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PubMed2003

Genetic variations of AA genome Oryza species measured by MITE-AFLP.

MITEs (miniature inverted-repeat transposable elements) are the major transposable elements in Oryza species. We have applied the MITE-AFLP technique to study the genetic variation and species relationship in the AA-genome Oryza species. High polymorphism was detected within and between species. The genetic variation in the cultivated species, Oryza sativa and Oryza glaberrima, was comparatively lower than in their ancestral wild species. In comparison between geographical lineages of the AA genome species, African taxa, O. glaberrima and Oryza barthii, showed lower variation than the Asian taxa, O. sativa, Oryza rufipogon, and Oryza nivara, and Australian taxon Oryza meridionalis. However, another African taxon, Oryza longistaminata, showed high genetic variation. Species relationships were analyzed by the pattern of presence or absence of homologous fragments, because nucleotide sequences of the detected MITE-AFLP fragments revealed that the same fragments in different species shared very high sequence homology. The clustering pattern of the AA-genome species matched well with the geographical origins (Asian, African and Australian), and with the Australian taxon being distant to the others. Therefore, this study demonstrated that the MITE-AFLP technique is amenable for studying the genetic variation and species relationship in rice.

Cluster Analysis↗
PubMed1996

Genetic variation in arthropod vectors of disease-causing organisms: obstacles and opportunities.

An overview of the genetic variation in arthropods that transmit pathogens to vertebrates is presented, emphasizing the genetics of vector-pathogen relationships and the biochemical genetics of vectors. Vector-pathogen interactions are reviewed briefly as a prelude to a discussion of the genetics of susceptibility and refractoriness in vectors. Susceptibility to pathogens is controlled by maternally inherited factors, sex-linked dominant alleles, and dominant and recessive autosomal genes. There is widespread interpopulation (including intercolony) and temporal variation in susceptibility to pathogens. The amount of biochemical genetic variation in vectors is similar to that found in other invertebrates. However, the amount varies widely among species, among populations within species, and temporally within populations. Biochemical genetic studies show that there is considerable genetic structuring of many vectors at the local, regional, and global levels. It is argued that genetic variation in vectors is critical in understanding vector-pathogen interactions and that genetic variation in vectors creates both obstacles to and opportunities for application of genetic techniques to the control of vectors.

Animals↗
PubMed1994

Genetic variation in parasitic nematodes and its implications.

An absolute pre-requisite for a genetic response to a selective pressure is genetic variation within the population under selection. Helminth populations are clearly able to respond to selective pressures and must, therefore, be genetically heterogeneous. While not quite tautological, this is at best indirect evidence for the existence of genetic variation but there are few examples of well documented helminth phenotypic variation with a proven genetic basis. Isozyme analysis has provided more direct evidence for variation but attempts to link this variation to responses to selection or to identify the forces maintaining that variation have been largely unsuccessful. Thus there is a clear need for new techniques. The recent application of PCR and direct sequencing technology to the study of helminth genetics has allowed the genotypes of individual worms to be determined and the first direct measurements of allele frequencies to be made in this group of organisms. In addition, the application of genetic and molecular data from Caenorhabditis elegans is a potentially rich source of new markers. These techniques do not require that the genetic basis of the phenotype in question be known since a large number of loci can be examined and selection detected through changes in the frequency of anonymous linked marker loci. Phenotypes with complex genetic bases can, therefore, be analysed. I have applied these techniques to the study of anthelmintic resistance genetics and others have applied them to the genetics of inhibited development in Ostertagia. Other phenotypes that are of great interest are the potential for selection of resistance to vaccination and the use of genetically resistant hosts. The ease with which helminths have countered all classes of anthelminitics and the apparently high levels of polymorphism in helminth populations suggest that immunological control methods may also prove to be vulnerable to the adaptive capabilities of the parasite. Evidence from a mouse-helminth model system has already provided evidence that worms can meet the challenge.

Animals↗
PubMed1991

Genetic variation in the Heterodoxus octoseriatus group (Phthiraptera): a test of Price's model of parasite evolution.

Most of the genetic variation in the H. octoseriatus group is present as fixed gene differences between species which have been described on morphological criteria. Based on allozymes, the taxonomic status of some species was challenged. There was insufficient evidence, however, to demonstrate that these were not 'good' biological species. Overall, the limited intraspecific variation was present as fixed gene differences among lice from different hosts and from different colonies of hosts; heterozygotes were rare. Two predictions derived from Price's model of parasite evolution were met: populations of lice were genetically homogeneous and, where genetic markers were present, we found substantial genetic variation among populations. These data contrast with those for endoparasitic helminths, where, in general, the amount of genetic variation is similar to that of free-living invertebrates.

Animals↗
PubMed2002

Resistance and tolerance in a host plant-holoparasitic plant interaction: genetic variation and costs.

Host organisms are believed to evolve defense mechanisms (i.e., resistance and/or tolerance) under selective pressures exerted by natural enemies. A prerequisite for the evolution of resistance and tolerance is the existence of genetic variation in these traits for natural selection to act. However, selection for resistance and/or tolerance may be constrained by negative genetic correlations with other traits that affect host fitness. We studied genetic variation in resistance and tolerance against parasitic infection and the potential fitness costs associated with these traits using a novel study system, namely the interaction between a flowering plant and a parasitic plant. In this system, parasitic infection has significant negative effects on host growth and reproduction and may thus act as a selective agent. We conducted a greenhouse experiment in which we grew host plants, Urtica dioica, that originated from a single natural population and represented 20 maternal families either uninfected or infected with the holoparasitic dodder, Cuscuta europaea. that originated from the same site. We calculated correlations among resistance, tolerance, and host performance to test for costs of resistance and tolerance. We measured resistance as parasite performance (quantitative resistance) and tolerance as the slopes of regressions relating the vegetative and reproductive biomass of host plants to damage level (measured as parasite biomass). We observed significant differences among host families in parasite resistance and in parasite tolerance in terms of reproductive biomass, a result that suggests genetic variation in these traits. Furthermore, we found differences in resistance and tolerance between female and male host plants. In addition, the correlations indicate costs of resistance in terms of host growth and reproduction and costs of tolerance in terms of host reproduction. Our results thus indicate that host tolerance and resistance can evolve as a response to infection by a parasitic plant and that costs of resistance and tolerance may be one factor maintaining genetic variation in these traits.

Analysis of Variance↗
PubMed2000

A yeast prion provides a mechanism for genetic variation and phenotypic diversity.

A major enigma in evolutionary biology is that new forms or functions often require the concerted effects of several independent genetic changes. It is unclear how such changes might accumulate when they are likely to be deleterious individually and be lost by selective pressure. The Saccharomyces cerevisiae prion [PSI+] is an epigenetic modifier of the fidelity of translation termination, but its impact on yeast biology has been unclear. Here we show that [PSI+] provides the means to uncover hidden genetic variation and produce new heritable phenotypes. Moreover, in each of the seven genetic backgrounds tested, the constellation of phenotypes produced was unique. We propose that the epigenetic and metastable nature of [PSI+] inheritance allows yeast cells to exploit pre-existing genetic variation to thrive in fluctuating environments. Further, the capacity of [PSI+] to convert previously neutral genetic variation to a non-neutral state may facilitate the evolution of new traits.

Anti-Bacterial Agents↗
PubMed2006

Genetic variation in the nucleotide excision repair pathway and bladder cancer risk.

Nucleotide excision repair (NER) is critical for protecting against damage from carcinogens in tobacco smoke. We evaluated the influence of common genetic variation in the NER pathway on bladder cancer risk by analyzing 22 single nucleotide polymorphisms (SNP) in seven NER genes (XPC, RAD23B, ERCC1, ERCC2, ERCC4, ERCC5, and ERCC6). Our study population included 1,150 patients with transitional cell carcinoma of the urinary bladder and 1,149 control subjects from Spain. Odds ratios (OR) and 95% confidence intervals (95% CI) were adjusted for age, gender, region, and smoking status. Subjects with the variant genotypes for SNPs in four of the seven genes evaluated had small increases in bladder cancer risk compared to subjects with the homozygous wild-type genotypes: RAD23B IVS5-15A>G (OR, 1.3; 95% CI, 1.1-1.5; P = 0.01), ERCC2 R156R (OR, 1.3; 95% CI, 1.1-1.6; P = 0.006), ERCC1 IVS5+33A>C (OR, 1.2; 95% CI, 1.0-1.5; P = 0.06; P(trend) = 0.04), and ERCC5 M254V (OR, 1.4; 95% CI, 1.0-2.0; P = 0.04). A global test for pathway effects indicated that genetic variation in NER characterized by the 22 SNPs analyzed in this study significantly predicts bladder cancer risk (P = 0.04). Pairwise comparisons suggested that carrying variants in two genes could result in substantial increases in risk. Classification tree analyses suggested the presence of subgroups of individuals defined by smoking and NER genotypes that could have substantial increases in risk. In conclusion, these findings provide support for the influence of genetic variation in NER on bladder cancer risk. A detailed characterization of genetic variation in key NER genes is warranted and might ultimately help identify multiple susceptibility variants that could be responsible for substantial joint increases in risk.

Adult↗
PubMed2006

Genetic variation at the mitochondrial DNA 9-bp repeat locus in the Sakha of Siberia.

Genetic variation at the mitochondrial DNA 9-bp repeat locus was assayed in 779 Sakha from Siberia. Fourteen deletion (1.8%), nine triplication (1.2%), and two 4-repeat alleles (0.26%) were identified. Several of these alleles were also detected as heteroplasmies. Among the four heteroplasmic individuals identified (0.51%), three different combinations of repeat alleles were present: 1/2, 2/3, and 2/3/4 copies. Hypervariable region I (HVRI) sequencing revealed that three different sets of haplogroups were associated with the three most frequent 9-bp polymorphisms: (1) haplo-groups B, T, and W for deletions; (2) haplogroups C, D, and K for triplications; and (3) haplogroups C, D, and T for heteroplasmies. Both of the two 4-repeat alleles were associated with haplogroup D. We detected more types of 9-bp polymorphisms and more genetic variation within classes of polymorphism than previously reported for any single population. We also present the largest and most geographically diverse sampling of the Sakha population to date. No neighboring populations have been reported to carry a non-haplogroup B deletion, triplication, or heteroplasmy, suggesting that shared ancestry or admixture or both are unlikely explanations for the presence of these polymorphisms in the Sakha. The identification of high levels of variation may be a function of the large sample size and the in-depth analysis of all derived polymorphisms. Further study of the Sakha is warranted to determine whether the level of variation is unexpectedly high, especially in light of the presence of different heteroplasmies, which suggests multiple recent events.

DNA, Mitochondrial↗
PubMed1999

An evaluation of the use of pooled samples in studies of genetic variation.

When using molecular markers to study genetic variation, either the sampled individuals can be analysed individually or the individuals can be pooled and only the pools analysed (pooled samples). A theoretical investigation was carried out into the use of pooled samples in the detection of alleles and providing maximum likelihood estimates of allele frequency. The results show that, in many cases, pooled samples are more efficient than samples of individuals. Of the different pool sizes studied, small pools containing two or three individuals showed the smallest expected squared error of allele frequency estimates.

Alleles↗
PubMed2006

Genetic variation in Opisthorchis viverrini (Trematoda: Opisthorchiidae) from northeast Thailand and Laos PDR based on random amplified polymorphic DNA analyses.

Genetic variation in Opisthorchis viverrini adults originating from different locations in northeast Thailand and Laos, People's Democratic Republic (PDR), was examined using random amplified polymorphic DNA (RAPD) analyses. In an initial analysis, the genomic DNA of one fluke from each of ten localities was amplified using 15 random primers (10-mers); however, genetic variation among O. viverrini specimens was detected reliably for only four primers. A more detailed RAPD analysis using these four primers was conducted on ten individuals from nine localities. Considerable genetic variation was detected among O. viverrini from different geographical areas and among some individuals from the same collecting locality. Comparison of the RAPD profiles revealed that O. viverrini adults from Laos PDR were genetically distinct from those from northeast Thailand. The taxonomic significance of this finding needs to be explored in more detail. The RAPD markers established in the present study provide opportunities to examine the biology and epidemiology of O. viverrini and fish-borne trematodes within the region. Additionally, application of these markers in such studies could have important implications in relation to the prevalence of cholangiocarcinoma in different regions of Asia.

Animals↗
PubMed1995

Genetic variation in plasma androgens and ovarian aromatase activity during mouse pregnancy.

Genetic variation in fetal survival, maternal plasma androgen levels, and ovarian aromatase activity was examined mid (Day 9) and late gestation (Day 16) in strains of mice that differ in reproductive performance (A/J, C57BL/6J, C8/JIs, C17/JIs, and S15/JIs). At both gestational stages, females selected for large litter size (S15/JIs) carried more fetuses than any of the other strains examined. Particularly at midpregnancy, S15/JIs females also maintained higher plasma levels of androstenedione and testosterone relative to both control strains, C8/JIs and C17/JIs. Consistent with previously reported changes in peripheral estrogen levels during mouse pregnancy, aromatase activity was higher on Day 16 than on Day 9. This study demonstrates genetic variation in fetal survival that is correlated with increased maternal androgen levels. A stage-specific gestational increase in aromatase activity occurs in several strains of mice and is associated with elevated plasma estrogen during the second half of pregnancy.

Androgens↗
PubMed1982

Two-dimensional gel electrophoresis of human brain proteins. III. Genetic and non-genetic variations in 145 brains.

To determine the frequency of genetic mutations, polymorphisms, and non-genetic variation in the major human brain proteins, I examined, by equilibrium two-dimensional gel electrophoresis, 145 brains from patients dying of a wide variety of psychiatric, neurological, and non-neurological disorders. Of 176 polypeptides screened, there was one polymorphism of glial fibrillary acidic protein (GFAP-Duarte). Chi square analysis indicated it was non-randomly distributed among different diseases. A possible mutation associated with Joseph's disease is being further investigated. Three examples of a possible mutation of protein 8c:1 were noted. No other genetic mutations were observed. This low frequency of polymorphisms is consistent with results for two-dimensional gel analysis of other tissue and species. The numerous non-genetic variations are described.

Brain Chemistry↗
PubMed2003

Genetic variation in Corynespora cassiicola: a possible relationship between host origin and virulence.

Genetic variation of 42 isolates of Corynespora cassiicola, a destructive fungal pathogen of many economically important crop plants including rubber, was investigated using RAPD-PCR analysis. Five genetic groups were identified using RAPD-PCR profiles generated by eight random primers. Results indicate that there is a significant genetic variation among C. cassiicola isolates collected from different host plants. These results should facilitate the development of rubber clones with enhanced resistance against all genetic groups of C. cassiicola.

Ascomycota↗
PubMed2001

Temporal changes in allele frequency, genetic variation and inbreeding depression in small populations of the guppy, Poecilia reticulata.

We established three closed lines of N = 10 for the guppy Poecilia reticulata, to evaluate the relationships among temporal changes in allele frequency, genetic variation and inbreeding depression for a fitness-related trait in small populations. Genetic variation at the allozyme loci, expressed by the proportion of polymorphic loci, number of alleles per locus and heterozygosity, decreased somewhat in two closed lines but it increased in one closed line over six generations. Effective population size (Ne) at each generation was estimated from the standardized variance in the allele frequencies. The average Ne was 24.4, 10.3 and 10.0 in the three closed lines. The inbreeding coefficient calculated from the Ne increased to 0.186, 0.321 and 0.414, respectively. As an index of the amount of inbreeding depression, changes in salinity tolerance were examined, because this trait is strongly sensitive to inbreeding depression and decreases linearly with an increase in inbreeding coefficient. The mean value of the salinity tolerance significantly decreased to 82.5%, 71.7% and 67.6% in the three closed lines during the six generations, suggesting inbreeding depression for salinity tolerance. Although a significant correlation was not observed between the amount of inbreeding depression and the genetic variation, the amount of inbreeding depression correlated with the inbreeding coefficient calculated from Ne. The regression line indicated an 8.4% decrease in the mean per 10% increase in the inbreeding coefficient and was similar to that obtained directly from full-sib matings. These results indicate that the temporal changes in the allele frequencies can provide an estimation of the amount of inbreeding depression during successive generations in small populations.

Adaptation, Physiological↗
PubMed2026

The contribution of common and rare genetic variation to emotional and behavioural symptoms in childhood and adolescence.

Genetic factors influence vulnerability to common mental health conditions, but their role in early-life mental health remains understudied. We analysed genotype array (n&#x2009;=&#x2009;4709-6687) and exome sequence data (n&#x2009;=&#x2009;4500-5424) from the Millennium Cohort Study (MCS) and Avon Longitudinal Study of Parents and Children (ALSPAC) to assess the contribution of common variants and rare deleterious coding variants to internalising and externalising symptoms across development. In longitudinal analysis spanning ages 5-17 years, we identified several associations between common genetic variation, indexed by polygenic indices (PGIs), and both symptom domains that generally remained stable across development. Effect sizes were modest, with the largest estimates observed for PGIs for attention deficit hyperactivity disorder (ADHD) and externalising behaviour with externalising symptoms (&#x3b2;&#x2009;=&#x2009;0.13-0.18; p-adj<3.5&#xd7;10&#x207b;29). Evidence for direct genetic effects was strongest for externalising symptoms, including for associations with the ADHD and externalising behaviour PGIs. Concordant results were observed in the Born in Bradford cohort. A higher exome-wide burden of deleterious rare variants was associated with increased externalising and internalising symptoms (&#x3b2;&#x2009;=&#x2009;0.04-0.06, p-adj<0.03); within-family models indicated direct genetic effects on externalising in MCS (&#x3b2;&#x2009;=&#x2009;0.07; p&#x2009;<&#x2009;0.05, p-adj>0.05) and on internalising symptoms in ALSPAC (&#x3b2;&#x2009;=&#x2009;0.12, p-adj<0.02). Common and rare genetic variants contributed independently, jointly explaining 2% of the variance in internalising and 5-7% in externalising symptoms. This study shows that early-life mental health is influenced by both common and rare genetic variation, with several associations explained by direct genetic effects.

Journal Article↗
PubMed2025

High-resolution, genotype-free mapping of genetic variation with CRI-SPA-Map.

Genetic variation within species shapes phenotypes, but identifying the specific genes and variants that cause phenotypic differences is costly and challenging. Here, we introduce CRI-SPA-Map, a genetic mapping strategy combining CRISPR-Cas9 genome engineering, selective ploidy ablation (SPA), and high-throughput phenotyping for precise genetic mapping with or without genotyping in the yeast Saccharomyces cerevisiae. In CRI-SPA-Map, a donor strain carrying SPA machinery is mated to a genetically different recipient strain harboring a genome-integrated selectable cassette. In the resulting diploid, CRISPR-Cas9 cuts the cassette for replacement with DNA from the homologous donor chromosome. Donor chromosomes are then removed using SPA to yield haploid recombinant strains. To establish CRI-SPA-Map, we mated a W303 SPA strain to 92 strains from the BY4742 yeast knockout collection that carry gene deletion cassettes on the left arm of chromosome XIV and created 1,451 recombinant isolates. Whole-genome sequencing verified that deletion cassette replacement introduced short donor DNA tracts of variable length, resulting in a finely recombined mapping population. Using only the known location of the gene deletions, which marks where donor DNA is introduced, we identified a 6.5 kb-region shaping yeast growth. Further dissection of this region pinpointed two causal variants in two genes, MKT1 and SAL1. Engineering these variants alone and in combination revealed gene-by-environment interactions at both genes, as well as epistatic interactions between them that were in turn dependent on the environment. CRI-SPA-Map is a cost-effective strategy for creating high-resolution recombinant panels of yeast strains for identifying the genetic basis of phenotypic variation.

Journal Article↗