Analysis of the genetic architecture of maize ear and grain morphological traits by combined linkage and association mapping

Key message

Using combined linkage and association mapping, 26 stable QTL and six stable SNPs were detected across multiple environments for eight ear and grain morphological traits in maize. One QTL, PKS2, might play an important role in maize yield improvement.

Abstract

In the present study, one bi-parental population and an association panel were used to identify quantitative trait loci (QTL) for eight ear and grain morphological traits. A total of 108 QTL related to these traits were detected across four environments using an ultra-high density bin map constructed using recombinant inbred lines (RILs) derived from a cross between Ye478 and Qi319, and 26 QTL were identified in more than two environments. Furthermore, 64 single nucleotide polymorphisms (SNPs) were found to be significantly associated with the eight ear and grain morphological traits (?log₁₀(P)?>?4) in an association panel of 240 maize inbred lines. Combining the two mapping populations, a total of 17 pleiotropic QTL/SNPs (pQTL/SNPs) were associated with various traits across multiple environments. PKS2, a stable locus influencing kernel shape identified on chromosome 2 in a genome-wide association study (GWAS), was within the QTL confidence interval defined by the RILs. The candidate region harbored a short 13-Kb LD block encompassing four SNPs (SYN11386, PHM14783.16, SYN11392, and SYN11378). In the association panel, 13 lines derived from the hybrid PI78599 possessed the same allele as Qi319 at the PHM14783.16 (GG) locus, with an average value of 0.21 for KS, significantly lower than that of the 34 lines derived from Ye478 that carried a different allele (0.25, P?<?0.05). Therefore, further fine mapping of PKS2 will provide valuable information for understanding the genetic components of grain yield and improving molecular marker-assisted selection (MAS) in maize.

     

Evaluation of European Schizophrenia GWAS Loci in Asian Populations via Comprehensive Meta-Analyses

Schizophrenia is a severe and highly heritable neuropsychiatric disorder. Recent genetic analyses including genome-wide association studies (GWAS) have implicated multiple genome-wide significant variants for schizophrenia among European populations. However, many of these risk variants were not largely validated in other populations of different ancestry such as Asians. To validate whether these European GWAS significant loci are associated with schizophrenia in Asian populations, we conducted a systematic literature search and meta-analyses on 19 single nucleotide polymorphisms (SNPs) in Asian populations by combining all available case-control and family-based samples, including up to 30,000 individuals. We employed classical fixed (or random) effects inverse variance weighted methods to calculate summary odds ratios (ORs) and 95 % confidence intervals (CIs). Among the 19 GWAS loci, we replicated the risk associations of nine markers (e.g., SNPs at VRK2, ITIH3/4, NDST3, NOTCH4) surpassing significance level (two-tailed P?<?0.05), and three additional SNPs in MIR137 and ZNF804A also showed trend associations (one-tailed P?<?0.05). These risk associations are in the same directions of allelic effects between Asian replication samples and initial European GWAS findings, and the successful replications of these GWAS loci in a different ethnic group provide stronger evidence for their clinical associations with schizophrenia. Further studies, focusing on the molecular mechanisms of these GWAS significant loci, will become increasingly important for understanding of the pathogenesis to schizophrenia.     

Genome-wide association study of <Emphasis Type="Italic">Mycobacterium avium</Emphasis> subspecies <Emphasis Type="Italic">Paratuberculosis</Emphasis> infection in Chinese Holstein

Background

Paratuberculosis is a contagious, chronic and enteric disease in ruminants, which is caused by Mycobacterium avium subspecies paratuberculosis (MAP) infection, resulting in enormous economic losses worldwide. There is currently no effective cure for MAP infection or a vaccine, it is thus important to explore the genetic variants that contribute to host susceptibility to infection by MAP, which may provide a better understanding of the mechanisms of paratuberculosis and benefit animal genetic improvement. Herein we performed a genome-wide association study (GWAS) to identify genomic regions and candidate genes associated with susceptibility to MAP infection in dairy cattle.

Results

Using Illumina Bovine 50?K (54,609 SNPs) and GeneSeek HD (138,893 SNPs) chips, two analytical approaches were performed, GRAMMAR-GC and ROADTRIPS in 937 Chinese Holstein cows, among which individuals genotyped by the 50?K chip were imputed to HD SNPs with Beagle software. Consequently, 15 and 11 significant SNPs (P?<?5?×?10^??5) were identified with GRAMMAR-GC and ROADTDRIPS, respectively. A total of 10 functional genes were in proximity to (i.e., within 1?Mb) these SNPs, including IL4, IL5, IL13, IRF1, MyD88, PACSIN1, DEF6, TDP2, ZAP70 and CSF2. Functional enrichment analysis showed that these genes were involved in immune related pathways, such as interleukin, T cell receptor signaling pathways and inflammatory bowel disease (IBD), implying their potential associations with susceptibility to MAP infection. In addition, by examining the publicly available cattle QTLdb, a previous QTL for MAP was found to be overlapped with one of regions detected currently at 32.5?Mb on BTA23, where the TDP2 gene was anchored.

Conclusions

In conclusion, we identified 26 SNPs located on 15 chromosomes in the Chinese Holstein population using two GWAS strategies with high density SNPs. Integrated analysis of GWAS, biological functions and the reported QTL information helps to detect positional candidate genes and the identification of regions associated with susceptibility to MAP traits in dairy cattle.

     

Rhizosphere processes induce changes in dissimilatory iron reduction in a tidal marsh soil: a rhizobox study

Background and aims

Although the role of microbial iron respiration in tidal marshes has been recognized for decades, the effect of rhizosphere processes on dissimilatory ferric iron reduction (FeR) is poorly known. Herein, we examined the FeR surrounding the root zone of three tidal marsh plants.

Methods

Using in situ rhizoboxes, we accurately separated rhizobox soil as one rhizosphere zone, and three bulk soil zones. Dissimilatory and sulfidic-mediated FeR were quantified by accumulation of non-sulfidic Fe(II) and Fe sulfides over time, respectively.

Results

The rates of dissimilatory FeR attained 42.5 μmol Fe g^?1 d^?1 in the rhizosphere, and logarithmically declined by up to 19.1 μmol Fe g^?1 d^?1 in the outer bulk soil. The rates of sulfidic-mediated FeR were less than 2 μmol Fe g^?1 d^?1 among all zones. Poorly crystalline Fe(III), DOC and DON, porewater Fe²⁺, and SO₄^2? were all enriched in the rhizosphere, whereas non-sulfidic Fe(II) and Fe sulfides gradually accumulated away from the roots. Iron reducers (Geobacter, Bacillus, Shewanella, and Clostridium) had higher populations in the rhizosphere than in the bulk soil. Higher rates of dissimilatory FeR were observed in the Phragmites australis and Spartina alterniflora rhizoboxes than in the Cyperus malaccensis rhizoboxes.

Conclusions

The radial change pattern of dissimilatory FeR rates were determined by allocation of poorly crystalline Fe(III) and dissolved organic carbon. The interspecies difference of rhizosphere dissimilatory FeR was associated with the root porosity and aerenchyma of the tidal marsh plants.

     

Genome-wide association study for soybean cyst nematode resistance in Chinese elite soybean cultivars

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is a highly recalcitrant endoparasite of soybean roots, causing more yield loss than any other pest. To identify quantitative trait loci (QTL) controlling resistance to SCN (HG type 2.5.7, race 1), a genome-wide association study (GWAS) was performed. The association panel, consisting of 120 Chinese soybean cultivars, was genotyped with 7189 single nucleotide polymorphism (SNPs). A total of 6204 SNPs with minor allele frequency >0.05 were used to estimate linkage disequilibrium (LD) and population structure. The mean level of LD measured by r ² declined very rapidly to half its maximum value (0.51) at 220 kb. The overall population structure was approximately coincident with geographic origin. The GWAS results identified 13 SNPs in 7 different genomic regions significantly associated with SCN resistance. Of these, three SNPs were localized in previously mapped QTL intervals, including rhg1 and Rhg4. The GWAS results also detected 10 SNPs in 5 different genomic regions associated with SCN resistance. The identified loci explained an average of 95.5% of the phenotypic variance. The proportion of phenotypic variance was due to additive genetic variance of the validated SNPs. The present study identified multiple new loci and refined chromosomal regions of known loci associated with SCN resistance. The loci and trait-associated SNPs identified in this study can be used for developing soybean cultivars with durable resistance against SCN.     

Short-term effects of crop rotation,residue management,and soil water on carbon mineralization in a tropical cropping system

The purpose of this study was to investigate the short-term effects of maize (Zea mays)-fallow rotation, residue management, and soil water on carbon mineralization in a tropical cropping system in Ghana. After 15 months of the trial, maize–legume rotation treatments had significantly (P?C ₀ (μg CO₂–C g^?1) than maize–elephant grass (Pennisetum purpureum) rotations. The C ₀ for maize–grass rotation treatments was significantly related to the biomass input (r?=?0.95; P?=?0.05), but that for the maize–legume rotation was not. The soil carbon mineralization rate constant, k (per day), was also significantly related to the rotation treatments (P?k values for maize–grass and maize–legume rotation treatments were 0.025 and 0.036 day^?1 respectively. The initial carbon mineralization rate, m ₀ (μg CO₂–C g^?1 day ^?1), was significantly (P?θ. The m ₀ ranged from 3.88 to 18.67 and from 2.30 to 15.35 μg CO₂–C g^?1 day^?1 for maize–legume and maize–grass rotation treatments, respectively, when the soil water varied from 28% to 95% field capacity (FC). A simple soil water content (θ)-based factor, f _w, formulated as: \(f_{\text{w}} = \left[ {\frac{{\theta - \theta _{\text{d}} }}{{\theta _{{\text{FC}}} - \theta _{\text{d}} }}} \right]\), where θ _d and θ _FC were the air-dry and field capacity soil water content, respectively, adequately described the variation of the m ₀ with respect to soil water (R ²?=?0.91; RMSE?=?1.6). Such a simple relationship could be useful for SOC modeling under variable soil water conditions.     

Rank-based genome-wide analysis reveals the association of Ryanodine receptor-2 gene variants with childhood asthma among human populations

Background

The standard approach to determine unique or shared genetic factors across populations is to identify risk alleles in one population and investigate replication in others. However, since populations differ in DNA sequence information, allele frequencies, effect sizes, and linkage disequilibrium patterns, SNP association using a uniform stringent threshold on p values may not be reproducible across populations. Here, we developed rank-based methods to investigate shared or population-specific loci and pathways for childhood asthma across individuals of diverse ancestry. We performed genome-wide association studies on 859,790 SNPs genotyped in 527 affected offspring trios of European, African, and Hispanic ancestry using publically available asthma database in the Genotypes and Phenotypes database.

Results

Rank-based analyses showed that there are shared genetic factors for asthma across populations, more at the gene and pathway levels than at the SNP level. Although the top 1,000 SNPs were not shared, 11 genes (RYR2, PDE4D, CSMD1, CDH13, ROBO2, RBFOX1, PTPRD, NPAS3, PDE1C, SEMA5A, and CTNNA2) mapped by these SNPs were shared across populations. Ryanodine receptor 2 (RYR2, a statin response-related gene) showed the strongest association in European (p value?=?2.55?×?10^?7) and was replicated in African (2.57?×?10^?4) and Hispanic (1.18?×?10^?3) Americans. Imputation analyses based on the 1000 Genomes Project uncovered additional RYR2 variants associated with asthma. Network and functional ontology analyses revealed that RYR2 is an integral part of dermatological or allergic disorder biological networks, specifically in the functional classes involving inflammatory, eosinophilic, and respiratory diseases.

Conclusion

Our rank-based genome-wide analysis revealed for the first time an association of RYR2 variants with asthma and replicated previously discovered PDE4D asthma gene across human populations. The replication of top-ranked asthma genes across populations suggests that such loci are less likely to be false positives and could indicate true associations. Variants that are associated with asthma across populations could be used to identify individuals who are at high risk for asthma regardless of genetic ancestry.

     

<Emphasis Type="Italic">HMG1A</Emphasis> and <Emphasis Type="Italic">PPARG</Emphasis> are differently expressed in the liver of fat and lean broilers

The expression of nine functional candidates for QT abdominal fat weight and relative abdominal fat content was investigated by real-time polymerase chain reaction (PCR) in the liver, adipose tissue, colon, muscle, pituitary gland and brain of broilers. The high mobility group AT-hook 1 (HMG1A) gene was up-regulated in liver with a ratio of means of 2.90 (P?≤?0.01) in the «fatty» group (relative abdominal fat content 3.5?±?0.18%, abdominal fat weight 35.4?±?6.09 g) relative to the «lean» group (relative abdominal fat content 1.9?±?0.56%, abdominal fat weight 19.2?±?5.06 g). Expression of this gene was highly correlated with the relative abdominal fat content (0.70, P?≤?0.01) and abdominal fat weight (0.70, P?≤?0.01). The peroxisome proliferator-activated receptor gamma (PPARG) gene was also up-regulated in the liver with a ratio of means of 3.34 (P?≤?0.01) in the «fatty» group relative to the «lean» group. Correlation of its expression was significant with both the relative abdominal fat content (0.55, P?≤?0.05) and the abdominal fat weight (0.57, P?≤?0.01). These data suggest that the HMG1A and PPARG genes were candidate genes for abdominal fat deposition in chickens. Searching of rSNPs in regulatory regions of the HMG1A and PPARG genes could provide a tool for gene-assisted selection.     

A GWA study reveals genetic loci for body conformation traits in Chinese Laiwu pigs and its implications for human BMI

Pigs share numerous physiological and phenotypic similarities with human and thus have been considered as a good model in nonrodent mammals for the study of genetic basis of human obesity. Researches on candidate genes for obesity traits have successfully identified some common genes between humans and pigs. However, few studies have assessed how many similarities exist between the genetic architecture of obesity in pigs and humans by large-scale comparative genomics. Here, we performed a genome-wide association study (GWAS) using the porcine 60 K SNP Beadchip for BMI and other four conformation traits at three different ages in a Chinese Laiwu pig population, which shows a large variability in fat deposition. In total, 35 SNPs were found to be significant at Bonferroni-corrected 5 % chromosome-wise level (P = 2.13 × 10^?5) and 88 SNPs had suggestive (P < 10^?4) association with the conformation traits. Some SNPs showed age-dependent association. Intriguingly, out of 32 regions associated with BMI in pigs, 18 were homologous with the loci for BMI in humans. Furthermore, five closest genes to GWAS peaks including HIF1AN, SMYD3, COX10, SLMAP, and GBE1 have been already associated with BMI in humans, which makes them very promising candidates for these QTLs. The result of GO analysis provided strong support to the fact that mitochondria and synapse play important roles in obesity susceptibility, which is consistent with previous findings on human obesity, and it also implicated new gene sets related to chromatin modification and Ig-like C2-type 5 domain. Therefore, these results not only provide new insights into the genetic architecture of BMI in pigs but also highlight that humans and pigs share the significant overlap of obesity-related genes.     

Genome-wide association study on chicken carcass traits using sequence data imputed from SNP array

Chicken carcass traits are economically important for the chicken industry. Detecting which genes affect chicken carcass traits is of great benefit to the genetic improvement of this important agricultural species. To investigate the genetic mechanism of carcass traits in chickens, we carried out a genome-wide association study (GWAS). A total of 435 Chinese indigenous chickens were phenotyped for carcass weight (CW), eviscerated weight with giblets (EWG), and eviscerated weight (EW) after slaughter at 91 days and were genotyped using a 600-K single nucleotide polymorphism (SNP) genotyping array. Twenty-four birds were selected for sequencing, and the 600 K SNP panel data were imputed to sequence data with the 24 birds as the reference. Univariate GWASs were performed with GEMMA software using the whole genome sequence data imputed from SNP chip data. Finally, 3, 25, and 63 suggestively significant SNPs were identified to be associated with carcass weight (CW), eviscerated weight with giblets (EWG), and eviscerated weight (EW), respectively. Six candidate genes, RNF219, SCEL, MYCBP2, ETS1, APLP2, and PRDM10 were detected. SCEL and MYCBP2 were potentially associated with these three traits, RNF219 and APLP2 were potentially associated with EWG and EW, and ETS1 and PRDM10 were only potentially associated with EWG and EW, respectively. Compared with forefathers’ research, 10 reported QTLs associated with CW were located within a 5-Mb distance near the SNPs with P value lower than 1×10^?5. This study enriched the knowledge of the genetic mechanisms of chicken carcass traits.     

HCV monoinfection and HIV/HCV coinfection enhance T-cell immune senescence in injecting drug users early during infection

Background

Injecting drug users (IDU) are at premature risk of developing multimorbidity and mortality from causes commonly observed in the elderly. Ageing of the immune system (immune-senescence) can lead to premature morbidity and mortality and can be accelerated by chronic viral infections. Here we investigated the impact of HCV monoinfection and HIV/HCV coinfection on immune parameters in (ex-) IDU. We analyzed telomere length and expression of activation, differentiation and exhaustion markers on T cells at baseline (t?=?1) and at follow-up (t?=?2) (median interval 16.9 years) in IDU who were: HCV mono-infected (n?=?21); HIV/HCV coinfected (n?=?23) or multiple exposed but uninfected (MEU) (n?=?8).

Results

The median time interval between t?=?1 and t?=?2 was 16.9 years. Telomere length within CD4⁺ and CD8⁺ T cells decreased significantly over time in all IDU groups (p?≤?0.012). CD4⁺ T-cell telomere length in HCV mono-infected IDU was significantly reduced compared to healthy donors at t?=?1 (p?<?0.008). HIV/HCV coinfected IDU had reduced CD4⁺ and CD8⁺ T-cell telomere lengths (p?≤?0.002) to healthy donors i at t?=?1. This was related to persistent levels of immune activation but not due to increased differentiation of T cells over time. Telomere length decrease was observed within all T-cell subsets, but mainly found in immature T cells (CD27⁺CD57⁺) (p?≤?0.015).

Conclusions

HCV mono-infection and HIV/HCV coinfection enhance T-cell immune-senescence. Our data suggest that this occurred early during infection, which warrants early treatment for both HCV and HIV to reduce immune senescence in later life.

     

Genome-wide association studies of net form of net blotch resistance at seedling and adult plant stages in spring barley collection

Net form of net blotch (NFNB) of barley (Hordeum vulgare L.), caused by Pyrenophora teres f. teres (Ptt) Drechsler (anamorph: Drechslera teres [Sacc.] Shoem.), is considered one of the major constraints of successful barley production in major barley growing regions of the world. Resistance to NFNB was evaluated in a barley collection of 336 genotypes (AM-2014), at seedling stage using isolates LGDPtt.19 and TD10 in the USA, and adult stage in seven hotspot environments in Morocco. The AM-2014 panel was genotyped with 9K SNP markers and genome-wide association studies (GWAS) were carried out using mixed linear model (MLM: Q?+?K) accounting for population structure (Q) and kinship (K) as covariates. Significant (P?<?0.001) marker trait associations were corrected for false discovery rate (FDR) at the q?<?0.05. Four genotypes showed an average infection response (IRs ≤ 2) to both isolates, LGDPttt.19 and TD10, at the seedling stage, and 30 genotypes showed resistance in all environments in the field while three genotypes exhibited the highest resistance at both stages. The GWAS of NFNB identified 31 distinct QTLs on all seven barley chromosomes, of which 8 with resistance at seedling stage, 21 were associated with resistance at the adult stage, and two QTLs, QRptt.2H-132.15 and QPtt.6H-54-55, conferred resistance at both stages. Of 31 resistance QTLs reported in this study, 10 QTLs coincided with previously mapped QTL while 21 are novel, thereby validating the GWAS approach used in this study. The resistance sources identified in AM-2014 and QTL mapped in this study are valuable resources for marker-assisted breeding for NFNB resistance in the future.     

Unlocking new alleles for leaf rust resistance in the Vavilov wheat collection

Key message

Thirteen potentially new leaf rust resistance loci were identified in a Vavilov wheat diversity panel. We demonstrated the potential of allele stacking to strengthen resistance against this important pathogen.

Abstract

Leaf rust (LR) caused by Puccinia triticina is an important disease of wheat (Triticum aestivum L.), and the deployment of genetically resistant cultivars is the most viable strategy to minimise yield losses. In this study, we evaluated a diversity panel of 295 bread wheat accessions from the N. I. Vavilov Institute of Plant Genetic Resources (St Petersburg, Russia) for LR resistance and performed genome-wide association studies (GWAS) using 10,748 polymorphic DArT-seq markers. The diversity panel was evaluated at seedling and adult plant growth stages using three P. triticina pathotypes prevalent in Australia. GWAS was applied to 11 phenotypic data sets which identified a total of 52 significant marker–trait associations representing 31 quantitative trait loci (QTL). Among them, 29 QTL were associated with adult plant resistance (APR). Of the 31 QTL, 13 were considered potentially new loci, whereas 4 co-located with previously catalogued Lr genes and 14 aligned to regions reported in other GWAS and genomic prediction studies. One seedling LR resistance QTL located on chromosome 3A showed pronounced levels of linkage disequilibrium among markers (r ² = 0.7), suggested a high allelic fixation. Subsequent haplotype analysis for this region found seven haplotype variants, of which two were strongly associated with LR resistance at seedling stage. Similarly, analysis of an APR QTL on chromosome 7B revealed 22 variants, of which 4 were associated with resistance at the adult plant stage. Furthermore, most of the tested lines in the diversity panel carried 10 or more combined resistance-associated marker alleles, highlighting the potential of allele stacking for long-lasting resistance.

     

Genome-wide association and validation of key loci for yield-related traits in wheat founder parent Xiaoyan 6

Xiaoyan 6, one of the most important founder parents in wheat, possesses many superior agronomic traits and has played a crucial role in Chinese wheat breeding programs. In this study, a panel of 66 elite wheat accessions derived from Xiaoyan 6 was planted in four growing seasons; genome-wide association study (GWAS) was performed for six yield-related traits using the wheat 90K genotyping assay. A total of 803 significant marker-trait associations (MTAs) that explained up to 35.0% of the phenotypic variation were detected. Of these, the locus QTkw-5B which contains 19 MTAs for thousand kernel weight (TKW) was consistently detected in three growing seasons and confirmed in a recombinant inbred line (RIL) population by developing simple sequence repeats (SSR) and kompetitive allele-specific PCR (KASP) markers. The locus QPh-3A containing eight repetitive MTAs for plant height (PH) was consistently identified in all the four growing seasons and validated in a RIL population by developing SSR markers. The transmission of Xiaoyan 6 allele indicated that the favorite allele of QPh-3A was strongly selected in breeding programs. Comparing with previous studies, QTkw-5B and QPh-3A should be novel QTL. The locus QFss-2D for fertile spikelet number per spike (FSS) was identified and then validated in three bi-parental populations. This locus controlled various spike-related traits and may be a key spike polymorphic locus. This study could provide insight into dissecting yield-related traits in the breeding population and reliable molecular markers that might be valuable for marker-assisted selection in wheat high-yield breeding programs.     

Identification of novel CSF biomarkers for neurodegeneration and their validation by a high-throughput multiplexed targeted proteomic assay

Background

Currently there are no effective treatments for many neurodegenerative diseases. Reliable biomarkers for identifying and stratifying these diseases will be important in the development of future novel therapies. Lewy Body Dementia (LBD) is considered an under diagnosed form of dementia for which markers are needed to discriminate LBD from other forms of dementia such as Alzheimer’s Disease (AD). This work describes a Label-Free proteomic profiling analysis of cerebral spinal fluid (CSF) from non-neurodegenerative controls and patients with LBD. Using this technology we identified several potential novel markers for LBD. These were then combined with other biomarkers from previously published studies, to create a 10 min multiplexed targeted and translational MRM-LC-MS/MS assay. This test was used to validate our new assay in a larger cohort of samples including controls and the other neurodegenerative conditions of Alzheimer’s and Parkinson’s disease (PD).

Results

Thirty eight proteins showed significantly (p?<?0.05) altered expression in LBD CSF by proteomic profiling. The targeted MRM-LC-MS/MS assay revealed 4 proteins that were specific for the identification of AD from LBD: ectonucleotide pyrophosphatase/phosphodiesterase 2 (p?<?0.0001), lysosome-associated membrane protein 1 (p?<?0.0001), pro-orexin (p?<?0.0017) and transthyretin (p?<?0.0001). Nineteen proteins were elevated significantly in both AD and LBD versus the control group of which 4 proteins are novel (malate dehydrogenase 1, serum amyloid A4, GM_2?activator protein, and prosaposin). Protein-DJ1 was only elevated significantly in the PD group and not in either LBD or AD samples. Correlations with Alzheimer-associated amyloid β-42 levels, determined by ELISA, were observed for transthyretin, GM2 activator protein and IGF2 in the AD disease group (r²?≥?0.39, p?≤?0.012). Cystatin C, ubiquitin and osteopontin showed a strong significant linear relationship (r²?≥?0.4, p?≤?0.03) with phosphorylated–tau levels in all groups, whilst malate dehydrogenase and apolipoprotein E demonstrated a linear relationship with phosphorylated-tau and total-tau levels in only AD and LBD disease groups.

Conclusions

Using proteomics we have identified several potential and novel markers of neurodegeneration and subsequently validated them using a rapid, multiplexed mass spectral test. This targeted proteomic platform can measure common markers of neurodegeneration that correlate with existing diagnostic makers as well as some that have potential to show changes between AD from LBD.

     

Iron homeostasis in tropical <Emphasis Type="Italic">indica</Emphasis> rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) cultivars having contrasting grain iron concentration

Iron homeostasis was studied in two tropical indica rice cultivars viz. Sharbati (high Fe) and Lalat (low Fe) having contrasting grain Fe concentration. Plants were hydroponically grown with 5 concentrations of Fe (0.05, 2, 5, 15, 50 mg L^?1) till maturity. The effect of incremental Fe treatment on the plant was followed by analyzing accumulation of ferritin protein, activities of aconitase enzyme, enzymes of anti-oxidative defense and accumulation of hydrogen peroxide and ascorbic acid. Plant growth was adversely affected beyond 15 mg L^?1 of Fe supplementation and effects of Fe stress (both deficiency and excess) were more apparent on the high Fe containing cultivar Sharbati than the low Fe containing Lalat. Level of ferritin protein and aconitase activity increased up to 5 mg L^?1 of Fe concentration. Lalat continued to synthesize ferritin protein at much higher Fe level than Sharbati and the cultivar also had higher activities of peroxidase, superoxide dismutase and glutathione reductase. It was concluded that the tolerance of Lalat to Fe stress was because of its higher intrinsic ability to scavenge free radicals of oxidative stress for possessing higher activity of antioxidative enzymes. This, together with its capacity to sequester the excess Fe in ferritin protein over a wider range of Fe concentrations made it more tolerant to Fe stress.     

Impact of plant growth-promoting bacteria on grain yield,protein content,and urea-<Superscript>15</Superscript> N recovery by maize in a Cerrado Oxisol

Background and aims

The inoculation of cereal crops with plant growth-promoting bacteria (PGPB) is a potential strategy to improve fertilizer-N acquisition by crops in soils with low capacity to supply N. A study was conducted to assess the impact of three inoculants on grain yield, protein content, and urea-¹⁵ N recovery in maize (Zea mays L.) under Cerrado soil and climate conditions.

Methods

The main treatments included inoculants containing (i) Azospirillum brasilense strain Sp245, (ii) A. brasilense strains AbV5 + AbV6, (iii) Herbaspirillum seropedicae strain ZAE94, and (iv) a non-inoculated control. The subtreatments were (i) urea-N fertilization (100 kg N ha^?1) at 30 days after sowing and (ii) no N addition at the stage. To determine fertilizer-N recovery, ¹⁵N–labelled urea was applied in microplots.

Results

Inoculants carrying A. brasilense improved urea-¹⁵ N acquisition efficiency in maize and also improved grain yield compared to the non-inoculated control, while urea-N fertilization enhanced grain quality by providing higher protein content.

Conclusion

Our results suggest that the inoculation of maize grains with PGPB represents a strategy to improve fertilizer-N recovery and maize yield in Cerrado soil with a low capacity to supply N.

     

A genome-wide association study on growth traits in orange-spotted grouper (<Emphasis Type="Italic">Epinephelus coioides</Emphasis>) with RAD-seq genotyping

The orange-spotted grouper, Epinephelus coioides, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study (GWAS) on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restrictionsite associated DNA sequencing. In this research, 261,366 single nucleotide polymorphisms (SNPs) were developed, in which 110 SNPs were identified to be correlated with growth and 20 SNPs were further confirmed to be associated with both body weight and total length. From these identified SNPs, we annotated a total of 34 genes, including adgrb2, csnkza1, cers5, col22a1, creb5, dnd1, dzank1, dnai1, npy2r, fat3, lrrk2, lrp5, map3k9, and so on. Among these candidate genes, npy2r (neuropeptide Y receptor Y2) was reported to play a critical role in growth of the orange-spotted grouper. In addition, population structure, principal component analysis, kinship matrix and linkage disequilibrium were examined to verify the accuracy and reliability of our GWAS results. Our data will also provide a valuable genetic resource for further marker-assisted selection program to improve growth quality in groupers.     

Multivariate eQTL mapping uncovers functional variation on the X-chromosome associated with complex disease traits

Very few studies have investigated the associations between genetic polymorphisms and gene expression on the X-chromosome. This is a major bottleneck when conducting functional follow-up studies of trait-associated variants, as those identified in genome-wide association studies (GWAS). We used a multivariate approach to test the association between individual single nucleotide polymorphisms (SNPs) and exon expression levels measured in 356 Epstein–Barr virus-transformed lymphoblastoid cell lines (LCLs) from the Geuvadis RNA sequencing project to identify SNPs associated with variation in gene expression on the X-chromosome, which we refer to as eSNPs. At an FDR of 5 %, we discovered 548 independent [linkage disequilibrium (LD) r ² < 0.1] eSNPs on the X-chromosome. Of these, 35 were in LD (r ² > 0.8) with previously published disease- or trait-associated variants identified through GWAS. One of the strongest eSNPs identified was rs35975601, which was associated with F8A1 expression (p value = 3 × 10^?20) and was in LD with a type 1 diabetes risk variant. Additionally, we identified a number of genes for which eSNPs were in LD with multiple diseases or traits, including DNASE1L1 which was mapped to bilirubin levels, type 1 diabetes and schizophrenia. Our results also indicate that multivariate exon-level analysis provides a more powerful approach than univariate gene-level analysis, particularly when SNPs influence the expression of different exons with different magnitude and/or direction of effect. The associations identified in our study may provide new insights into the molecular process by which gene expression may contribute to trait variation or disease risk in humans.