Common single-nucleotide polymorphisms (SNPs) are predicted to collectively explain 40–50% of phenotypic variation in human height, but identifying the specific variants and associated regions requires huge sample sizes1. Here, using data from a genome-wide association study of 5.4 million individuals of diverse ancestries, we show that 12,111 independent SNPs that are significantly associated with height account for nearly all of the common SNP-based heritability. These SNPs are clustered within 7,209 non-overlapping genomic segments with a mean size of around 90 kb, covering about 21% of the genome. The density of independent associations varies across the genome and the regions of increased density are enriched for biologically relevant genes. In out-of-sample estimation and prediction, the 12,111 SNPs (or all SNPs in the HapMap 3 panel2) account for 40% (45%) of phenotypic variance in populations of European ancestry but only around 10–20% (14–24%) in populations of other ancestries. Effect sizes, associated regions and gene prioritization are similar across ancestries, indicating that reduced prediction accuracy is likely to be explained by linkage disequilibrium and differences in allele frequency within associated regions. Finally, we show that the relevant biological pathways are detectable with smaller sample sizes than are needed to implicate causal genes and variants. Overall, this study provides a comprehensive map of specific genomic regions that contain the vast majority of common height-associated variants. Although this map is saturated for populations of European ancestry, further research is needed to achieve equivalent saturation in other ancestries.
Symbiotic bacteria are important drivers of phenotypic diversity in insects. One of the widespread symbionts to have emerged belongs to the genus Arsenophonus, however, its biological functions in most host insects remain entirely unknown. Here we report two distinct Arsenophonus strains in the brown planthopper (BPH), Nilaparvata lugens, a major pest insect in Asian countries that causes significant economic damage through rice crop destruction. Genomic resequencing data suggested that one Arsenophonus strain (S-type) negatively affected the insecticide resistance of the host. Indeed, replacement of the resident Arsenophonus with the S-type Arsenophonus significantly decreased host insecticide resistance. Transcriptome and metabolome analysis revealed down-regulation of xenobiotic metabolism and increased amino acid accumulation in the S-type Arsenophonus infected host. This study demonstrates how a symbiont-mediated phenotypic change can occur. The results of this study will aid in developing strategies that work through imposing an ecological disadvantage on insect pests, which will be of great value for pest control in agricultural industry.
As an r-strategy insect species, the brown planthopper (BPH) Nilaparvata lugens (Stål) is a serious pest of rice crops in the temperate and tropical regions of Asia and Australia, which may be due to its robust fecundity. Here we combined 2-DE comparative proteomic and RNA-seq transcriptomic analyses to identify fecundity-related proteins and genes. Using high- and low-fecundity populations as sample groups, a total of 54 and 75 proteins were significantly altered in the third and sixth day brachypterous female stages, respectively, and 39 and 54 of these proteins were identified by MALDI-TOF/TOF MS. In addition, 71,966 unigenes were quantified by Illumina sequencing. On the basis of the transcriptomic analysis, 7408 and 1639 unigenes demonstrated higher expression levels in the high-fecundity population in the second day brachypterous female adults and the second day fifth instar nymphs, respectively, and 411 unigenes were up-regulated in both groups. Of these dozens of proteins and thousands of unigenes, five were differentially expressed at both the protein and mRNA levels at all four time points, suggesting that these genes may regulate fecundity. Glutamine synthetase (GS) was chosen for further functional studies. RNAi knockdown of the GS gene reduced the fecundity of N. lugens by 64.6%, disrupted ovary development, and inhibited vitellogenin (Vg) expression. Our results show that a combination of proteomic and transcriptomic analyses provided five candidate proteins and genes for further study. The knowledge gained from this study may lead to a more fundamental understanding of the fecundity of this important agricultural insect pest.
The target of rapamycin (TOR) positively controls cell growth in response to nutrients such as amino acids. However, research on the specific nutrients sensed by TOR is limited. Glutamine (Gln), a particularly important amino acid involved in metabolism in organisms, is synthesised and catalysed exclusively by glutamine synthetase (GS), and our previous studies have shown that Gln may regulate fecundity in vivo levels of the brown planthopper (BPH) Nilaparvata lugens. Until now, it has remained unclear whether Gln activates or inhibits the TOR signalling pathway. Here, we performed the combined analyses of iTRAQ (isobaric tags for relative and absolute quantification) and DGE (tag-based digital gene expression) data in N.lugens at the protein and transcript levels after GS RNAi, and we found that 52 pathways overlap, including the TOR pathway. We further experimentally demonstrate that Gln activates the TOR pathway by promoting the serine/threonine protein kinase AKT and inhibiting the 5′AMP-activated protein kinase AMPK phosphorylation activity in the pest. Furthermore, TOR regulates the fecundity of N. lugens probably by mediating vitellogenin (Vg) expression. This work is the first report that Gln activates the TOR pathway in vivo.
There was a significant difference in the microbial community composition between diabetic patients and healthy subjects. A high abundance of Acinetobacter in the OS of diabetic patients may arise from the unique characteristics of the OS compared with those of other organ surfaces.
Introduction The brown planthopper (BPH, Nilaparvata lugens Stål, Hemiptera: Delphacidae) is one of the most devastating insect pests of the crucially important cereal crop, rice ( Oryza sativa L.). Currently, multiple BPH-resistant rice varieties have been cultivated and generalized to control BPH. However, the defence metabolic responses and their modes of action against BPH in different rice cultivars remain uncharacterized. Objective We used a non-biased metabolomics approach to explore the differences in metabolite profiles in response to BPH infestation in the susceptible TN1 rice cultivar and two resistant cultivars (IR36 and IR56). Methods The metabolomic detection based on gas chromatography–mass spectrometry (GC–MS) and liquid chromatography–mass spectrometry (LC–MS) was performed to investigate the content changes of identified metabolites in TN1, IR36 and IR56 rice varieties at various time points (0 h, 24 h, 48 h and 96 h) post BPH feeding. The differentially expressed metabolites were screened and the corresponding metabolic pathways were further enriched. Results The results showed that compared to that in TN1, the content changes of most primary metabolites were more stable, but the concentration alterations of some defence-related metabolites were more acute and persistent in IR36 and IR56. Furthermore, the differentially expressed pathways analysis revealed that cyanoamino acids and lipids metabolism was persistently induced in IR36, but changes in thiamine, taurine and hypotaurine metabolism were more significant in IR56 during BPH infestation. Besides, the contents of quercetin and spermidine which were harmful to BPH fitness, were significantly elevated by BPH in TN1 and IR36, and the quercetin level was significantly decreased during BPH feeding in IR56. Conclusion The results of the differences in metabolite profiles in response to BPH infestation in different rice cultivars were useful to clarify the metabolic mechanism of rice plants during BPH infestation and to provide new resources to control this insect pest. Electronic supplementary material The online version of this article (10.1007/s11306-019-1523-4) contains supplementary material, which is available to authorized users.
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