Number Of Different Loci Research Articles

Screening of 200 Core SNPs and the Construction of a Systematic SNP-DNA Standard Fingerprint Database with More Than 20,000 Maize Varieties

To strengthen the management of maize varieties and the protection of intellectual property rights to new varieties, we constructed a comprehensive single nucleotide polymorphism (SNP)-DNA standard fingerprint database of 20,075 materials covering nationally and provincially approved maize hybrid lines, hybridized combinations, and inbred lines. The database was based on 200 core SNPs selected from 60 K SNPs distributed in intragenic regions, including 106 (53.0%) located in exons. Average minor allele frequencies (MAF) of the 200 SNPs in 6755 maize hybrids, 7837 hybridized combinations, and 3478 inbred lines were 0.385, 0.350, and 0.378, respectively, with corresponding average polymorphism information content (PIC) values of 0.354, 0.335, and 0.351. Heterozygous genotype frequencies of maize hybrids, hybridized combinations, and inbred lines averaged 0.48, 0.47, and 0.012, respectively. The number of different loci in the three different maize groups ranged from one up to 164, 160, and 140, respectively. The percentage of different SNPs within 5% (the number of difference SNPs is less than 10) accounted for 0.013%, 0.011%, and 0.030% among pairwise comparisons of samples within hybrid lines, hybridized combinations and inbred lines, respectively. Genetic distances between varieties based on the 200 core SNPs were highly correlated with those obtained using 60 K SNPs, with a correlation coefficient of 0.82 and 0.87 in in inbred and hybrid lines, respectively. The maize SNP-DNA fingerprint database established in this study can play an important role in variety authentication, purity determination and the protection of variety rights, thereby providing reliable, comprehensive data support for use in the seed industry.

Molecular characterization of fluoroquinolones, macrolides, and imipenem resistance in Haemophilus influenzae: analysis of the mutations in QRDRs and assessment of the extent of the AcrAB-TolC-mediated resistance.

The aims of the present study were to characterize the mechanisms of resistance to fluoroquinolones, macrolides, and imipenem in Haemophilus influenzae, to assess the extent of the AcrAB-TolC-mediated resistance, and to define a core genome multilocus sequence typing (cgMLST) scheme for H. influenzae by using whole-genome sequencing. Four amino acid substitutions in GyrA (at Ser84 and Asp88), ParC (at Ser84), and ParE (at Asp420) were found to be closely associated to the MICs. We did not find any amino acid substitution surrounding the three highly conserved amino acid motifs in PBP3 related to imipenem resistance. All the isolates possessed the ermB gene. Carbonyl cyanide m-chlorophenylhydrazone (CCCP) decreased the MIC of imipenem by twofold for FQR-6 and fourfold for GE47 and GE88 strains. For erythromycin, the MICs were decreased by twofold. We found that the six FQR isolates were clustered in two groups. The number of different loci within FQR-1_FQR-3_FQR-5 cluster was 6, while FQR-2 and FQR-4 differed for 21 loci. FQR-1_FQR-3_FQR-5 and FQR-2_FQR-4 clusters were distant among each other and compared to 19 genomes downloaded from NCBI, to 8 strains heteroresistant to imipenem, and to 4 strains monoresistant to ciprofloxacin isolated in Denmark. We confirmed that specific amino acid substitutions in GyrA, ParC, and ParE are implicated in quinolone resistance. Additionally, the degree of resistance is related to the number of these amino acid substitutions. We provide robust evidence that drug efflux is one of the substantial mechanisms of imipenem and erythromycin resistance in H. influenzae.

A new gene controlling hybrid sterility in rice (Oryza sativa L.)

Hybrids between rice subspecies indica and japonica display strong heterosis. However, semi-sterility of inter-subspecific hybrids between indica and japonica varieties is a major obstacle for application of hybrid vigor in rice production. Semi-sterility was previously ascribed to allelic interaction at a number of different loci, whereas, wide-compatibility varieties can overcome hybrid sterility. Variety Nekken 2, which is a source of wide compatibility genes, showed sterility when crossed to the Korean variety Yeong Pung. Genetic and cytological analyses revealed that the semi-sterility was caused by partial abortion of the embryo sac. Genome-wide analysis of the backcross population, Nekken 2/Yeong Pung//Nekken 2 identified two independent loci for hybrid sterility on chromosomes 1 and 12, explaining 18.99 and 18.03% of the phenotypic variance, respectively. To confirm this result, another population of the same backcross containing 216 individuals was tested at a different site in a different year. The locus on chromosome 12 was detected again. Based on the study, the stable QTL on chromosome 12 appeared to be different from previously reported genes for this trait, and was designated as S35(t).

The miswired brain: making connections from neurodevelopment to psychopathology

Developmental neurobiologists have made great progress in elucidating the molecular mechanisms underlying nervous system development. Th ere has been less focus, however, on the consequences when these processes go wrong. As the evidence increases that mutations in neurodevelopmental genes are associated with major psychiatric disorders, defi ning these consequences assumes paramount importance in elucidating pathogenic mechanisms. The convergence of psychiatry and developmental neurobiology Mutations in many diff erent genes controlling cell migration, axon guidance and especially synaptogenesis are being found at an increasing rate in patients with schizophrenia, autism, epilepsy, mental retardation and other disorders [1]. Th ese discoveries are prompting a paradigm shift regarding models of the genetic architecture of these disorders, which can be seen to be highly heterogeneous and primarily due to rare mutations in any of a large number of diff erent loci [2]. Th ey also indicate that these distinct clinical categories share over lapping etiologies and strongly implicate neuro develop mental processes in a signifi cant proportion of cases. In this context, investigating the genetics of neurodevelopment in animals assumes greater importance. Many researchers have used genetic approaches in model organisms to dissect how neurodevelopmental processes work - to infer the normal function of a protein and to identify the cellular processes it is involved in. Th e application of these approaches in mice has revealed a wealth of information on how the brain gets wired. Th e converse question - how the brain can be miswired - has received less direct attention. With the evidence of relevance to human disease, the phenotypes that arise in mice due to mutations in neurodevelopmental genes become of interest in themselves, not just as indicators of the normal function of the gene. It is important to ask: what happens to brain circuitry when a mutation aff ecting a process such as cell migration or synaptogenesis is mutated? Th e primary defects due to impairment of that protein are just the start of the story. How does miswiring of the circuit aff ect its function? What are the secondary consequences of altered activity in developing circuits? How does the developing brain react to such changes? How does the ultimate anatomical outcome aff ect brain functions, as indexed by physiology and behavior? Answering these questions will be a major challenge for the future and will require an integration of expertise from diverse fi elds and disciplinary traditions [3].

Tracing isolates of bacterial species by multilocus variable number of tandem repeat analysis (MLVA)

All bacterial genomes contain multiple loci of repetitive DNA. Repeat unit sizes and repeat sequences may vary when multiple loci are considered for different isolates of an individual microbial species. Moreover, it has been documented on many occasions that the number of repeat units per locus is a strain-defining parameter. Consequently, there is isolate-specificity in the number of repeats per locus when different strains of a given bacterial species are compared. The experimental assessment of this variability for a number of different loci has been called 'multilocus variable number of tandem repeat analysis' (MLVA). The approach can be supported or extended by locus-specific DNA sequencing for establishing mutations in the individual repeat units, which usually enhances the resolution of the approach considerably. Essentially, MLVA with or without supportive sequencing has been developed for all of the medically relevant bacterial species and can be used effectively for tracing outbreaks or other forms of bacterial dissemination. MLVA is a modern, timely and versatile bacterial typing methodology.

Interspecific hybridization in vanilla and molecular characterization of hybrids and selfed progenies using RAPD and AFLP markers

Vanilla, Vanilla planifolia Andrews, is native to Mexico and Central America, but is now cultivated in other parts of the tropics. Continuous clonal propagation has resulted in very little variability for crop improvement programmes in vanilla. In this study, an attempt has been made to increase the spectrum of variation by interspecific hybridization with Vanilla aphylla, an Indian species which is tolerant to Fusarium. Interspecific hybrids were successfully produced and morphological characters and molecular profiles revealed the true hybridity of the progenies. Ten seedling progenies of V. planifolia, and four interspecific hybrids obtained from crosses between V. planifolia (female) and V. aphylla (male) using a number of different loci as markers were evaluated and 319 amplified fragment length polymorphisms (AFLPs) and 83 random amplified polymorphic DNAs (RAPDs) loci were marked. The profiles indicate similarity between the parents, selfed progenies and interspecific hybrids and that all the progenies tested were variable when compared to each other, which can be exploited for crop improvement in vanilla. This is the first report in vanilla, indicating that RAPD and AFLP profiles coupled with morphological characters can be utilized to assess the variability and hybrid nature of genotypes and of successful interspecific hybridization and production of hybrids between V. planifolia and V. aphylla.

Paucimorphic Alleles versus Polymorphic Alleles and Rare Mutations in Disease Causation: Theory, Observation and Detection

Definitions of polymorphism in a gene include occurrence of a rarer allele of at least 1% frequency; or occurrence of the commonest allele at less than 95% frequency. Many alleles of single nucleotide polymorphisms (SNPs) in genes occur at much higher frequency (up to 50%). Many common diseases have a substantial genetic component. The prevailing hypothesis for the molecular basis of common diseases is that it involves the combinatoric action of common polymorphic alleles of minor effect (common disease / common variant, CD / CV hypothesis). The ready development of genome-wide databases of high frequency SNPs is enabling the testing of this hypothesis. A contrasting approach has been the study of very highly selected cases and families by linkage and mutation detection techniques to identify rare mutations of large effect on a gene, often private to a single family (rare disease / rare variant, RD / RV hypothesis. These approaches have formed the mainstay of disease gene discovery, the latter having been feasible for a decade, the former just now becoming feasible. However, an intermediate possibility exists. Sequence changes at an intermediate frequency (herewith, “paucimorphisms”, arbitrarily 0.0005<q<0.05) may exist and may have a moderate effect. A number of different loci may predispose to the same disease, although only one paucimorphic allele of one particular gene will be found in any one individual. Exploring the “paucimorphisms hypothesis” will require mutation detection applied both at the level of large numbers of relatively unselected cases and at the population level. In this review we consider the foundations of this hypothesis, relevant available technologies and possible future approaches to systematically explore this hypothesis.

Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines

In order to compare their relative efficiencies as markers and to find the most suitable marker for maize diversity studies we evaluated 18 inbred tropical maize lines using a number of different loci as markers. The loci used were: 774 amplified fragment length polymorphisms (AFLPs); 262 random amplified polymorphic DNAs (RAPDs); 185 restriction fragment length polymorphisms (RFLPs); and 68 simple sequence repeats (SSR). For estimating genetic distance the AFLP and RFLP markers gave the most correlated results, with a correlation coefficient of r = 0.87. Bootstrap analysis were used to evaluate the number of loci for the markers and the coefficients of variation (CV) revealed a skewed distribution. The dominant markers (AFLP and RAPD) had small CV values indicating a skewed distribution while the codominant markers gave high CV values. The use of maximum values of genetic distance CVs within each sample size was efficient in determining the number of loci needed to obtain a maximum CV of 10%. The number of RFLP and AFLP loci used was enough to give CV values of below 5%, while the SSRs and RAPD loci gave higher CV values. Except for the RAPD markers, all the markers correlated genetic distance with single cross performance and heterosis which showed that they could be useful in predicting single cross performance and heterosis in intrapopulation crosses for broad-based populations. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationships among tropical maize inbred lines with high accuracy.

Splicing-independent processing of plant box C/D and box H/ACA small nucleolar RNAs.

Small nucleolar RNAs (snoRNAs) are involved in various aspects of ribosome biogenesis and rRNA maturation. Plants have a unique organisation of snoRNA genes where multiple, different genes are tightly clustered at a number of different loci. The maize gene clusters studied here include genes from both of the two major classes of snoRNAs (box C/D and box H/ACA) and are transcribed as a polycistronic pre-snoRNA transcript from an upstream promoter. In contrast to vertebrate and yeast intron-encoded snoRNAs, which are processed from debranched introns by exonuclease activity, the particular organisation of plant snoRNA genes suggests a different mode of expression and processing. Here we show that single and multiple plant snoRNAs can be processed from both non-intronic and intronic transcripts such that processing is splicing-independent and requires endonucleolytic activity. Processing of these different snoRNAs from the same polycistronic transcript suggests that the processing machineries needed by each class are not spatially separated in the nucleolus/nucleus.

Heterokaryon incompatibility in fungi—more than just another way to die

In filamentous fungi heterokaryon (vegetative) compatibility is regulated by a number of different loci. Vegetative incompatibility is most often detected as the inability to form a prototrophic heterokaryon under forcing conditions, or as the formation of a barrage when two incompatible strains interact. Vegetative compatibility has been used as a multilocus phenotype in analysis of fungal populations. In some highly clonal populations the vegetative-compatibility phenotype is correlated with pathogenicity. The molecular basis for vegetative compatibility is not well understood. Fourhet loci have been cloned fromNeurospora crasset orPodospora anserina, inch but no two are alike and it is clear that thehet genes themselves do not encode the gene products that are directly responsible for cell death. We suggest that a broader view of vegetative compatibility would include genes that are responsible for prefusion, fusion, and postfusion activities. Postfusion activities could include the fungal apoptotic apparatus since microscopic observations of cell death resemble those in higher plants and animals.

Markers, maps and the detection of trait loci

Naturally occurring genetic variation is the basis for differences in performance and appearance between and within different breeds and lines of livestock. In a few instances (e.g. coat colour, polling) the genes (or loci) which control the variation between animals and breeds have a large enough effect to be individually recognisable. For many traits, however, the combined effects of many different genes act together to control quantitative differences between breeds and individuals within breeds (hence such genes are often referred to as quantitative trait loci or QTLs). Thus the dramatic successes of modern breeding result from generations of selection which has produced accumulated changes at a number of different loci. The genome contains up to 100,000 different genes and identifying those which contribute to variation in traits of interest is a difficult task. One first step is to identify regions of the genome containing loci of potential interest through their linkage to genetic markers.

Markers, maps and the detection of trait loci

Naturally occurring genetic variation is the basis for differences in performance and appearance between and within different breeds and lines of livestock. In a few instances (e.g. coat colour, polling) the genes (or loci) which control the variation between animals and breeds have a large enough effect to be individually recognisable. For many traits, however, the combined effects of many different genes act together to control quantitative differences between breeds and individuals within breeds (hence such genes are often referred to as quantitative trait loci or QTLs). Thus the dramatic successes of modern breeding result from generations of selection which has produced accumulated changes at a number of different loci. The genome contains up to 100,000 different genes and identifying those which contribute to variation in traits of interest is a difficult task. One first step is to identify regions of the genome containing loci of potential interest through their linkage to genetic markers.

Isozyme procedures for the characterization of germplasm, exemplified by the collection ofLolium perenne L.

The utility of isozymes for the characterization of genetic resources is widely recognised and routinely applied to many species. For theLolium genus a number of different loci and alleles have been identified and used in the characterization of collections and for allied breeding purposes, however confusion has arisen between different sets of results due to the various technical systems applied. Coupled with this is the problem of identification of the products of specific loci and the common designation of alleles at these loci.

Genetic analysis of inbreeding depression caused by chlorophyll-deficient lethals in Mimulus guttatus

Two Oregon populations of the partially self-fertilizing Mimulus guttatus, located on Iron Mountain and Cone Peak, were surveyed for the frequency of recessive chlorophyll-deficient lethals by selfing plants collected as seed from the wild. Allelism tests were used to determine the number of different loci with lethal alleles present in the carriers isolated in the population surveys. The frequency of carriers was 0.065 for the Iron Mountain population (23/356) and 0.024 for the Cone Peak population (8/327). Allelism tests of the 31 carriers isolated from both populations revealed the existence of 26 different independently acting loci and two different duplicate locus systems with lethal alleles. These results indicate that the component of inbreeding depression caused by chlorophyll-deficient lethals is not due to single locus heterozygote advantage and is probably caused by mutation-selection balance at many loci. Estimates of the genomic and per locus mutation rates for this class of lethals are in close agreement with those obtained in studies of chlorophyll-deficient lethals in several agricultural plant species. Genetic analysis of a California population of M. guttatus, reported in the literature to exhibit an unusually high per locus mutation rate and segregation distortion for a chlorophyll-deficient lethal, revealed that chlorophyll-deficiency is inherited as a duplicate gene system. This mode of inheritance, not recognized previously, can explain the appearance of unusually high mutation rates and segregation distortion.

Genetic analysis of long-flagella mutants of Chlamydomonas reinhardtii.

The length of the flagella of Chlamydomonas reinhardtii cells is tightly regulated; both short-flagella and long-flagella mutants have been described. This report characterizes ten long-flagella mutants, including five newly isolated mutants, to determine the number of different loci conferring this phenotype, and to study interactions of mutants at different loci. The mutants, each of which was recessive in heterozygous diploids with wild type, fall into three unlinked complementation groups. One of these defines a new gene, lf3, which maps near the centromere of linkage group I. The flagellar length distributions in populations of each mutant were broad, with the longest flagella measuring four times the length of the longest flagella seen on wild-type cells. Each of the ten mutants had defective flagellar regrowth after amputation. Some of the mutants showed no regrowth within the time required for wild-type cells to regenerate flagella completely. Other mutants had subpopulations with rapid regeneration kinetics, and subpopulations with no observable regeneration. The mutants were each crossed to wild type to form temporary quadriflagellate, dikaryon cells; in each case the long flagella were rapidly shortened in the presence of the wild-type cytoplasm, demonstrating that the mutants were recessive, and that length control could be exerted on already assembled flagella.

COMPOSITION VARIATIONS IN OBSIDIAN SOURCES AND THE ARCHAEOLOGICAL IMPLICATIONS*

ABSTRACTSAn obsidian source can exhibit considerable variations in chemical composition. One such flow at Borax Lake in Lake County, California has been carefully investigated by neutron activation analysis of specimens from a number of different loci. It was found that the variable elements were completely coherent, and thus judgements concerning provenience could be just as definitive as with extremely homogeneous materials.

Transplantation. II.

Immunogenetics and Tissue Typing in ManThe antigenic polymorphism discussed in the first section of this review is maintained through the action of many genes at a number of different loci. Analysis of the mode of transmission and mechanisms of action of these genes constitutes a formidable problem.The availability of highly inbred mouse strains has permitted a formal genetic analysis of histocompatibility in that species, in which 15 independent loci have been positively identified and partially characterized.55 Of these, the H-2 locus and its associated antigenic specificities constitute the most thoroughly studied histocompatibility system in any species. The present . . .

Genetic Analysis of the First Steps of Sulphate Metabolism in Aspergillus nidulans

PHENOTYPIC analysis of interactions between different mutations in the same genome often helps elucidate the structure and function of the loci in question. If, in a series of mutations affecting a linear pathway, each non-allelic mutation has a characteristic phenotype, then the order of the steps they affect can be determined from the phenotypes of double mutants. A (“non-leaky”) mutation blocking one step in the pathway will be epistatic to all those blocking later steps. The minimum number of different double mutants sufficient to determine unequivocally the order of loci participation on a linear pathway equals the number of different loci (the total number of different double mutants equals n(n−l)/2 where n equals the number of different loci). This communication reports application of this method in Aspergillus nidulans to four loci where mutation can result in loss of ability to use sulphate but not sulphite as a sulphur source and indicates that these four loci are involved in the conversion of sulphate to a metabolite which interferes with utilization of exogenous choline O-sulphate.