Potential Genetic Markers Research Articles

The complement system in schizophrenia: where are we now and what’s next?

The complement system is a set of immune proteins involved in first-line defense against pathogens and removal of waste materials. Recent evidence has implicated the complement cascade in diseases involving the central nervous system, including schizophrenia. Here, we provide an up-to-date narrative review and critique of the literature on the relationship between schizophrenia and complement gene polymorphisms, gene expression, protein concentration, and pathway activity. A literature search identified 23 new studies since the first review on this topic in 2008. Overall complement pathway activity appears to be elevated in schizophrenia. Recent studies have identified complement component 4 (C4) and CUB and Sushi Multiple Domains 1 (CSMD1) as potential genetic markers of schizophrenia. In particular, there is some evidence of higher rates of C4B/C4S deficiency, reduced peripheral C4B concentration, and elevated brain C4A mRNA expression in schizophrenia patients compared to controls. To better elucidate the additive effects of multiple complement genotypes, we also conducted gene- and gene-set analysis through MAGMA which supported the role of Human Leukocyte Antigen class (HLA) III genes and, to a lesser extent, CSMD1 in schizophrenia; however, the HLA-schizophrenia association was likely driven by the C4 gene. Lastly, we identified several limitations of the literature on the complement system and schizophrenia, including: small sample sizes, inconsistent methodologies, limited measurements of neural concentrations of complement proteins, little exploration of the link between complement and schizophrenia phenotype, and lack of studies exploring schizophrenia treatment response. Overall, recent findings highlight complement components-in particular, C4 and CSMD1-as potential novel drug targets in schizophrenia. Given the growing availability of complement-targeted therapies, future clinical studies evaluating their efficacy in schizophrenia hold the potential to accelerate treatment advances.

Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes.

Fritillaria cirrhosa D. Don, whose bulb is used in a well-known traditional Chinese medicine to relieve cough and eliminate phlegm, is one of the most important medicinal plants of Fritillaria L. The species is widely distributed among the alpine regions in southwestern China and possesses complex morphological variations in different distributions. A series of newly related species were reported, based on obscure morphological differences. As a result, F. cirrhosa and its closely related species constitute a taxonomically complex group. However, it is difficult to accurately identify these species and reveal their phylogenetic relationships using traditional taxonomy. Molecular markers and gene fragments have been adopted but they are not able to afford sufficient phylogenetic resolution in the genus. Here, we report the complete chloroplast genome sequences of F. cirrhosa and its closely related species using next generation sequencing (NGS) technology. Eight plastid genomes ranged from 151,058 bp to 152,064 bp in length and consisted of 115 genes. Gene content, gene order, GC content, and IR/SC boundary structures were highly similar among these genomes. SSRs and five large repeat sequences were identified and the total number of them ranged from 73 to 79 and 63 to 75, respectively. Six highly divergent regions were successfully identified that could be used as potential genetic markers of Fritillaria. Phylogenetic analyses revealed that eight Fritillaria species were clustered into three clades with strong supports and F. cirrhosa was closely related to F. przewalskii and F. sinica. Overall, this study indicated that the complete chloroplast genome sequence was an efficient tool for identifying species in taxonomically complex groups and exploring their phylogenetic relationships.

Polymorphism in the Promoter Region of NFE2L2 Gene Is a Genetic Marker of Susceptibility to Cirrhosis Associated with Alcohol Abuse.

Alcoholic liver disease (ALD) is a highly prevalent spectrum of pathologies caused by alcohol overconsumption. Morbidity and mortality related to ALD are increasing worldwide, thereby demanding strategies for early diagnosis and detection of ALD predisposition. A potential candidate as a marker for ALD susceptibility is the transcription factor nuclear factor erythroid-related factor 2 (Nrf2), codified by the nuclear factor erythroid 2-related factor 2 gene (NFE2L2). Nrf2 regulates expression of proteins that protect against oxidative stress and inflammation caused by alcohol overconsumption. Here, we assessed genetic variants of NFE2L2 for association with ALD. Specimens from patients diagnosed with cirrhosis caused by ALD were genotyped for three NFE2L2 single nucleotide polymorphisms (SNP) (SNPs: rs35652124, rs4893819, and rs6721961). Hematoxylin & eosin and immunohistochemistry were performed to determine the inflammatory score and Nrf2 expression, respectively. SNPs rs4893819 and rs6721961 were not specifically associated with ALD, but analysis of SNP rs35652124 suggested that this polymorphism predisposes to ALD. Furthermore, SNP rs35652124 was associated with a lower level of Nrf2 expression. Moreover, liver samples from ALD patients with this polymorphism displayed more severe inflammatory activity. Together, these findings provide evidence that the SNP rs35652124 variation in the Nrf2-encoding gene NFE2L2 is a potential genetic marker for susceptibility to ALD.

Detection of Bovine TMEM95 p.Cys161X Mutation in 13 Chinese Indigenous Cattle Breeds.

Simple SummaryChinese indigenous cattle are economically important cattle breeds for animal husbandry development. The promotion and development of Chinese cattle breeds is essential. A previous study found that a nonsense mutation (rs378652941, c.483C > A, p.Cys161X) in bovine transmembrane protein 95 gene (TMEM95) seriously reduced reproductive performance in male Fleckvieh cattle; therefore, this locus was considered a candidate genetic marker in bovine marker-assisted selection (MAS) breeding. Until now, no study has identified this mutation in Chinese cattle breeds. Herein, we detected this c.483C > A mutation in 13 Chinese cattle breeds. Importantly, we found that this mutation did not exist at this locus in our analyzed breeds. Interestingly, we first identified a frameshift insertion/deletion (indel) mutation (NC_037346.1: g.27056998_27057000delCT) in the bovine TMEM95 gene in 11 cattle breeds. Together, the results of this study suggest that the mutation c.483C > A cannot serve as a genetic marker for molecular breeding among Chinese indigenous cattle breeds.Chinese indigenous cattle breeds have abundant genetic resources, which are valuable for the molecular breeding of cattle around the world. Thus, identifying important candidate genes and their genetic markers is very important for cattle molecular breeding. A previous study found that a nonsense mutation (rs378652941, c.483C > A, p.Cys161X) in the bovine transmembrane protein 95 gene (TMEM95) seriously reduced the reproductive performance in bulls, but few studies have detected this mutation in Chinese indigenous cattle breeds. Since the mutation c.483C > A may serve as a potential genetic marker for selecting higher fertility bulls, in the present study, using tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR), forced PCR restriction fragment length polymorphism (forced PCR-RFLP), and DNA sequencing methods, the mutation c.483C > A was detected in 765 individuals from 13 Chinese cattle breeds. However, the results showed that this mutation did not exist at this locus in our analyzed breeds. Interestingly, we identified a newly frameshift insertion/deletion (indel) mutation (NC_037346.1: g.27056998_27057000delCT) in the bovine TMEM95 gene in 11 cattle breeds, which changed the location of the termination codon and changed the 16 amino acids in the C-terminal to 21 amino acids. Combined with previous studies, our study provides evidence that in Chinese cattle breeds the mutation c.483C > A cannot be used as a genetic marker in molecular breeding.

Associations of MTRR and TSER polymorphisms related to folate metabolism with susceptibility to metabolic syndrome.

Hyperhomocysteinemia is a potential risk factor for the development of metabolic syndrome (MetS). Among genes involved in homocysteine metabolism, polymorphisms of methylenetetrahydrofolate reductase (MTHFR) gene are known to be associated with MetS incidence. However, effects of polymorphisms of other folate metabolism-related genes on MetS susceptibility are not well known yet. This study was to determine whether methionine synthase (MTR) 2756A > G, methionine synthase reductase (MTRR) 66A > G, and thymidylate synthase enhancer region (TSER) 2R/3R polymorphisms might be associated with risks of MetS development in the Korean population. Genotype analysis of the three polymorphisms was performed for a total of 483 subjects including 236 MetS patients and 247 unrelated healthy controls using polymerase chain reaction-restriction fragment length polymorphism technique. The present study revealed that MTRR and TSER polymorphisms were associated with susceptibility to MetS. Several genotypes and allele combinations from the three polymorphisms were also related to the MetS prevalence. When polymorphism data were stratified according to the risk components of MetS, MTR polymorphism was significantly associated with an increased risk of MetS in subjects with systolic blood pressure < 132.7mmHg (AOR 1.842, 95% CI 1.039-3.266, P = 0.037) and fasting blood glucose level < 106.3mg/dL (AOR 1.772, 95% CI 1.069-2.937, P = 0.027). MTRR polymorphism was significantly associated with a decreased risk of MetS in subjects with triglyceride level < 216.3mg/dL (AOR 0.616, 95% CI 0.399-0.951, P = 0.029). To the best of our knowledge, this is the first to provide reliable evidence about the association of other folate metabolism-related gene polymorphisms besides MTHFR with MetS susceptibility and its risk factors. Results of this study suggest that MTRR and TSER polymorphisms might be potential genetic markers for the risk of MetS development in Korean population.

Functional Analysis of Genes Involved in Glycerolipids Biosynthesis (GPAT1 and GPAT2) in Pigs

Simple SummaryPork consumption is the highest among all meats in Poland and in the world. Current breeding programs were designed to obtain high meat content and low levels of fat in pork carcasses. This resulted in a decrease in the quality of meat. Numerous researchers indicated that intramuscular fat content (IMF) is the determining factor for meat quality and consumer’s acceptance of meat. The genes GPAT1 and GPAT2, being the objective of this study are involved in triacylglycerol (TAG) synthesis. TAGs are the main constituents of animal fat as well as of IMF. The aim of this study was to assess the expression level of the GPAT1 and GPAT2 genes in musculus longissimus lumborum, subcutaneous fat and liver of pigs. Moreover, association analysis between the genes’ expression, production traits, quality and sensory parameters of pork was carried out. The results obtained showed significant differences in the mRNA expression of analyzed genes between tissues and breeds of pigs. Furthermore, association analysis showed significant associations between expression level of the genes and some of the production traits, sensory and quality parameters of pork. The results of this study indicated the possibility of modification of desired traits through transcriptional control of gene expression.Glycerol-3-phosphate acyltransferase (GPAT) enzymes catalyze the first step in triacylglycerol (TAG) synthesis. Genes that belong to the GPAT family are potential genetic markers for intramuscular fat content (IMF) content and thus meat quality. The objective of this study was to analyze the expression of GPAT1 and GPAT2 genes in musculus longissimus lumborum, liver and subcutaneous fat of various breeds of pigs. Furthermore, correlations between the genes’ expression abundance and utility traits, meat quality and meat texture parameters of pork were determined. The results obtained showed significant differences in the mRNA level of GPAT1 between analyzed tissues and breeds. The highest expression of GPAT1 gene was observed in liver tissue (p ≤ 0.01). Furthermore, significantly higher GPAT1 transcript level in the m. longissimus lumborum was observed for duroc in comparison to other analyzed breeds (p ≤ 0.05). Expression of the GPAT2 gene was shown only in the liver tissues, however statistically significant differences between the analyzed breeds were not observed. Correlation analysis confirmed the highest association between GPAT2 gene expression level in liver and cohesiveness and resilience traits of m. longissimus lumborum (p ≤ 0.01).

Low density lipoprotein receptor (LDLR) gene and ocular manifestation in Malay patients with familial hypercholesterolaemia

Introduction: Corneal arcus and eyelid xanthelasma are the common ocular findings but not exclusively found in familial hypercholesterolaemia (FH) patients. Low density lipoprotein receptor (LDLR) gene is the one of the most common genes investigated in FH. There is no study predicting ocular manifestations with genetic variations of the LDLR gene.Purpose: To associate common ocular manifestations of FH and LDLR gene in Malays.Material and methods: A cross-sectional study involving 50 unrelated Malay patients with FH were recruited. FH was diagnosed based on Dutch Lipid Clinic Network diagnostic criteria. The right eye was examined for eyelid xanthelasma and corneal arcus, while mean retinal nerve fibre layer thickness (RNFL) was assessed using Heidelberg retinal tomography II. Venepuncture was performed and genomic deoxyribonucleotide acid (DNA) was extracted. LDLR gene variations were screened using denaturing high-performance liquid chromatography and confirmed through DNA sequencing.Results: Corneal arcus was detected in 86.0% of patients, while eyelid xanthelasma was detected in 2.0% of patients. Mean RNFL thickness was 254.16 μm (SD: 60.67 μm). LDLR gene variations were identified in 32 patients (64.0%), including 5 mutations and 9 single nucleotide polymorphisms (SNPs). Two novel mutations were detected: c.1705+117T&gt;G and p.Asp139His. There was significant association between genotype frequency of LDLR variations c.940+36G&gt;A, p.Glu201Lys and p.Asp304Asn with FH, p.Glu201Lys with corneal arcus, and p.Cys255Ser and c.1705+117T&gt;G with mean RNFL thickness.Conclusion: LDLR gene variations were not uncommon in Malay patients with FH. Two novel variations, c.1705+117T&gt;G and p.Asp139His, were identified. LDLR gene is a potential predictor genetic marker for corneal arcus in Malay patients with FH. c.1705+117T&gt;G is associated with thinner mean RNFL thickness.

Novel Polymorphisms in RAPGEF6 Gene Associated with Egg-Laying Rate in Chinese Jing Hong Chicken using Genome-Wide SNP Scan.

The improvement of egg production is of vital importance in the chicken industry to maintain optimum output throughout the laying period. Because of the elongation of the egg-laying cycle, a drop in egg-laying rates in the late laying period has provoked great concern in the poultry industry. In this study, we calculated the egg-laying rate at weeks 61–69 (60 days) of Jing Hong chickens parent generation as the phenotype, and the genotype were detected by the chicken 600K Affymetrix Axiom High Density (HD) Single Nucleotide Polymorphisms (SNP)-array. The Genome-Wide Association Study (GWAS) result showed that the egg production trait is significantly associated with five SNPs (AX-75745366, AX-75745380, AX-75745340, AX-75745388, and AX-75745341), which are in the rap guanine nucleotide exchange factor 6 (RAPGEF6) gene on chicken chromosome 13. A total of 1676 Chinese commercial Jing Hong laying hens—including two populations, P1 population (858 hens) and P2 population (818 hens)—were genotyped using the Polymerase Chain Reaction-Restriction Fragments Length Polymorphisms (PCR-RFLP) method for the association analysis of egg-laying rates for the verification of the GWAS results. Genotypic and allelic frequencies of five SNPs were inconsistent with Hardy–Weinberg equilibrium, and the average population genetics parameters considering all the SNP values; i.e., gene homozygosity (Ho), gene heterozygosity (He), the effective number of alleles (Ne), and the polymorphism information content (PIC) were 0.75, 0.25, 1.40, and 0.20 in P1; 0.71, 0.29, 1.46, and 0.24 in P2; and 0.73, 0.27, 1.43, and 0.22 in P1 + P2 populations, respectively. The association analysis results revealed that out of the five polymorphisms, three of them (AX-75745366, AX-75745340, and AX-75745341; Patent applying No: 201810428916.5) had highly significant effects on egg-laying rates according to the GWAS results. Population-specific association analyses also showed similar significant association effects with this trait. Four haplotypes (AAGG, AAAG, AGGG, and AGAG) were inferred based on significant loci (AX-75745340 and AX-75745341) and also showed significant associations with the egg-laying rate, where haplotype AAGG had the highest egg-laying rate, with the exception of the egg-laying rate in P1 population, followed by other haplotypes. Furthermore, genotypes TT, AA, and GG showed the highest egg-laying rate compared to the corresponding genotypes at AX-75745366, AX-75745340, and AX-75745341 SNP loci in P1+P2, respectively. A similar result was found in the population-specific analysis except for the P1 population, in which TC genotype showed the highest egg-laying rate. No significant association was found in the egg-laying rate during the 60 days laying period for the SNPs (AX-75745380 and AX-75745388) in any group of population (p ≥ 0.05). Collectively, we report for the first time that 3 SNPs in the RAPGEF6 gene were significantly associated with the egg-laying rate during the later stage of egg production, which could be used as the potential candidate molecular genetic markers that would be able to facilitate in the selection and improvement of egg production traits through chicken breeding.

Mitochondrial Gene Heterogeneity and Population Genetics of Haemaphysalis longicornis (Acari: Ixodidae) in China.

Haemaphysalis longicornis is an important ectoparasite of domestic and wild animals that can transmit many pathogens including viruses, fungi, bacteria and protozoa. In this study, we examined genetic variation and population genetics in three mitochondrial (mt) genes [cox1 (cytochrome c subunit 1), rrnL (large subunit ribosomal RNA) and nad5 (NADH dehydrogenase 5)] among four H. longicornis populations from China. The sizes of the partial sequences of cox1, rrnL and nad5 were 776bp, 409bp, 510bp, respectively. Among the obtained sequences, we identified 22 haplotypes for cox1, 2 haplotypes for rrnL and 17 haplotypes for nad5. Low gene flow and significant genetic differentiation (66.2%) were detected among H. longicornis populations. There was no rapid expansion event in the demographic history of four H. longicornis populations in China. In addition, phylogenetic analyses confirmed that all the Haemaphysalis isolates were H. longicornis which were segregated into two major clades. The mt DNA genes provide a potential novel genetic marker for molecular epidemiology of H. longicornis and assist in the control of tick and tick-borne diseases in humans and animals.

Limited genetic variability of Cytauxzoon felis apical membrane antigen-1 (ama1) from domestic cats and bobcats

BackgroundCytauxzoon felis is a tick-transmitted apicomplexan that causes cytauxzoonosis in domestic cats (Felis catus). Even with intensive care, the mortality rate of acute cytauxzoonosis approaches 40% in domestic cats, while bobcats (Lynx rufus), the natural intermediate host of C. felis, remain clinically asymptomatic. However, multiple reports of domestic cats surviving acute disease without any treatment exist. One hypothesis for survival of these cats is infection with unique C. felis genotypes of lower pathogenicity. Prior studies have identified genetically distinct C. felis isolates containing polymorphisms within internal transcribed spacer regions (ITS) of the rRNA operon. However, these polymorphisms do not correlate with the clinical outcome of cytauxzoonosis, and so additional genetic markers are needed to test this hypothesis. We selected C. felis apical membrane antigen-1 (ama1) as a potential genetic marker of differential pathogenicity. AMA1 is a vaccine candidate for relatives of C. felis within Plasmodium spp.; however its historically high level of genetic polymorphism has resulted in escape from vaccine-induced immunity. While such diversity has hindered vaccine development, the expected polymorphism within the ama1 gene may be useful to evaluate population genetics.ResultsA 677 bp sequence of the C. felis ama1 gene was PCR-amplified from 84 domestic cats and 9 bobcats and demonstrated 99.9% sequence identity across all samples. A single nucleotide polymorphism (SNP) was identified in domestic cats and bobcats with evidence for co-infection with both genotypes identified in two domestic cats. The prevalence of the two genotypes varied with geographical distribution in domestic cats. Nucleotide diversity (π) and haplotype diversity (H) were calculated for C. felis ama1 and ama1 of related apicomplexans to assess genetic diversity. Based on these values (π = 0.00067 and H = 0.457), the diversity of the C. felis ama1 gene region analyzed is considerably lower than what is documented in related apicomplexans.ConclusionsIn surprising contrast to related apicomplexans, our results support that the sequence of the C. felis ama1 gene is highly conserved. While lack of genetic diversity limits utility of C. felis AMA1 as a genetic marker for clinical outcome, it supports further investigation as a vaccine candidate for cytauxzoonosis.

Novel mutations in WEE2: Expanding the spectrum of mutations responsible for human fertilization failure.

Successful fertilization is fundamental for sexual reproduction. After undergoing a series of molecular and morphological changes, the haploid sperm fuses with the haploid oocyte to create a diploid zygote. Defects in this process might lead to human fertilization failure. We have previously found homozygous mutations in WEE2 that are responsible for human fertilization failure, but the genetic basis of human fertilization failure requires further investigation. In the present study, we screened for WEE2 mutations in a new cohort of patients with fertilization failure. Through Sanger sequencing of WEE2 exons, we identified seven novel mutations and two reported mutations in WEE2 from six affected individuals. Morphologically normal PB1 oocytes can be retrieved from all patients. However, most of the oocytes cannot be fertilized successfully. These findings confirmed our previous research and expanded the mutational spectrum of WEE2, making it a potential genetic diagnostic marker for those suffering from human fertilization failure.

Decreased expression of microRNA-30b promotes the development of pulpitis by upregulating the expression of interleukin-6 receptor.

The present study aimed to examine the expression of interleukin-6 receptor (IL-6R) mRNA and protein in pulp tissues, blood and saliva from patients with pulpitis. It also investigated the association between IL-6R and microRNA (miR)-30b, as well as their effects on pulpitis. A total of 28 patients with pulpitis were recruited into the experimental group and 16 subjects with no pulpitis who also underwent tooth extraction were recruited into the control group. Pulp tissues, plasma and saliva were collected from all participants. Reverse transcription-quantitative polymerase chain reaction was used to determine the expression of IL-6R mRNA and miR-30b in all sample types. Western blot analysis was performed to examine the protein expression of IL-6R in pulp tissues, while ELISA was used to determine the contents of IL-6R protein in the plasma and saliva samples. A dual luciferase reporter assay was performed to verify the interactions between IL-6R and miR-30b. The expression of IL-6R mRNA in the pulp tissues, plasma and saliva was significantly increased in patients with pulpitis compared with the control group. Similarly, the IL-6R protein expression in the samples from patients with pulpitis were also significantly increased compared with the control group. Conversely, the expression of miR-30b was significantly reduced in the samples from patients with pulpitis compared with the control group. The dual luciferase reporter assay revealed that miR-30b may bind with the 3'-untranslated seed region of IL-6R mRNA to regulate its expression. The present study demonstrated that the upregulated expression of IL-6R in pulp tissues, plasma and saliva from patients with pulpitis was associated with the downregulation of miR-30b expression. In addition, miR-30b may affect the progression of pulpitis via IL-6R and may be a potential genetic marker for the diagnosis of pulpitis.

Polymorphisms of exon 10 in the BPI gene and its association analysis with some reproductive traits and partial immune indexes in Meishan pigs

This study was conducted to detect polymorphisms of BPI gene exon 10 by PCR-RFLP in Meishan pigs and their associations with some important cytokine levels (IL-1s, IL-4, IL-6, IL-8, IL-10, TGF-1s, IFN-γ, TNF-α) and reproductive traits (total number born (TNB), number born alive (NBA), birth litter weight (BLW), and weaning litter weight (WLW)), with the aim of identifying effective genetic markers for molecular breeding. The results revealed three genotypes, including AA, AB, and BB, with the trend of AA > BB > AB in reproductive traits. Pigs with the AA genotype were significantly higher than the AB genotype in TNB and IFN-γ (P 0.05). Comprehensive analysis indicated that the polymorphisms of exon 10 in the BPI gene have significant genetic effects on some reproductive traits and cytokines in Meishan pigs, for which the AA genotype was demonstrated to be the favorable genotype, which could be used as potential genetic markers for in-depth research and examination.

Transcriptome analysis of the endangered Notopterygium incisum: Cold-tolerance gene discovery and identification of EST-SSR and SNP markers

Notopterygium incisum C. C. Ting ex H. T. Chang (Apiaceae) is an endangered perennial herb in China. The lack of transcriptomic and genomic resources for N. incisum greatly hinders studies of its population genetics and conservation. In this study, we employed RNA-seq technology to characterize transcriptomes for the flowers, leaves, and stems of this endangered herb. A total of 56 million clean reads were assembled into 120,716 unigenes with an N50 length of 850 bp. Among these unigenes, 70,245 (58.19%) were successfully annotated and 65,965 (54.64%) were identified as coding sequences based on their similarities with sequences in public databases. We identified 21 unigenes that had significant relationships with cold tolerance in N. incisum according to gene ontology (GO) annotation analysis. In addition, 13,149 simple sequence repeats (SSRs) and 85,681 single nucleotide polymorphisms were detected as potential molecular genetic markers. Ninety-six primer pairs of SSRs were randomly selected to validate their amplification efficiency and polymorphism. Nineteen SSR loci exhibited polymorphism in three natural populations of N. incisum. These results provide valuable resources to facilitate future functional genomics and conservation genetics studies of N. incisum.

Potential biochemical, genetic and molecular markers of deterioration advancement in seeds of oilseed rape (Brassica napus L.)

Seed aging occurs relatively fast in crops and it is a process that delays germination as well as reducing its rate and even causing total loss of seed viability. Hence, it is a problem for seed banks, farmers and seed companies that deal with seed storage. The purpose of the research was to unravel genetic, biochemical and molecular events accompanying natural oilseed rape (Brassica napus L.) seed aging and thus to find potential markers of seed deterioration advancement, in order to facilitate the checking of seed quality and the ability to quickly take measures to protect them from dying. In this study, it is shown that low seed vigour is characterised by low intensity of DNA synthesis, which can quickly be measured by means of flow cytometry, changes in RNA quality, low sugar levels, increased proline content and superoxide dismutase activity, decreased ascorbate peroxidase activity, as well as abscisic acid content. Furthermore, it is demonstrated that the expression of BnRSH1 and BnRSH3, encoding for enzymes responsible for metabolism of the effectors of the stringent response (guanosine tetra- and pentaphosphate) that function in chloroplasts to regulate transcription, translation and metabolites levels, is downregulated in seeds of low vigour. Besides indicating potential markers of oilseed rape seed quality, we also propose a mechanism of seed dormancy regulation via the abscisic acid-stringent response module.

Rs2651899 variant is associated with risk for migraine without aura from North Indian population.

Recently a GWAS study had identified 38 genomic variants commonly found in humans that influence migraine risk. For further replicate these findings, we selected two SNPs; rs2651899 on chromosome 1p36.32 in PRDM16 gene and rs10166942 on chromosome 2q37.1 close to TRPM8 gene for their associations with migraine in the North Indian population as much work has not been done on these variants before from this population. In this case-control association study, 300 unrelated subjects, including 150 migraineurs (43 migraine with aura and 107 migraine without aura) and 150 healthy controls were selected to collect genomic DNA. Polymerase chain reaction and restriction-fragment-length polymorphism methods were performed for genotyping of these variants. Univariate and multivariate analyses were done to find the association of different genotypes and alleles of these SNPs with migraine and its subgroups. We found a statistically significant difference in migraineurs with control for PRDM16 rs2651899 polymorphism at genotypic (p < 0.05), allelic (p = 0.022; OR 1.462; 95% CI 1.058-2.022) and for dominant model (p = 0.011; OR 1.957; 95% CI 1.169-3.276). A similar trend was observed both on subgroup and gender analysis in migraine without aura (MO) and females respectively for rs2651899 variant. For the other SNP (rs10166942), statistically non-significant differences were reported in the allelic/genotypic frequencies between migraineurs and controls as p > 0.05. However, on subgroup analysis we found statistically significant differences at genotypic (p < 0.05) and dominant models in migraine with aura (MA) and in males with that of entire controls. But no significant association was found at allelic level in both subgroup and gender analysis for rs10166942. This research study showed that rs2651899 is a potential genetic marker for migraine susceptibility in MO and female subgroup at both genotypic and allelic level in the North Indian population and found that rs10166942 variant may be a potential marker for MA and male subgroup. Further work with large sample size is required for these SNPs to understand their functional mechanisms and to strengthen our results.

Association between Interleukin-21 and Interleukin-21 receptor gene polymorphisms with susceptibility to chronic hepatitis B virus infection and HBV spontaneous clearance in Iranian population

Hepatitis B virus (HBV) infection is a major public health concern due to the infection often leads to chronic infection, liver cirrhosis and also liver cancer. The host immune response to HBV infection and also genetic background play significant role in outcome of infection. Single nucleotide polymorphisms (SNPs) are the most important kind of variation in genetic sequences that caused by point mutations. As cytokines have major roles in viral infections, it seems that cytokine gene polymorphisms are independently associated with response to viral infections. Interleukin 21 (IL-21) plays an influential role in both innate and adaptive immune responses. Its specific receptor, IL-21R, produced and located on the surface of T, B and natural killer (NK) cells and is critical for the proliferation and differentiation of these immune effector cells. Many studies confirmed that the IL-21 involved in response to viral infections.We aimed to investigate the association of G/T IL-21 (rs2055979) and C/T IL-21R (rs3093390) gene polymorphisms with chronic hepatitis B virus infection and HBV spontaneous clearance in Iranian population. MethodsIn this study, blood samples were gathered from 320 patients with chronic HBV and 310 healthy controls and also 120 HBV spontaneous clearance individuals. Following genomic DNA extraction, genotypes of the selected SNPs determined by PCR and restriction fragment length polymorphism (RFLP) method. The results were analyzed by SPSS software using Chi-square, Logistic Regression, ANOVA and Independent Samples t-Test. ResultsAccording to our results, in IL-21R (rs3093390 C/T) gene polymorphism, allele frequency of T is statistically different in the HBV spontaneous clearance group compared to chronic HBV cases. But there is no significant difference between G/T IL-21 (rs2055979) and C/T IL-21R (rs3093390) genotypes distribution in three groups.Also we found that higher serum aspartate transaminase (AST) level in HBV spontaneous clearance group is significantly associated with TT genotype of IL-21 (rs2055979) compared to GG genotype (P value = 0.006). DiscussionOur results showed that T allele frequency in IL-21R (rs3093390 C/T) gene polymorphism could consider as a host genetic factor for HBV spontaneous clearance. Probably we can serve it as a potential prognostic genetic marker for spontaneous clearance of HBV infection.

Characterization of B-BOX gene family and their expression profiles under hormonal, abiotic and metal stresses in Poaceae plants

BackgroundB-box (BBX) proteins play important roles in plant growth regulation and development including photomorphogenesis, photoperiodic regulation of flowering, and responses to biotic and abiotic stresses.ResultsIn the present study we retrieved total 131 BBX members from five Poaceae species including 36 from maize, 30 from rice, 24 from sorghum, 22 from stiff brome, and 19 from Millet. All the BBX genes were grouped into five subfamilies on the basis of their phylogenetic relationships and structural features. The expression profiles of 12 OsBBX genes in different tissues were evaluated through qRT-PCR, and we found that most rice BBX members showed high expression level in the heading stage compared to seedling and booting stages. The expression of OsBBX1, OsBBX2, OsBBX8, OsBBX19, and OsBBX24 was strongly induced by abiotic stresses such as drought, cold and salt stresses. Furthermore, the expression of OsBBX2, OsBBX7, OsBBX17, OsBBX19, and OsBBX24 genes was up-regulated under GA, SA and MeJA hormones at different time points. Similarly, the transcripts level of OsBBX1, OsBBX7, OsBBX8, OsBBX17, and OsBBX19 genes were significantly affected by heavy metals such as Fe, Ni, Cr and Cd.ConclusionChange in the expression pattern of BBX members in response to abiotic, hormone and heavy metal stresses signifies their potential roles in plant growth and development and in response to multivariate stresses. The findings suggest that BBX genes could be used as potential genetic markers for the plants, particularly in functional analysis and determining their roles under multivariate stresses.

Association analysis of polymorphisms of G protein-coupled receptor 54 gene exons with reproductive traits in Jiaxing Black sows.

ObjectiveThe aim of this study was to detect single nucleotide polymorphisms (SNP) of G protein-coupled receptor 54 (GPR54) gene and explore association of this candidate gene with reproductive traits in Jiaxing Black sows.MethodsSix pairs of primers of the gene were designed to amplify all exons thus sequences of which were detected by means of direct sequencing and then SNP loci were scanned. The effects of SNPs on total number of piglets born (TNB), number of piglets born alive (NBA), number of still born piglets (NSB), and litter weight at birth (LWB) of Jiaxing Black sows were analyzed.ResultsThree SNP loci, including T3739C, C3878T and T6789C, were identified via comparison of sequencing and two genotypes (AB, BB) at each SNP site were observed. T3739C resulted in the change of amino acid (Leu→Pro) in corresponding protein, and C3878T resulted in synonymous mutation (Ile→Ile). Statistical results demonstrated that allele B was the preponderant allele at the three SNP loci and Genotype BB was the preponderant genotype. Meanwhile, Chi-Square test of these three SNPs indicated that all mutation sites fitted in Hardy-Weinberg equilibrium (p>0.05). For GPR54-T3739C locus, Jiaxing Black sows with genotype BB had 1.23 TNB and 1.28 NBA (p<0.01) that were more than those with genotype AB, respectively. Jiaxing Black sows that had the first two parities with genotype BB had additional 2.23 TNB, 2.27 NBA (p<0.01), and 1.94 LWB (p<0.05) compared to those with genotype AB, respectively. However, for other two loci, no significant difference was found between TNB, NBA, NSB, and LWB, and different genotypes of Jiaxing Black sows.ConclusionIn conclusion, the polymorphisms of GPR54-T3739C locus were significantly associated to TNB, NBA, and LWB and could be used as a potential genetic marker to improve reproductive function of Jiaxing black sows.

SA45 - AFFECTIVE TEMPERAMENT AND DEPRESSIVE SYMPTOMS IN OBESE INDIVIDUALS IN THE CONTEXT OF SEROTONERGIC TRANSCRIPTIONAL GENE POLYMORPHISMS

Background Patients with obesity experience many psychological burdens. Some of them result directly from the load that jets excessive weight. Nevertheless, it seems that the susceptibility of obese people to accompanying mental disorders can be ingested not only by the environment, but also genetically. The aim of this work was to determine the correlation of the genetic aspects of serotoninergic (SERT, 5-HT2A) transmission with the severity of depressive symptoms and the affective temperament profile in subjects with simple obesity. Methods The study included 506 patients with simple obesity who were excluded secondary causes of obesity and significant mental illness. Clinical, psychological and genetic analyzes were performed. To assess the severity of depressive symptoms, Beck Depression Inventory and the Hamilton Depression Scale were used. Affective temperament was assessed using the TEMPS-A questionnaire. Polymorphism of serotonin transporter (SERT 44-bp insertion/deletion) and serotonin receptor 2 A type (1438 G/A) were evaluated as potential genetic markers of psychological factors. Results The long allele of SERT gene was associated with significantly higher BMI and more pronounced depressive, cyclothymic and hyperthymic dimensions of affective temperament. Interestingly, these subjects obtained the lowest scores of both scales, which measured the severity of depressive symptoms. Adenine homozygotes in examined 5-HT2A polymorphism were characterized by higher BMI and more pronounced anxious and, in particular, hyperthymic dimension of temperament. Carriers of particular polymorphisms in this gene did not differ significantly in the clinical scale evaluating the severity of depressive symptoms. Discussion Polymorphisms of both examined genes revealed correlations in affective temperamental dimensions. Acknowledgments in the SERT polymorphism seems to play a more important role in the regulation of reactive depressive symptoms.