcate and flanked by a pair of low internal carinae. This alternative set of hypotheses of homology makes the argument for a conulariid affinity for Vendoconularia stronger.     

Natural Variation in Maize Aphid Resistance Is Associated with 2,4-Dihydroxy-7-Methoxy-1,4-Benzoxazin-3-One Glucoside Methyltransferase Activity

Plants differ greatly in their susceptibility to insect herbivory, suggesting both local adaptation and resistance tradeoffs. We used maize (Zea mays) recombinant inbred lines to map a quantitative trait locus (QTL) for the maize leaf aphid (Rhopalosiphum maidis) susceptibility to maize Chromosome 1. Phytochemical analysis revealed that the same locus was also associated with high levels of 2-hydroxy-4,7-dimethoxy-1,4-benzoxazin-3-one glucoside (HDMBOA-Glc) and low levels of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one glucoside (DIMBOA-Glc). In vitro enzyme assays with candidate genes from the region of the QTL identified three O-methyltransferases (Bx10a-c) that convert DIMBOA-Glc to HDMBOA-Glc. Variation in HDMBOA-Glc production was attributed to a natural CACTA family transposon insertion that inactivates Bx10c in maize lines with low HDMBOA-Glc accumulation. When tested with a population of 26 diverse maize inbred lines, R. maidis produced more progeny on those with high HDMBOA-Glc and low DIMBOA-Glc. Although HDMBOA-Glc was more toxic to R. maidis than DIMBOA-Glc in vitro, BX10c activity and the resulting decline of DIMBOA-Glc upon methylation to HDMBOA-Glc were associated with reduced callose deposition as an aphid defense response in vivo. Thus, a natural transposon insertion appears to mediate an ecologically relevant trade-off between the direct toxicity and defense-inducing properties of maize benzoxazinoids.     

Comprehensive genotyping of the USA national maize inbred seed bank

Background

Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world.

Results

The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits.

Conclusions

The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.     

Extrafloral nectaries as a deterrent mechanism against seed predators in the chemically protected weed Crotalaria pallida (Leguminosae)

Abstract In several plants, extrafloral nectaries (EFN) are located close to the reproductive structures, suggesting that ants may act as a defence against specialized seed predators that overcome chemical defences. Alternatively, ants may also deter herbivores in a generalized manner, thereby protecting the whole plant. In this work, we examined the relationship between the chemically protected weed Crotalaria pallida Ait. (Leguminosae) that bears EFN, its specialized seed predator, the larvae of the arctiid moth Utetheisa ornatrix L. (Arctiidae) and ants. We tested two hypotheses related to the type of deterrence caused by ants. The Seed Predator Deterrence Hypothesis predicts that ant deterrence is directed primarily towards herbivores that destroy seeds and other reproductive structures, without attacking herbivores on vegetative structures. The General Deterrence Hypothesis states that ants are general in their effects, equally deterring herbivores in vegetative and reproductive structures. Our results supported the predictions of the Seed Predator Deterrence Hypothesis, namely, that (i) ant activity on EFN was related to the vulnerability of reproductive structures to attack by U. ornatrix; (ii) ant patrolling was restricted almost entirely to racemes; (iii) ants removed termites used as baits more frequently on racemes than on leaves; and (iv) U. ornatrix larvae were often expulsed from the racemes. These results indicate that EFN can act as another deterrent mechanism in chemically protected plants by promoting the expulsion of specialist seed predators.     

Testing the quick meal hypothesis: The effect of pulp on hoarding and seed predation of Hymenaea courbaril by red‐rumped agoutis (Dasyprocta leporina)

Abstract: Red‐rumped agoutis (Dasyprocta leporina) are important seed dispersers/predators of Neotropical large‐seeded plants. Several species of seeds cached by agoutis have an edible reward, in contrast to temperate rodent‐dispersed diaspores. The quick meal hypothesis states that the presence of a reward such as edible pulp will enhance the efficiency of rodents as seed disperses by satiating the animal and, consequently, reducing seed predation and enhancing hoarding. In this study, this hypothesis was tested using as the reference system the pulp and seeds of Hymenaea courbaril. Seeds with and without pulp were offered to agoutis and the behaviour of each individual was recorded. Since the probability of predation and hoarding were complementary, we used the probability of predation. The proportion of agoutis that preyed on at least one seed was similar for seeds with (42.8% of individuals) and without (40.0% of individuals) pulp. In agoutis that preyed upon at least one seed, the probability that they killed a seed did not differ between seeds with (0.17 ± 0.03) and without (0.20 ± 0.08) pulp. Hence, these results do not support the ‘quick meal hypothesis’.     

Prediction of indirect interactions in proteins

Background  

Both direct and indirect interactions determine molecular recognition of ligands by proteins. Indirect interactions can be defined as effects on recognition controlled from distant sites in the proteins, e.g. by changes in protein conformation and mobility, whereas direct interactions occur in close proximity of the protein's amino acids and the ligand. Molecular recognition is traditionally studied using three-dimensional methods, but with such techniques it is difficult to predict the effects caused by mutational changes of amino acids located far away from the ligand-binding site. We recently developed an approach, proteochemometrics, to the study of molecular recognition that models the chemical effects involved in the recognition of ligands by proteins using statistical sampling and mathematical modelling.     

Genome-Wide Association of Carbon and Nitrogen Metabolism in the Maize Nested Association Mapping Population

Carbon (C) and nitrogen (N) metabolism are critical to plant growth and development and are at the basis of crop yield and adaptation. We performed high-throughput metabolite analyses on over 12,000 samples from the nested association mapping population to identify genetic variation in C and N metabolism in maize (Zea mays ssp. mays). All samples were grown in the same field and used to identify natural variation controlling the levels of 12 key C and N metabolites, namely chlorophyll a, chlorophyll b, fructose, fumarate, glucose, glutamate, malate, nitrate, starch, sucrose, total amino acids, and total protein, along with the first two principal components derived from them. Our genome-wide association results frequently identified hits with single-gene resolution. In addition to expected genes such as invertases, natural variation was identified in key C₄ metabolism genes, including carbonic anhydrases and a malate transporter. Unlike several prior maize studies, extensive pleiotropy was found for C and N metabolites. This integration of field-derived metabolite data with powerful mapping and genomics resources allows for the dissection of key metabolic pathways, providing avenues for future genetic improvement.Carbon (C) and nitrogen (N) metabolism are the basis for life on Earth. The production, balance, and tradeoffs of C and N metabolism are critical to all plant growth, yield, and local adaptation (Coruzzi and Bush, 2001; Coruzzi et al., 2007). In plants, there is a critical balance between the tissues that are producing energy (sources) and those using it (sinks), as the identities and locations of these vary through time and developmental stage (Smith et al., 2004). While a great deal of research has focused on the key genes and proteins involved in these processes (Wang et al., 1993; Kim et al., 2000; Takahashi et al., 2009), relatively little is known about the natural variation within a species that fine-tunes these processes in individual plants.In addition, a key aspect of core C metabolism involves the nature of plant photosynthesis. While the majority of plants use standard C₃ photosynthetic pathways, some, including maize (Zea mays) and many other grasses, use C₄ photosynthesis to concentrate CO₂ in bundle sheath cells to avoid wasteful photorespiration (Sage, 2004). Under some conditions (such as drought or high temperatures), C₄ photosynthesis is much more efficient than C₃ photosynthesis. Since these conditions are expected to become more prevalent in the near future due to climate change, various research groups are working to convert C₃ crop species to C₄ metabolism in order to boost crop production and food security (Sage and Zhu, 2011). Beyond this, better understanding of both C₃ and C₄ metabolic pathways will aid efforts to breed crops for superior yield, N-use efficiency, and other traits important for global food production.In the last two decades, quantitative trait locus (QTL) mapping, first with linkage analysis and later with association mapping, has been used to dissect C and N metabolism in several species, including Arabidopsis (Arabidopsis thaliana; Mitchell-Olds and Pedersen, 1998; Keurentjes et al., 2008; Lisec et al., 2008; Sulpice et al., 2009), tomato (Solanum lycopersicum; Schauer et al., 2006), and maize (Hirel et al., 2001; Limami et al., 2002; Zhang et al., 2006, 2010a, 2010b). These studies identified key genetic regions underlying variation in core C and N metabolism, many of which include candidate genes known to be involved in these processes.Previous studies of genetic variation for C and N metabolism are limited by the fact that they identified trait loci only through linkage mapping in artificial families or through association mapping across populations of unrelated individuals. Linkage mapping benefits from high statistical power due to many individuals sharing the same genotype at any given location, but it suffers from low resolution due to the limited number of generations (and hence recombination events) since the initial founders. Association mapping, in turn, enjoys high resolution due to the long recombination histories of natural populations but suffers from low power, since most genotypes occur in only a few individuals. In addition, many of these studies focused on C and N in artificial settings (e.g. greenhouses or growth chambers) instead of field conditions, running the risk that important genetic loci could be missed if the conditions do not include important (and potentially unknown) natural environmental variables.To address these issues and improve our understanding of C and N metabolism in maize, we used a massive and diverse germplasm resource, the maize nested association mapping (NAM) population (Buckler et al., 2009; McMullen et al., 2009), to evaluate genetic variation underlying the accumulation of 12 targeted metabolites in maize leaf tissue under field conditions. This population was formed by mating 25 diverse maize lines to the reference line, B73, and creating a 200-member biparental family from each of these crosses. The entire 5,000-member NAM population thus combines the strengths of both linkage and association mapping (McMullen et al., 2009), and it has been used to identify QTLs for important traits such as flowering time (Buckler et al., 2009), disease resistance (Kump et al., 2011; Poland et al., 2011), and plant architecture (Tian et al., 2011; Peiffer et al., 2013). Most importantly, this combination of power and resolution frequently resolves associations down to the single-gene level, even when using field-based data.The metabolites we profiled are key indicators of photosynthesis, respiration, glycolysis, and protein and sugar metabolism in the plant (Sulpice et al., 2009). By taking advantage of a robotized metabolic phenotyping platform (Gibon et al., 2004), we performed more than 100,000 assays across 12,000 samples, with two independent samples per experimental plot. Raw data and the best linear unbiased predictors (BLUPs) of these data were included as part of a study of general functional variation in maize (Wallace et al., 2014), but, to our knowledge, this is the first in-depth analysis of these metabolic data. We find strong correlations among several of the metabolites, and we also find extensive pleiotropy among the different traits. Many of the top QTLs are also near or within candidate genes relating to C and N metabolism, thus identifying targets for future breeding and selection. These results provide a powerful resource for those working with core C and N metabolism in plants and for improving maize performance in particular.     

Variants in the interleukin-1 alpha and beta genes,and the risk for periodontal disease in dogs

Elevated levels of interleukin-1 (IL-1) have been shown to amplify the inflammatory response against periodontopathogenic bacteria. In humans, polymorphisms in the IL1A and IL1B genes are the most well-studied genetic polymorphisms associated with periodontal disease (PD). In contrast to human, there is a lack of knowledge on the genetic basis of canine PD. A case–control study was conducted in which a molecular analysis of dog IL1A and IL1B genes was performed. Of the eight genetic variants identified, seven in IL1A gene and one in IL1B gene, IL1A/1_g.388A >C and IL1A/1_g.521T >A showed statistically significant differences between groups (adjusted OR (95% CI): 0.15 (0.03–0.76), P= 0.022; 5.76 (1.03–32.1), P= 0.046, respectively). It suggests that in the studied population the IL1A/1_g.388C allele is associated with a decreased PD risk, whereas the IL1A/1_g.521A allele can confer an increased risk. Additionally, the IL1A/2_g.515G >T variation resulted in a change of amino acid, i.e. glycine to valine. In silico analysis suggests that this change can alter protein structure and function, predicting it to be deleterious or damaging. This work suggests that IL1 genetic variants may be important in PD susceptibility in canines.     

Independent Molecular Basis of Convergent Highland Adaptation in Maize

Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America, using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.