Linking the CHRNA5 SNP to drug abuse liability: From circuitry to cellular mechanisms.

Genetics are known to be a significant risk factor for drug abuse. In human populations, the single nucleotide polymorphism (SNP) D398N in the gene CHRNA5 has been associated with addiction to nicotine, opioids, cocaine, and alcohol. In this paper, we review findings from studies in humans, rodent models, and cell lines and provide evidence that collectively suggests that the Chrna5 SNP broadly influences the response to drugs of abuse in a manner that is not substance-specific. This finding has important implications for our understanding of the role of the cholinergic system in reward and addiction vulnerability. This article is part of the special issue on 'Vulnerabilities to Substance Abuse.'

Eukaryotic peptide chain release factor 1 participates in translation termination of specific cysteine-poor prolamines in rice endosperm.

Prolamines are alcohol-soluble proteins classified as either cysteine-poor (CysP) or cysteine-rich (CysR) based on whether they can be alcohol-extracted without or with reducing agents, respectively. In rice esp1 mutants, various CysP prolamines exhibit both reduced and normal amounts of isoelectric focusing bands, indicating that the mutation affects only certain prolamine classes. To examine the genetic regulation of CysP prolamine synthesis and accumulation, we constructed a high-resolution genetic linkage map of ESP1. The ESP1 gene was mapped to within a 20 kb region on rice chromosome 7. Sequencing analysis of annotated genes in this region revealed a single-nucleotide polymorphism within eukaryotic peptide chain release factor (eRF1), which participates in stop-codon recognition and nascent-polypeptide release from ribosomes during translation. A subsequent complementation test revealed that ESP1 encodes eRF1. We also identified UAA as the stop codon of CysP prolamines with reduced concentration in esp1 mutants. Recognition assays and microarray analysis confirmed that ESP1/eRF1 recognizes UAA/UAG, but not UGA. Our results provide convincing evidence that ESP1/eRF1 participates in the translation termination of CysP prolamines during seed development.

Why Do Sex Chromosomes Stop Recombining?

It is commonly assumed that sex chromosomes evolve recombination suppression because selection favours linkage between sex-determining and sexually antagonistic genes. However, although the role of sexual antagonism during sex chromosome evolution has attained strong support from theory, experimental and observational evidence is rare or equivocal. Here, we highlight alternative, often neglected, hypotheses for recombination suppression on sex chromosomes, which invoke meiotic drive, heterozygote advantage, and genetic drift, respectively. We contrast the hypotheses, the situations when they are likely to be of importance, and outline why it is surprisingly difficult to test them. Lastly, we discuss future research directions (including modelling, population genomics, comparative approaches, and experiments) to disentangle the different hypotheses of sex chromosome evolution.

Mapping a male-fertility restoration locus for the A4 cytoplasmic-genic male-sterility system in pearl millet using a genotyping-by-sequencing-based linkage map.

BACKGROUND: Pearl millet (Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) R. Br) is an important cereal and fodder crop in hot and arid environments. There is great potential to improve pearl millet production through hybrid breeding. Cytoplasmic male sterility (CMS) and the corresponding nuclear fertility restoration / sterility maintenance genes (Rfs) are essential tools for economic hybrid seed production in pearl millet. Mapping the Rf genes of the A4 CMS system in pearl millet would enable more efficient introgression of both dominant male-fertility restoration alleles (Rf) and their recessive male-sterility maintenance counterparts (rf). RESULTS: A high density linkage map based on single nucleotide polymorphism (SNP) markers was generated using an F2 mapping population and genotyping-by-sequencing (GBS). The parents of this cross were 'ICMA 02777' and 'ICMR 08888', which segregate for the A4 Rf locus. The linkage map consists of 460 SNP markers distributed mostly evenly and has a total length of 462 cM. The segregation ratio of male-fertile and male-sterile plants (3:1) based on pollen production (presence/absence) indicated monogenic dominant inheritance of male-fertility restoration. Correspondingly, a major quantitative trait locus (QTL) for pollen production was found on linkage group 2, with cross-validation showing a very high QTL occurrence (97%). The major QTL was confirmed using selfed seed set as phenotypic trait, though with a lower precision. However, these QTL explained only 14.5% and 9.9% of the phenotypic variance of pollen production and selfed seed set, respectively, which was below expectation. Two functional KASP markers were developed for the identified locus. CONCLUSION: This study identified a major QTL for male-fertility restoration using a GBS-based linkage map and developed KASP markers which support high-throughput screening of the haploblock. This is a first step toward marker-assisted selection of A4 male-fertility restoration and male-sterility maintenance in pearl millet.

Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in Populus tomentosa†.

Economically important traits in many species generally show polygenic, quantitative inheritance. The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined. Here, we investigated 11 full-length genes in cellulose biosynthesis, on 10 growth and wood-property traits, within a population of 460 unrelated Populus tomentosa individuals, via multi-gene association. To validate positive associations, we conducted single-marker analysis in a linkage population of 1,200 individuals. We identified 118, 121, and 43 associations (P< 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R(2)). Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume. Single-marker analysis validated 61 associations (false discovery rate, Q ≤ 0.10), representing 38 SNPs from nine genes, and its average effect (R(2) = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants. Moreover, a structural gene-gene network based on tissue-specific transcript abundances provides a better understanding of the multi-gene pathway affecting tree growth and lignocellulose biosynthesis. Our study highlights the importance of pathway-based multiple gene associations to uncover the nature of genetic variance for quantitative traits and may drive novel progress in molecular breeding.

An integrated genomic approach for rapid delineation of candidate genes regulating agro-morphological traits in chickpea.

The identification and fine mapping of robust quantitative trait loci (QTLs)/genes governing important agro-morphological traits in chickpea still lacks systematic efforts at a genome-wide scale involving wild Cicer accessions. In this context, an 834 simple sequence repeat and single-nucleotide polymorphism marker-based high-density genetic linkage map between cultivated and wild parental accessions (Cicer arietinum desi cv. ICC 4958 and Cicer reticulatum wild cv. ICC 17160) was constructed. This inter-specific genetic map comprising eight linkage groups spanned a map length of 949.4 cM with an average inter-marker distance of 1.14 cM. Eleven novel major genomic regions harbouring 15 robust QTLs (15.6-39.8% R(2) at 4.2-15.7 logarithm of odds) associated with four agro-morphological traits (100-seed weight, pod and branch number/plant and plant hairiness) were identified and mapped on chickpea chromosomes. Most of these QTLs showed positive additive gene effects with effective allelic contribution from ICC 4958, particularly for increasing seed weight (SW) and pod and branch number. One robust SW-influencing major QTL region (qSW4.2) has been narrowed down by combining QTL mapping with high-resolution QTL region-specific association analysis, differential expression profiling and gene haplotype-based association/LD mapping. This enabled to delineate a strong SW-regulating ABI3VP1 transcription factor (TF) gene at trait-specific QTL interval and consequently identified favourable natural allelic variants and superior high seed weight-specific haplotypes in the upstream regulatory region of this gene showing increased transcript expression during seed development. The genes (TFs) harbouring diverse trait-regulating QTLs, once validated and fine-mapped by our developed rapid integrated genomic approach and through gene/QTL map-based cloning, can be utilized as potential candidates for marker-assisted genetic enhancement of chickpea.

A statistical framework to guide sequencing choices in pedigrees.

The use of large pedigrees is an effective design for identifying rare functional variants affecting heritable traits. Cost-effective studies using sequence data can be achieved via pedigree-based genotype imputation in which some subjects are sequenced and missing genotypes are inferred on the remaining subjects. Because of high cost, it is important to carefully prioritize subjects for sequencing. Here, we introduce a statistical framework that enables systematic comparison among subject-selection choices for sequencing. We introduce a metric "local coverage," which allows the use of inferred inheritance vectors to measure genotype-imputation ability specifically in a region of interest, such as one with prior evidence of linkage. In the absence of linkage information, we can instead use a "genome-wide coverage" metric computed with the pedigree structure. These metrics enable the development of a method that identifies efficient selection choices for sequencing. As implemented in GIGI-Pick, this method also flexibly allows initial manual selection of subjects and optimizes selections within the constraint that only some subjects might be available for sequencing. In the present study, we used simulations to compare GIGI-Pick with PRIMUS, ExomePicks, and common ad hoc methods of selecting subjects. In genotype imputation of both common and rare alleles, GIGI-Pick substantially outperformed all other methods considered and had the added advantage of incorporating prior linkage information. We also used a real pedigree to demonstrate the utility of our approach in identifying causal mutations. Our work enables prioritization of subjects for sequencing to facilitate dissection of the genetic basis of heritable traits.

Quantitative high resolution mapping of HvMLH3 foci in barley pachytene nuclei reveals a strong distal bias and weak interference.

In barley (Hordeum vulgare L.), chiasmata (the physical sites of genetic crossovers) are skewed towards the distal ends of chromosomes, effectively consigning a large proportion of genes to recombination coldspots. This has the effect of limiting potential genetic variability, and of reducing the efficiency of map-based cloning and breeding approaches for this crop. Shifting the sites of recombination to more proximal chromosome regions by forward and reverse genetic means may be profitable in terms of realizing the genetic potential of the species, but is predicated upon a better understanding of the mechanisms governing the sites of these events, and upon the ability to recognize real changes in recombination patterns. The barley MutL Homologue (HvMLH3), a marker for class I interfering crossovers, has been isolated and a specific antibody has been raised. Immunolocalization of HvMLH3 along with the synaptonemal complex transverse filament protein ZYP1, used in conjunction with fluorescence in situ hybridization (FISH) tagging of specific barley chromosomes, has enabled access to the physical recombination landscape of the barley cultivars Morex and Bowman. Consistent distal localization of HvMLH3 foci throughout the genome, and similar patterns of HvMLH3 foci within bivalents 2H and 3H have been observed. A difference in total numbers of HvMLH3 foci between these two cultivars has been quantified, which is interpreted as representing genotypic variation in class I crossover frequency. Discrepancies between the frequencies of HvMLH3 foci and crossover frequencies derived from linkage analysis point to the existence of at least two crossover pathways in barley. It is also shown that interference of HvMLH3 foci is relatively weak compared with other plant species.

Epileptic encephalopathies of the Landau-Kleffner and continuous spike and waves during slow-wave sleep types: genomic dissection makes the link with autism.

PURPOSE: The continuous spike and waves during slow-wave sleep syndrome (CSWSS) and the Landau-Kleffner (LKS) syndrome are two rare epileptic encephalopathies sharing common clinical features including seizures and regression. Both CSWSS and LKS can be associated with the electroencephalography pattern of electrical status epilepticus during slow-wave sleep and are part of a clinical continuum that at its benign end also includes rolandic epilepsy (RE) with centrotemporal spikes. The CSWSS and LKS patients can also have behavioral manifestations that overlap the spectrum of autism disorders (ASD). An impairment of brain development and/or maturation with complex interplay between genetic predisposition and nongenetic factors has been suspected. A role for autoimmunity has been proposed but the pathophysiology of CSWSS and of LKS remains uncharacterized. METHODS: In recent years, the participation of rare genomic alterations in the susceptibility to epileptic and autistic disorders has been demonstrated. The involvement of copy number variations (CNVs) in 61 CSWSS and LKS patients was questioned using comparative genomic hybridization assays coupled with validation by quantitative polymerase chain reaction (PCR). KEY FINDINGS: Whereas the patients showed highly heterogeneous in genomic architecture, several potentially pathogenic alterations were detected. A large number of these corresponded to genomic regions or genes (ATP13A4, CDH9, CDH13, CNTNAP2, CTNNA3, DIAPH3, GRIN2A, MDGA2, SHANK3) that have been either associated with ASD for most of them, or involved in speech or language impairment, or in RE. Particularly, CNVs encoding cell adhesion proteins (cadherins, protocadherins, contactins, catenins) were detected with high frequency (≈20% of the patients) and significant enrichment (cell adhesion: p = 0.027; cell adhesion molecule binding: p = 9.27 × 10(-7)). SIGNIFICANCE: Overall our data bring the first insights into the possible molecular pathophysiology of CSWSS and LKS. The overrepresentation of cell adhesion genes and the strong overlap with the genetic, genomic and molecular ASD networks, provide an exciting and unifying view on the clinical links among CSWSS, LKS, and ASD.

Hormesis and epigenetics: is there a link?

Epigenetic regulation of gene expression is a key molecular mechanism linking environmental factors with the genome with consequences for health status throughout the life course. According to the modern view, epigenetic changes are far more likely than genetic changes to be directed, and many of these changes are manifestly adaptive. Recent experimental studies clearly indicate that environmental fluctuations can induce specific and predictable epigenetic-related molecular changes, and support the possibility of adaptive epigenetic phenomenon. The epigenetic adaptation processes implying alterations of gene expression to buffer the organism against environmental changes support adaptability to the expected life-course conditions. It appears likely that adaptive epigenetic rearrangements can occur not only during early developmental stages but also through the adulthood, and they can cause hormesis, a phenomenon in which adaptive responses to low doses of otherwise harmful conditions improve the functional ability of cells and organisms. In this review, several lines of evidence are presented that epigenetic mechanisms can be involved in hormesis-like responses.

Homozygosity mapping with SNP arrays confirms 3p21 as a recessive locus for gray platelet syndrome and narrows the interval significantly.

Gray platelet syndrome (GPS) is an inherited bleeding disorder characterized by thrombocytopenia and the absence of α-granules in platelets. Patients with GPS present with mild to moderate bleeding and many develop myelofibrosis. The genetic cause of GPS is unknown. We present 2 Native American families with a total of 5 affected persons and a single affected patient of Pakistani origin in which GPS appears to be inherited in an autosomal recessive manner. Homozygosity mapping using the Affymetrix 6.0 chips demonstrates that all 6 GPS-affected persons studied are homozygous for a 1.7-Mb region in 3p21. Linkage analysis confirmed the region with a logarithm of the odds score of 2.7. Data from our families enabled us to significantly decrease the size of the critical region for GPS from the previously reported 9.4-Mb region at 3p21.

Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors.

In vertebrates, including humans, individuals harbor gut microbial communities whose species composition and relative proportions of dominant microbial groups are tremendously varied. Although external and stochastic factors clearly contribute to the individuality of the microbiota, the fundamental principles dictating how environmental factors and host genetic factors combine to shape this complex ecosystem are largely unknown and require systematic study. Here we examined factors that affect microbiota composition in a large (n = 645) mouse advanced intercross line originating from a cross between C57BL/6J and an ICR-derived outbred line (HR). Quantitative pyrosequencing of the microbiota defined a core measurable microbiota (CMM) of 64 conserved taxonomic groups that varied quantitatively across most animals in the population. Although some of this variation can be explained by litter and cohort effects, individual host genotype had a measurable contribution. Testing of the CMM abundances for cosegregation with 530 fully informative SNP markers identified 18 host quantitative trait loci (QTL) that show significant or suggestive genome-wide linkage with relative abundances of specific microbial taxa. These QTL affect microbiota composition in three ways; some loci control individual microbial species, some control groups of related taxa, and some have putative pleiotropic effects on groups of distantly related organisms. These data provide clear evidence for the importance of host genetic control in shaping individual microbiome diversity in mammals, a key step toward understanding the factors that govern the assemblages of gut microbiota associated with complex diseases.

Mapping of autosomal dominant cerebellar ataxia without the pathogenic PPP2R2B mutation to the locus for spinocerebellar ataxia 12.

OBJECTIVES: To map the disease locus and to identify a gene mutation in a Japanese family with autosomal dominant cerebellar ataxia. DESIGN: A genome-wide linkage analysis was performed using the Affymetrix genome-wide human single-nucleotide polymorphism array containing 909 622 single-nucleotide polymorphisms. Direct nucleotide sequencing of a candidate gene was performed. SETTING: Hokkaido University Graduate School of Medicine and Tokyo University Graduate School of Medicine. Patients  Four affected and 6 healthy individuals in a family with autosomal dominant cerebellar ataxia. RESULTS: One locus on chromosome 5q had a multipoint logarithm of odds score of 2.408, the theoretical maximum. This locus was flanked by markers rs681591 and rs32582 and includes PPP2R2B (protein phosphatase 2, regulatory subunit B, beta isoform), the causative gene of autosomal dominant spinocerebellar ataxia 12 (SCA12). However, unlike SCA12, no CAG repeat expansions in the promoter region and no nucleotide substitution or insertion-deletion mutations in the exons of the PPP2R2B gene were found. CONCLUSION: Autosomal dominant cerebellar ataxia mapping to 5q31-q33.1 has no CAG repeat expansion or other mutations of the PPP2R2B gene.

DOK7 mutations presenting as a proximal myopathy in French Canadians.

DOK7 mutations cause a congenital myasthenic syndrome (OMIM 254300) characterized by a "limb-girdle" phenotype. We identified 7 French-Canadian patients with a previously undiagnosed proximal myopathy. A genome wide scan was performed. Homozygosity mapping identified a locus on chromosome 4p16.2 containing DOK7. Sequencing of DOK7 revealed homozygous 1124_1127dupTGCC mutations in all individuals. SNP genotyping of 42kb surrounding DOK7 in our cohort and in 9 patients of various European origins demonstrated a shared haplotype suggesting a common ancestral European mutation. In our cohort, fatigability was not prominent; rather patients reported prolonged periods of increased weakness. Abnormalities on repetitive nerve stimulation and single fiber EMG were not invariably present. There was considerable intra-familial phenotypic variability, and we report an asymptomatic individual. DOK7 mutations should be considered in patients with early-onset myopathy, even in the absence of symptoms suggesting a possible myasthenia.

[Microsatellites from the linkage groups E26C13 and E50C23 are located on the Gallus gallus domesticus microchromosomes 20 and 21].

Using the method of dual color fluorescence in situ hybridization and a set of chromosome-specific BAC clones, localization of microsatellites LEI0345 and LEI0336 on chicken (Gallus gallus domesticus) mitotic chromosomes was performed. Microsatellite LEI0345 (TAM 32, BAC clones r49A10 and r55M23) from the linkage group E26C13 was mapped to microchromosome 20, while microsatellite LEI0336 (TAM 32, BAC clones r19E22 and r13C08) from the linkage E50C23 was assigned to microchromosome 21. Using the PCR technique, an attempt to assign the suitable markers to chromosome-specific BAC clones was made. The PCR data confirmed the microsatellite localization performed with the help of FISH technique and showed the presence of the LEI0345 microsatellite sequence on many other chicken microchromosomes, except for microchromosomes 19 and 22. Linkage groups E26C13 and E50C23 were assigned to microchromosomes 20 and 21, respectively.

Comprehensive genetic and mutation analysis of familial dementia with Lewy bodies linked to 2q35-q36.

The second most frequent form of neurodegenerative dementia after Alzheimer's disease is dementia with Lewy bodies (DLB). Since informative DLB families are scarce, little is presently known about the molecular genetic etiology of DLB. We recently mapped the first locus for DLB on chromosome 2q35-q36 in a multiplex Belgian family, DR246, with autopsy-proven DLB pathology in a region of 9.2 Mb. Here, we describe the ascertainment of additional DR246 family members and significant finemapping of the DLB locus to 3.3 Mb based on informative meiotic recombinants. Extensive sequencing of the 42 positional candidate genes within the DLB region did not identify a simple pathogenic mutation that co-segregated with disease in family DR246. Also high resolution analysis of copy number variations in the DLB locus did not provide evidence for a complex mutation. In conclusion, we confirmed the DLB locus at 2q35-q36 as a genetic entity but candidate gene-based sequencing and copy number variation analysis did not identify the pathogenic mutation in family DR246. Other detection strategies will be needed to reveal the underlying mutation explaining the linkage of DLB to 2q35-q26. Possibly the disease mutation in this family acts through a more complex mechanism than generally envisaged for monogenic disorders. Nevertheless, identifying the first familial DLB gene is likely to contribute an entry point into the pathogenic cascades underlying DLB pathology.

Genome-wide linkage scans for major depression in individuals with alcohol dependence.

Major depression is more prevalent among individuals with alcoholism than in the general population. Twin studies have found a moderate degree of genetic correlation for alcohol dependence (AD) and major depression (MD), suggesting the existence of loci that confer susceptibility to both disorders. The aim of the present study was to conduct genome-wide linkage analyses to identify loci and to replicate prior evidence for linkage to MD, and to search for linkage regions that may confer risk to the co-occurrence of depression and alcoholism in a sample of sib-pairs affected with AD. A set of 1020 microsatellite markers (average marker spacing of 4cM) were genotyped in 1289 subjects, which consisted of 473 informative families for analysis of depressive traits and 626 sibling pairs for analysis of symptoms of MD and AD. For univariate linkage results for depression, there were six regions (1q, 2p, 4q, 12q, 13q, and 22q) with multipoint LOD scores in excess of 1.00; the highest peak was on chromosome 4q32.3 near marker D4S2952 (LOD=2.17, p=0.0008) for symptoms of MD. Bivariate linkage analysis of symptoms of MD and AD identified only one region at 22q11.21 with LOD>1, which overlapped with the region for symptoms of MD. Several of these regions replicate previously reported linkage results for major depression and emotion-related traits and events, such as neuroticism and suicide attempts. These identified genomic locations, together with results from prior studies, indicate potential regions of interests that may contain susceptibility loci to the risk of depression among individuals with alcohol dependence.

Rank transformation in Haseman-Elston regression using scores for location-scale alternatives.

The Haseman-Elston method is a simple regression approach for detecting genetic linkage to quantitative traits in sib-pair studies. Although this method and especially the new extended Haseman-Elston approach are quite robust, there might be some loss of power for non-normally distributed traits. We propose using rank transformation techniques, which either combine the information on a trend in locations and in scales or detect a trend only for a subset of the trait variables for genetically different sibs under linkage. As this rank transformation is based on linear regression, no exact grouping of identity by descent proportions has to be assumed. Simulation results indicate a gain in power compared to recently suggested nonparametric methods.

Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map.

BACKGROUND: Determining the position and order of contigs and scaffolds from a genome assembly within an organism's genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies for DNA sequencing, we developed a strategy for whole genome single nucleotide polymorphism sequencing allowing the positioning of sequence contigs onto a linkage map using the bin mapping method. RESULTS: The strategy was tested on a draft genome of the fungal pathogen Venturia inaequalis, the causal agent of apple scab, and further validated using sequence contigs derived from the diploid plant genome Fragaria vesca. Using our novel method we were able to anchor 70% and 92% of sequences assemblies for V. inaequalis and F. vesca, respectively, to genetic linkage maps. CONCLUSIONS: We demonstrated the utility of this approach by accurately determining the bin map positions of the majority of the large sequence contigs from each genome sequence and validated our method by mapping single sequence repeat markers derived from sequence contigs on a full mapping population.