Unique characteristics of the genetics epidemiology of amyotrophic lateral sclerosis in China

Continual discoveries of new genes and unraveling the genetic etiology in amyotrophic lateral sclerosis(ALS) have provided greater insight into the underlying pathogenesis in motor neuron degeneration, as well as facilitating the disease modeling and the testing of targeted therapeutics. While, the genetic etiology accounted for two-thirds of FALS and approximately 11% of SALS in Caucasians. However, the contributions of these causative genes to ALS vary among different populations. Furthermore, the prominent difference between Chinese population and other ethnics remains a source of ongoing debate. We systemically reviewed genetics literature of Chinese ALS populations and updated the mutation frequencies of the main ALS-implicated genes aiming to determine the genetic features of ALS in Chinese population. We also reviewed the associations between ALSimplicated single nucleotide polymorphisms(SNPs) and the risk of ALS in Chinese population. A total of 116 studies were included in this analysis(86 gene mutation study articles and 30 SNPs study articles). The results showed that the overall gene mutation rates of ALS-related causative genes were 55.0% in familial ALS(FALS) and 11.7% in sporadic ALS(SALS) in Chinese population. In Chinese FALS, the highest mutation frequency was found in SOD1 gene(25.6%), followed by FUS(5.8%), TARDBP(5.8%), DCTN1(3.6%) and C9 orf 72(3.5%). In Chinese SALS, the highest mutation frequency was also identified in SOD1 gene(1.6%), followed by ANXA11(1.4%), FUS(1.3%), SQSTM1(1.0%), OPTN(0.9%) and CCNF(0.8%).The associations between several SNPs and risk of ALS were also reported in Chinese population. The genetic features of ALS in Chinese population are significantly different from those in Caucasian population, indicating an association between genetic susceptibility and origin of population. Further explorations are required to understand the gene complexity of ALS, including the contribution of most minor genes and the molecular mechanisms in ALS pathologies.     

Genetic basis of maize stalk strength decoded via linkage and association mapping

Stalk lodging is a severe problem that limits maize production worldwide, although little attention has been given to its genetic basis. Here we measured rind penetrometer resistance (RPR), an effective index for stalk lodging, in a multi-parent population of 1948 recombinant inbred lines (RILs) and an association population of 508 inbred lines (AMP508). Linkage and association mapping identified 53 and 29 single quantitative trait loci (QTLs) and 50 and 19 pairs of epistatic interactions for RPR in the multi-parent population and AMP508 population, respectively. Phenotypic variation explained by all identified epistatic QTLs (up to ~5%) was much less than that explained by all single additive QTLs (up to ~33% in the multi-parent population and ~ 60% in the AMP508 population). Among all detected QTLs, only eight single QTLs explained >10% of phenotypic variation in single RIL populations. Alleles that increased RPR were enriched in tropical/subtropical (TST) groups from the AMP508 population. Based on genome-wide association studies in both populations, we identified 137 candidate genes affecting RPR, which were assigned to multiple biological processes, such as the biosynthesis of cell wall components. Sixty-six candidate genes were cross-validated by multiple methods or populations. Most importantly, 23 candidate genes were upregulated or downregulated in high-RPR lines relative to low-RPR lines, supporting the associations between candidate genes and RPR. These findings reveal the complex nature of the genetic basis underlying RPR and provide loci or candidate genes for developing elite varieties that are resistant to stalk lodging via molecular breeding.     

Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce

Conifers are characterized by a large genome size and a rapid decay of linkage disequilibrium, most often within gene limits. Genome scans based on noncoding markers are less likely to detect molecular adaptation linked to genes in these species. In this study, we assessed the effectiveness of a genome-wide single nucleotide polymorphism (SNP) scan focused on expressed genes in detecting local adaptation in a conifer species. Samples were collected from six natural populations of white spruce ( Picea glauca ) moderately differentiated for several quantitative characters. A total of 534 SNPs representing 345 expressed genes were analysed. Genes potentially under natural selection were identified by estimating the differentiation in SNP frequencies among populations ( F _ST) and identifying outliers, and by estimating local differentiation using a Bayesian approach. Both average expected heterozygosity and population differentiation estimates ( H _E = 0.270 and F _ST = 0.006) were comparable to those obtained with other genetic markers. Of all genes, 5.5% were identified as outliers with F _ST at the 95% confidence level, while 14% were identified as candidates for local adaptation with the Bayesian method. There was some overlap between the two gene sets. More than half of the candidate genes for local adaptation were specific to the warmest population, about 20% to the most arid population, and 15% to the coldest and most humid higher altitude population. These adaptive trends were consistent with the genes' putative functions and the divergence in quantitative traits noted among the populations. The results suggest that an approach separating the locus and population effects is useful to identify genes potentially under selection. These candidates are worth exploring in more details at the physiological and ecological levels.     

Copy number of DAZ genes in Slovenian and Bosnian general population

Deletions of two of four DAZ (Deleted in AZoospermia) gene copies located on the Y chromosome were associated with spermatogenic failure, but the information on DAZ copy number is still very scarce. The aim of this study was to determine the frequency of partial DAZ gene deletions and to analyze the existence of duplications in general Slovenian and Bosnian population. To answer these questions, we used real time PCR. We analyzed 100 male samples from Slovenian and Bosnian general population. The incidence of two DAZ gene copies was 6% (3/50) in Slovenian population. The incidence of more than four DAZ genes was 2% (1/50) in Slovenian population and 8% (4/50) in Bosnian population. Observed differences have not reached statistical significance. In conclusion we demonstrate that DAZ genes are not only prone to deletions but also to duplication events. Further studies are needed to estimate the prevalence of these mutations and its' relevance to male infertility.     

Etiologic impact of known cancer susceptibility genes

The impact of a gene variant on the population burden of cancer can be measured by the population attributable fraction (PAF), which depends on the risk conferred by the variant, genotype relative risk (GRR), the frequency of the variant in the population and the mode of inheritance. PAF defines the proportion of the disease in the study population due to a gene variant, hence the synonymic term, etiologic fraction. After a review of the literature, 27 confirmed cancer susceptibility genes, groups of genes and loci were selected for analysis on the basis of their prevalence and availability of validated GRR data. The covered variants represent the most common established cancer susceptibility genes; those not included have marginal PAFs on common cancers. The PAF due to known genes at the covered sites was highest for brain hemangioblastoma (19%), conferred by the VHL gene. For colorectal cancer, the PAF estimates amounted to 7.0%. Including genes and identified loci from whole genome scans, PAFs for both breast and prostate cancers summed up to 70%. The derived estimates should rectify common overstatements on the contribution of individual high penetrance genes on common cancers at the population level. More dramatically, the estimates show the large PAFs conferred by the recently discovered breast, prostate and colorectal cancer loci, most of which are not known to alter coding sequences or expression patterns and they thus act through yet unexplained mechanisms. Although of low risk, these common variants appear to explain large proportions of breast and prostate cancers in the population.     

SNP detection and genetic mapping of porcine genes encoding enzymes in hepatic metabolic pathways and evaluation of linkage with carcass traits

We have previously identified and mapped porcine expressed sequence tags (ESTs) derived from genes that are preferentially expressed in liver. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) in porcine genes encoding enzymes in hepatic metabolic pathways and use the SNPs for mapping. Furthermore, these genes, which are involved in utilization and partitioning of nutrients, were examined for their effects on carcass and meat quality traits by linkage analyses. In total, 100 ESTs were screened for SNPs by single strand conformation polymorphism analyses across a diverse panel of animals with a 36% success rate. Twelve of 36 polymorphic loci segregated in a three-generation Duroc x Berlin Miniature Pig (F2) resource population, the DUMI resource population, and were genetically mapped. Interval mapping of the corresponding chromosomes was performed to verify mapping of the genes within quantitative trait loci (QTL) regions detected in this resource population. QTL with genome-wide significance were detected in the vicinity of GNMT, ESTL147 and HGD. These loci therefore are positional candidate genes.     

Spatial divergence in the proportions of genes encoding toxic peptide synthesis among populations of the cyanobacterium Planktothrix in European lakes

It has been frequently reported that seasonal changes in toxin production by cyanobacteria are due to changes in the proportion of toxic/nontoxic genotypes in parallel to increases or decreases in population density during the seasonal cycle of bloom formation. In order to find out whether there is a relationship between the proportion of genes encoding toxic peptide synthesis and population density of Planktothrix spp. we compared the proportion of three gene regions that are indicative of the synthesis of the toxic heptapeptide microcystin (mcyB), and the bioactive peptides aeruginoside (aerB) and anabaenopeptin (apnC) in samples from 23 lakes of five European countries (n=153). The mcyB, aerB, and apnC genes occurred in 99%, 99%, and 97% of the samples, respectively, and on average comprised 60 ± 3%, 22 ± 2%, and 54 ± 4% of the total population, respectively. Although the populations differed widely in abundance (10(-3)-10(3) mm(3) L(-1)) no dependence of the proportion of the mcyB, aerB, and apnC genes on the density of the total population was found. In contrast populations differed significantly in their average mcyB, aerB, and apnC gene proportions, with no change between prebloom and bloom conditions. These results emphasize stable population-specific differences in mcyB, aerB, and apnC proportions that are independent from seasonal influences.     

Extensive Copy-Number Variation of Young Genes across Stickleback Populations

Duplicate genes emerge as copy-number variations (CNVs) at the population level, and remain copy-number polymorphic until they are fixed or lost. The successful establishment of such structural polymorphisms in the genome plays an important role in evolution by promoting genetic diversity, complexity and innovation. To characterize the early evolutionary stages of duplicate genes and their potential adaptive benefits, we combine comparative genomics with population genomics analyses to evaluate the distribution and impact of CNVs across natural populations of an eco-genomic model, the three-spined stickleback. With whole genome sequences of 66 individuals from populations inhabiting three distinct habitats, we find that CNVs generally occur at low frequencies and are often only found in one of the 11 populations surveyed. A subset of CNVs, however, displays copy-number differentiation between populations, showing elevated within-population frequencies consistent with local adaptation. By comparing teleost genomes to identify lineage-specific genes and duplications in sticklebacks, we highlight rampant gene content differences among individuals in which over 30% of young duplicate genes are CNVs. These CNV genes are evolving rapidly at the molecular level and are enriched with functional categories associated with environmental interactions, depicting the dynamic early copy-number polymorphic stage of genes during population differentiation.     

Comparative Analysis of Flanking Sequence Tags of T-DNA/Transposon Insertional Mutants and Genetic Variations of Fast-neutron Treated Mutants in Rice

Whole genome sequencing analyses of 1,504 fast-neutron (FN)-induced mutants of ‘Kitaake’ rice variety have revealed a new mutant population covering 58.6% of transposable element (TE) genes and 47.6% of non-TE genes throughout the rice genome. Mutation rate for TE gene is much higher in FN-induced mutants (58.6%) than in flanking sequence tag (FST) population (25.7%), implying that the former are more randomly generated than the latter. By adding this resource to FST population, we found that the mutation rate for the rice genome increases from 53.1% to 78.1% and more importantly, the rate with multiple alleles increases from 35.2% to 56.1%. To test the functional significance of mutants produced by both FN-induction and T-DNA/transposon insertions, we analyzed the coverage of functionally characterized genes by using the Overview of functionally characterized Genes in Rice Online database (OGRO, http://qtaro.abr.affrc.go.jp/ogro/table). These combined genetic resources cover the mutations for 90.9% of functionally characterized genes for morphological traits, 91.0% for physiological traits, and 92.6% for resistance or tolerance traits, indicating that a gene-indexed mutant population that includes FN-induced mutants is valuable to future research for improving most of the important agronomic traits.     

Killer cell immunoglobulin-like receptor gene diversity in the Saudi population

Killer cell immunoglobulin-like receptors (KIRs) influence the outcome of haematopoetic stem cell transplantation by modulating the cytotoxic ability of natural killer (NK) cells and a subset of T cells. KIRs are also highly polymorphic and could therefore be good population genetic markers, much like their human leukocyte antigen (HLA) ligands. This study represents the first report on distribution of 16 KIR genes in 162 unrelated healthy Saudi individuals. All the 16 KIR genes were observed in the studied population and the four framework genes (KIR2DL4, 3DL2, 3DL3 and 3DP1) were present in all individuals. Forty- one distinct KIR profiles were expressed in our population, 11 of which had not been previously described in other populations including the Middle Eastern population. AA1, the most common genotypic profile was observed at a frequency of 26.5%. The group A haplotype was more frequent (53%) in the Saudi population compared to the group B haplotype (47%). The pattern of the inhibitory KIR/HLA ligands were also analyzed and 52.3% of the Saudi population was found to express two pairs of the inhibitory KIR/HLA-C. The KIR gene frequencies suggests that the Saudi population shares common general features with the Middle Eastern and other populations, but still has its own unique frequencies of several KIR loci.     

HLA polymorphism and evaluation of European, African, and Amerindian contribution to the white and mulatto populations from Paraná, Brazil

Polymorphism of classical HLA-A, HLA-B, HLA-C, HLA-DR, and HLA-DQ genes differs greatly among populations, both in frequencies and in the presence of alleles and haplotypes particular to population groups, making these genes powerful tools for the study of origins of populations and their degree of admixture. Antigen, allele, and haplotype frequencies, together with linkage disequilibrium patterns, are reported for 2 populations in the southern Brazilian state of Paraná, one of predominantly European ancestry (white), the other of predominantly African and European ancestry (mulatto). Genetic distance estimates between the 2 groups and other populations studied previously, and of degree of admixture, were performed. In accordance with phenotypic classification, the white population is of predominantly European origin (80.6%), with a smaller contribution of African (12.5%) and Amerindian (7.0%) genes. The mulatto population consists of African (49.5%) and European (41.8%) ancestry, with a smaller but significant contribution of Amerindian (8.7%) ancestry. On the basis of history and population genetics, there is controversy regarding the Amerindian contribution to Paraná's gene pool. These results provide a better picture of Paraná's ethnic constitution and on the Amerindian contribution to the white and mulatto populations.     

MHC class I A region diversity and polymorphism in macaque species

The HLA-A locus represents a single copy gene that displays abundant allelic polymorphism in the human population, whereas, in contrast, a nonhuman primate species such as the rhesus macaque (Macaca mulatta) possesses multiple HLA-A-like (Mamu-A) genes, which parade varying degrees of polymorphism. The number and combination of transcribed Mamu-A genes present per chromosome display diversity in a population of Indian animals. At present, it is not clearly understood whether these different A region configurations are evolutionarily stable entities. To shed light on this issue, rhesus macaques from a Chinese population and a panel of cynomolgus monkeys (Macaca fascicularis) were screened for various A region-linked variations. Comparisons demonstrated that most A region configurations are old entities predating macaque speciation, whereas most allelic variation (>95%) is of more recent origin. The latter situation contrasts the observations of the major histocompatibility complex class II genes in rhesus and cynomolgus macaques, which share a high number of identical alleles (>30%) as defined by exon 2 sequencing.     

Genotypic diversity of the Killer Cell Immunoglobulin-like Receptors (KIR) and their HLA class I Ligands in a Saudi population

Killer Cell Immunoglobulin-like Receptors (KIR) have been used as good markers for the study of genetic predisposition in many diseases and in human genetic population dynamics. In this context, we have investigated the genetic diversity of KIR genes and their main HLA class I ligands in Saudi population and compared the data with other studies of neighboring populations. One hundred and fourteen randomly selected healthy Saudi subjects were genotyped for the presence or absence of 16 KIR genes and their HLA-C1, -C2, -Bw4^Thr80 and Bw4^Ile80 groups, using a PCR-SSP technique. The results show the occurrence of the framework genes (3DL2, 3DL3 and 2DL4) and the pseudogenes (2DP1 and 3DP1) at highest frequencies. All inhibitory KIR (iKIR) genes appeared at higher frequencies than activating genes (aKIR), except for 2DS4 with a frequency of 90.35%. A total of 55 different genotypes were observed appearing at different frequencies, where 12 are considered novel. Two haplotypes were characterized, AA and Bx (BB and AB), which were observed in 24.5% and 75.5% respectively of the studied group. The frequencies of iKIR + HLA associations were found to be much higher than aKIR + HLA. KIR genes frequencies in the Saudi population are comparable with other Middle Eastern and North African populations.     

Genetic characteristics of recessive sensorineural hearing loss

Genetic characteristics of recessive sensorineural hearing impairment mediated by 5 recessive genes were studied. One of these is responsible for early progressive hearing loss, others causing congenital deafness. The incidence of early progressive recessive hearing loss in a population is 1:20,000, gene frequency being 0.007; the incidence of heterozygotes for this gene is 1.4%. The incidence of each of 4 forms of recessive congenital hearing loss in a population is 1.125:10,000, the frequency of these genes being 0.0106; the incidence of heterozygotes for each of these genes is 2.1%. The total frequency of all recessive genes for sensorineural hearing impairment is 0.0494 and the incidence of heterozygotes for all genes is 9.9%. The frequency of different genotypes for recessive genes specifying sensorineural hearing loss was established, based on the data obtained.     

A DNA marker for the duplicated cytosolic PGI genes in sheep's fescue (Festuca ovina L.)

Active duplicate PgiC genes in sheep's fescue, Festuca ovina, are associated with a PCR marker of specific length (about 370 bp, of which 231 are in an intron). Using this marker, the frequency of plants with duplicate genes is estimated to be about 10% in a population from southern Sweden. The close molecular similarity between the electrophoretically different duplicated genes is in accordance with the conclusion reached earlier that they are indeed alleles at the same locus.     

Genetic variability in Scotch pine in the southeastern part of its range

The main parameters of genetic variability have been determined in an isolated natural Scotch pine population from Chita oblast' (Tsasuchei Forest) by analysis of 19 genes coding for nine enzymes: GDH, IDH, LAP, PGM, AAT, ADH, MDH, 6-PGD, and DIA. Polymorphic genes constituted 63.2% of all structural genes studied in the population at the 99% polymorphism criterion. The mean number of alleles per locus was 1.63. The observed and expected heterozygosities were 0.237 and 0.251, respectively. These estimates are close to the corresponding mean values for Scotch pine according to the data on 18 or more structural genes.     

Strikingly high levels of heterozygosity despite 20 years of inbreeding in a clonal honey bee

Inbreeding (the mating between closely related individuals) often has detrimental effects that are associated with loss of heterozygosity at overdominant loci, and the expression of deleterious recessive alleles. However, determining which loci are detrimental when homozygous, and the extent of their phenotypic effects, remains poorly understood. Here, we utilize a unique inbred population of clonal (thelytokous) honey bees, Apis mellifera capensis, to determine which loci reduce individual fitness when homozygous. This asexual population arose from a single worker ancestor approximately 20 years ago and has persisted for at least 100 generations. Thelytokous parthenogenesis results in a 1/3 of loss of heterozygosity with each generation. Yet, this population retains heterozygosity throughout its genome due to selection against homozygotes. Deep sequencing of one bee from each of the three known sub‐lineages of the population revealed that 3,766 of 10,884 genes (34%) have retained heterozygosity across all sub‐lineages, suggesting that these genes have heterozygote advantage. The maintenance of heterozygosity in the same genes and genomic regions in all three sub‐lineages suggests that nearly every chromosome carries genes that show sufficient heterozygote advantage to be selectively detrimental when homozygous.     

Genetic Variability in Scotch Pine in the Southeastern Part of Its Range

The main parameters of genetic variability have been determined in an isolated natural Scotch pine population from Chita oblast (Tsasuchei Forest) by analysis of 19 genes coding for nine enzymes: GDH, IDH, LAP, PGM, AAT, ADH, MDH, 6-PGD, and DIA. Polymorphic genes constituted 63.2% of all structural genes studied in the population at the 99% polymorphism criterion. The mean number of alleles per locus was 1.63. The observed and expected heterozygosities were 0.237 and 0.251, respectively. These estimates are close to the corresponding mean values for Scotch pine according to the data on 18 or more structural genes.     

Theoretical aspects of extinction by inbreeding depression

Populational extinction due to inbreeding depression is analyzed with simple population genetic and population ecological models. Two alternative genetic mechanisms of inbreeding depression, i.e. recessive deleterious genes and overdominant genes, are assumed in separate analyses in order to examine their relative importance. With both mechanisms the population size and the coefficient of inbreeding are maintained at stable equilibria if there is no non-genetic demographic disturbance or stress. With a certain amount of demographic disturbance the population declines rapidly due to interaction between the decrease of population size and the increase of inbreeding coefficient. Such rapid extinction occurs with both genetic mechanisms. However, in the case of overdominant genes extinction happens only if the equilibrium population size is small and the selection coefficient is large such that segregation load is large. In nature, extinction due to overdominant genes is considered to be much less likely than extinction due to recessive deleterious genes.     

Gene Genealogy in Three Related Populations: Consistency Probability between Gene and Population Trees

A genealogical relationship among genes at a locus (gene tree) sampled from three related populations was examined with special reference to population relatedness (population tree). A phylogenetically informative event in a gene tree constructed from nucleotide differences consists of interspecific coalescences of genes in each of which two genes sampled from different populations are descended from a common ancestor. The consistency probability between gene and population trees in which they are topologically identical was formulated in terms of interspecific coalescences. It was found that the consistency probability thus derived substantially increases as the sample size of genes increases, unless the divergence time of populations is very long compared to population sizes. Hence, there are cases where large samples at a locus are very useful in inferring a population tree.