Common variants at 6q22 and 17q21 are associated with intracranial volume

During aging, intracranial volume remains unchanged and represents maximally attained brain size, while various interacting biological phenomena lead to brain volume loss. Consequently, intracranial volume and brain volume in late life reflect different genetic influences. Our genome-wide association study (GWAS) in 8,175 community-dwelling elderly persons did not reveal any associations at genome-wide significance (P < 5 × 10(-8)) for brain volume. In contrast, intracranial volume was significantly associated with two loci: rs4273712 (P = 3.4 × 10(-11)), a known height-associated locus on chromosome 6q22, and rs9915547 (P = 1.5 × 10(-12)), localized to the inversion on chromosome 17q21. We replicated the associations of these loci with intracranial volume in a separate sample of 1,752 elderly persons (P = 1.1 × 10(-3) for 6q22 and 1.2 × 10(-3) for 17q21). Furthermore, we also found suggestive associations of the 17q21 locus with head circumference in 10,768 children (mean age of 14.5 months). Our data identify two loci associated with head size, with the inversion at 17q21 also likely to be involved in attaining maximal brain size.     

The molecular mechanism of zinc and cadmium stress response in plants

When plants are subjected to high metal exposure, different plant species take different strategies in response to metal-induced stress. Largely, plants can be distinguished in four groups: metal-sensitive species, metal-resistant excluder species, metal-tolerant non-hyperaccumulator species, and metal-hypertolerant hyperaccumulator species, each having different molecular mechanisms to accomplish their resistance/tolerance to metal stress or reduce the negative consequences of metal toxicity. Plant responses to heavy metals are molecularly regulated in a process called metal homeostasis, which also includes regulation of the metal-induced reactive oxygen species (ROS) signaling pathway. ROS generation and signaling plays an important duel role in heavy metal detoxification and tolerance. In this review, we will compare the different molecular mechanisms of nutritional (Zn) and non-nutritional (Cd) metal homeostasis between metal-sensitive and metal-adapted species. We will also include the role of metal-induced ROS signal transduction in this comparison, with the aim to provide a comprehensive overview on how plants cope with Zn/Cd stress at the molecular level.     

Genomic and metabolic prediction of complex heterotic traits in hybrid maize

Maize is both an exciting model organism in plant genetics and also the most important crop worldwide for food, animal feed and bioenergy production. Recent genome-wide association and metabolic profiling studies aimed to resolve quantitative traits to their causal genetic loci and key metabolic regulators. Here we present a complementary approach that exploits large-scale genomic and metabolic information to predict complex, highly polygenic traits in hybrid testcrosses. We crossed 285 diverse Dent inbred lines from worldwide sources with two testers and predicted their combining abilities for seven biomass- and bioenergy-related traits using 56,110 SNPs and 130 metabolites. Whole-genome and metabolic prediction models were built by fitting effects for all SNPs or metabolites. Prediction accuracies ranged from 0.72 to 0.81 for SNPs and from 0.60 to 0.80 for metabolites, allowing a reliable screening of large collections of diverse inbred lines for their potential to create superior hybrids.     

Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population

Rheumatoid arthritis is a common autoimmune disease characterized by chronic inflammation. We report a meta-analysis of genome-wide association studies (GWAS) in a Japanese population including 4,074 individuals with rheumatoid arthritis (cases) and 16,891 controls, followed by a replication in 5,277 rheumatoid arthritis cases and 21,684 controls. Our study identified nine loci newly associated with rheumatoid arthritis at a threshold of P < 5.0 × 10(-8), including B3GNT2, ANXA3, CSF2, CD83, NFKBIE, ARID5B, PDE2A-ARAP1, PLD4 and PTPN2. ANXA3 was also associated with susceptibility to systemic lupus erythematosus (P = 0.0040), and B3GNT2 and ARID5B were associated with Graves' disease (P = 3.5 × 10(-4) and 2.9 × 10(-4), respectively). We conducted a multi-ancestry comparative analysis with a previous meta-analysis in individuals of European descent (5,539 rheumatoid arthritis cases and 20,169 controls). This provided evidence of shared genetic risks of rheumatoid arthritis between the populations.     

Multiple-scale roost habitat comparisons of female Merriam’s Wild Turkeys in the southern Black Hills, South Dakota

Because quantity and quality of roosting habitat can affect Merriam’s Wild Turkey ( Meleagris gallopavo merriami ) distribution, we described habitat characteristics of Merriam’s turkey roost sites in the southern Black Hills of South Dakota. Varying proportions of Merriam’s turkeys in the southern Black Hills depended on supplemental feed from livestock operations during the 2 winters of our study, whereas the remainder wintered in forested habitat away from supplemental feed. We compared characteristics of roost habitat occupied by female turkeys from both groups. We located turkeys with radio-transmitters in the early morning and late evening to find roost sites. Female Merriam’s turkeys in the southern Black Hills roosted exclusively in ponderosa pine trees, primarily on the upper portions of ridges on easterly aspects. Generally, trees >30 cm diameter at breast height (dbh) were chosen for roosting, but turkeys also roosted in trees with smaller dbh. During winter months, turkeys that relied on supplemental feeding roosted adjacent to the ranch-farmstead where the supplemental food was located. Generally, these turkeys used the same roost site(s) throughout the winter, whereas turkeys that remained in the forest during winter used multiple roost sites. We suggest maintaining stands of trees >30 cm dbh on the upper portions of easterly aspects to provide suitable roosting habitat for female Merriam’s Wild Turkeys in the southern Black Hills.     

Comparative tolerance of four stocks of cuttthroat trout to extremes in temperature, salinity, and hypoxia

Four stocks of cutthroat trout ( Oncorhynchus clarki ) were exposed to high temperature, high salinity, and low dissolved oxygen to determine inherent differences. The fish tested included 2 stocks of Bonneville cutthroat trout ( O. c. utah ), a lacustrine stock derived from Bear Lake and a fluvial-origin stock from southern Utah (Manning Meadow Reservoir). The other 2 stocks tested were from Electric Lake (largely Yellowstone cutthroat trout, O. c. bouvieri ) and Jackson Hole, Wyoming (fine-spotted Snake River cutthroat trout, O. c. subsp.). Temperature tests were either critical thermal maximum (CTM) or 96-hour trials using juveniles acclimated between 12.5° C and 18.0° C. Two CTM end points were temperature at first loss of equilibrium (CTM eq ) and onset of spasms (CTM s ). There were no significant differences in CTM eq among test fish acclimated to 18.0° C, but CTM s was significantly higher for Bear Lake Bonneville (30.0°C) than for Snake River (29.6° C) or southern Bonneville (29.7° C) stocks. With fish acclimated at 13.0° C, there were no significant differences among the stocks in CTM eq or CTM s . Differences among stocks varied significantly among nine 96-hour tests. Overall, it appeared that the southern Bonneville stock had slightly better survival at warmer temperatures than other stocks. In 24-hour survival tests at high salinities, the Snake River stock had the lowest tolerance, with significant mortality occuring at 18% (29.5 mS · cm -1 conductivity). The southern Bonneville stock had the highest tolerance, with no mortality until 22% (38 mS · cm -1 ). Bear Lake Bonneville and Electric Lake stocks had 60% and 30% mortality, respectively, at 21% (36 mS · cm -1 ). Hypoxia tolerance measured by resistance time, 24-hour mortality, or probit analysis (LEC 50 ) did not differ among stocks. The 24-hour LEC 50 was 2.34 mg O 2 · L -1 for all stocks combined.     

A framework for variation discovery and genotyping using next-generation DNA sequencing data

Recent advances in sequencing technology make it possible to comprehensively catalog genetic variation in population samples, creating a foundation for understanding human disease, ancestry and evolution. The amounts of raw data produced are prodigious, and many computational steps are required to translate this output into high-quality variant calls. We present a unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs. Our process includes (i) initial read mapping; (ii) local realignment around indels; (iii) base quality score recalibration; (iv) SNP discovery and genotyping to find all potential variants; and (v) machine learning to separate true segregating variation from machine artifacts common to next-generation sequencing technologies. We here discuss the application of these tools, instantiated in the Genome Analysis Toolkit, to deep whole-genome, whole-exome capture and multi-sample low-pass (～4×) 1000 Genomes Project datasets.     

The genome of Theobroma cacao

We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.