Genomic organization, sequence and polymorphism of the human chromosome 4-specific a-satellite DNA

Two -satellite fragments specific for human chromosome 4 have been cloned and characterized. Under stringent annealing conditions, they hybridized in situ only to the pericentromeric region of chromosome 4, but under nonstringent conditions they hybridized to all chromosomes containing the sequences of -satellite suprachromosomal family 2 (viz., chromosomes 2, 4, 8, 9, 13, 14, 15, 18, 20, 21 and 22). Southern blot analysis reveals the 3.2-kb higher-order repeated unit which exists in two forms: as a single MspI fragment or a combination of the 2.6-kb and 0.6-kb MspI fragments. The two chromosome-4-specific cloned sequences appear to be different parts of this repeated unit. Taken together they constitute about 60% of its length. The primary structure of the higher-order repeated unit is characterized by a dimeric periodicity of the D1-D2 type which is usual to suprachromosomal family 2. At least in one site this regularity is disrupted by monomer deletion leading to the D2-D2 monomeric order. The most likely mechanism of this monomer excision is homologous unequal crossing-over. These sequences may serve as both cytogenetic and restriction-fragment length polymorphism (RFLP) markers for the pericentromeric region of chromosome 4.     

Restriction Fragment Length Polymorphism (RFLP) of Genomic DNA of Moraxella (Branhamella) catarrhalis Isolates in a Hospital

Epidemiological typing, based on restriction fragment length polymorphism (RFLP) by pulsed-field gel electrophoresis (PFGE), was attempted for the 38 clinical isolates of Moraxella catarrhalis obtained at Shinshu University Hospital during the years 1987 and 1993. Digestion with SmaI or NotI generated well separable, 12 to 5 genomic DNA fragments ranging from 1,000 kb to 30 kb and the strains could be classified into 14 or 13 types, respectively. The electrophoretic profile differed with the strain in most of them and was hence useful to distinguish the each strain. Investigation for their RFLP have, however, suggested that majority of them, including the type strain ATCC25238, may have derived from a common ancestor.     

Enhanced detection of polymorphic DNA by multiple arbitrary amplicon profiling of endonuclease-digested DNA: identification of markers tightly linked to the supernodulation locus in soybean

Multiple endonuclease digestion of template DNA or amplification products can increase significantly the detection of polymorphic DNA in fingerprints generated by multiple arbitrary amplicon profiling (MAAP). This coupling of endonuclease cleavage and amplification of arbitrary stretches of DNA, directed by short oligonucleotide primers, readily allowed distinction of closely related fungal and bacterial isolates and plant cultivars. MAAP analysis of cleaved template DNA enabled the identification of molecular markers linked to a developmental locus of soybean (Glycine max L. Merrill). Ethyl methane sulfonate (EMS)-induced supernodulating, near-isogenic lines altered in the nts locus, which controls nodule formation, could be distinguished from each other and from the parent cultivar by amplification of template pre-digested with 2–3 restriction enzymes. A total of 42 DNA polymorphisms were detected using only 19 octamer primers. In the absence of digestion, 25 primers failed to differentiate these soybean genotypes. Several polymorphic products co-segregated tightly with the nts locus in F₂ families from crosses between the allelic mutants nts382 and nts1007 and the ancestral G. soja Sieb. & Succ. PI468.397. Our results suggest that EMS is capable of inducing extensive DNA alterations, probably around discrete mutational hot-spots. EMS-induced DNA polymorphisms may constitute sequence-tagged markers diagnostic of specific genomic regions.     

ABSENCE OF POLLEN DISCOUNTING IN A GENOTYPE OF IPOMOEA PURPUREA EXHIBITING INCREASED SELFING

Throughout southeastern North America, the annual morning glory Ipomoea purpurea exhibits a polymorphism at a locus that influences the intensity of floral pigmentation. Previous studies have shown that when rare, the homozygous white genotype has a greater selfing rate than the homozygous dark genotype. In the absence of pollen discounting (a reduction in transmission of pollen to other plants by genotypes that exhibit increased selfing) and inbreeding depression, this increased selfing rate should favor the white allele. Experiments reported here confirm that the white genotype has elevated selfing rates when rare but indicate pollen discounting is not associated with elevated selfing. Rather, white genotypes contribute more pollen to the outcross pollen pool. The disparity between genotypes in both selfing rates and success at pollen contribution to other plants disappears at intermediate to high frequencies of the white allele. Pollinator movements are consistent with the pattern of selfing. These results suggest that elevated selfing and enhanced success at pollen donation contribute to maintenance of the white allele in natural populations of morning glories.     

EVOLUTION OF HOST-PARASITE DIVERSITY

Hosts and parasites often have extensive genetic diversity for resistance and virulence (host range). Qualitative diversity occurs when the success of attack is an all-or-nothing response that varies according to the genotypes of the host and parasite. Quantitative diversity occurs when the success of attack is a graded response that depends on additive genetic variation in the host and parasite. Community diversity occurs when parasites vary in the success with which they can attack different host species, leading to a mixture of specialists and generalists. I developed a series of models that classify components of host-parasite interactions according to whether they cause stabilizing or disruptive selection for resistance and virulence. Stabilizing selection reduces diversity by favoring a single optimal phenotype. Disruptive selection creates diversity by favoring a mixture of widely separated phenotypes. The evolution of maximal resistance and virulence are opposed by one of three forces: metabolic costs, frequency dependence, or negative genetic correlations among beneficial traits. The models predict that qualitatively inherited resistance and virulence traits typically cause greater diversity than quantitatively inherited traits. However, each natural system is composed of many stabilizing factors that reduce diversity and disruptive factors that promote diversity. I advocate a style of modeling in which families of related assumptions are compared by their equilibrium properties, and general conclusions from equilibrium properties are tested by complete dynamical analysis. The comparison among models highlights the need for empirical studies that compare levels of diversity among related host-parasite systems.     

Shaping intraspecific variation: Development,ecology and the evolution of morphology and life history variation in tiger salamanders

The tiger salamander,Ambystoma tigrinum, is a geographically widespread, morphologically variable, polytipic species. It is among the most variable species of salamanders in morphology and life history with two larval morphs (typical and cannibal) and three adult morphs (metamorphosed, typical branchiate, cannibal branchiate) that vary in frequency between subspecies and between populations within subspecies. We report morphometric evidence suggesting that branchiate cannibals arose through intraspecific change in the onset or timing of development resulting in the wider head and hypertrophied tooth-bearing skull bones characteristic of this phenotype. We also quantified bilateral symmetry of gill raker counts and abnormalities, then evaluated fluctuating asymmetry as a measure of the developmental stability of each morph. There was a significant interaction between fluctuating asymmetry of developmental abnormalities in cannibals and typicals and the locality where they were collected, suggesting that relative stability of each phenotype could vary among populations. While altered timing of developmental events appears to have a role in the evolution and maintenance of morphs, novel phenotypes persist only under favorable ecological conditions. Predictability of the aquatic habitat, genetic variation, kinship, body size, intraspecific competition and predation all affect expression and survival of the morphs inA. tigrinum. This taxon provides an excellent model for understanding the diversity and complexity of developmental and ecological variables controlling the evolution and maintenance of novel phenotypes.     

Opa-like repeats in the genome of the Medfly Ceratitis capitata

The sequence determination of several genomic clones isolated from the Mediterranean fruitfly Ceratitis capitata identified the existence of opa-like repeats, often more than one being clustered in small chromosomal segments. These repeats have previously been shown to consist of stretches of tandemly reiterated glutamine-encoding residues, and they are found in multiple genes of several organisms. Most of the repeats described here are flanked or interrupted by stop codons in all reading frames and, thus, could not possibly be part of protein-coding sequences. Furthermore, these repeats, of which there are several hundred in the genome of the Medfly, can be used effectively for the determination of sequence polymorphisms, providing a convenient approach to obtain additional landmarks for the construction of genomic maps of this economically important insect.This paper is dedicated to the memory of our colleague and friend Dr. Jim Flach who took part in the initial phase of this work and died during the course of the investigation.     

Quantitative trait loci influencing protein and starch concentration in the Illinois Long Term Selection maize strains

A study was initiated to determine the number, chromosomal location, and magnitude of effect of QTL (quantitative trait loci or locus depending on context) controlling protein and starch concentration in the maize (Zea mays L.) kernel. Restriction fragment length polymorphism (RFLP) analysis was performed on 100 F₃ families derived from a cross of two strains, Illinois High Protein (IHP), X Illinois Low Protein (ILP), which had been divergently selected for protein concentration for 76 generations as part of the Illinois Long Term Selection Experiment. These families were analyzed for kernel protein and starch in replicated field trials during 1990 and 1991. A series of 90 genomic and cDNA clones distributed throughout the maize genome were chosen for their ability to detect RFLP between IHP and ILP. These clones were hybridized with DNA extracted from the 100 F₃ families, revealing 100 polymorphic loci. Single factor analysis of variance revealed significant QTL associations of many loci with both protein and starch concentration (P < 0.05 level). Twenty-two loci distributed on 10 chromosome arms were significantly associated with protein concentration, 19 loci on 9 chromosome arms were significantly associated with starch concentration. Sixteen of these loci were significant for both protein and starch concentration. Clusters of 3 or more significant loci were detected on chromosome arms 3L, 5S, and 7L for protein concentration, suggesting the presence of QTL with large effects at these locations. A QTL with large additive effects on protein and starch concentration was detected on chromosome arm 3L. RFLP alleles at this QTL were found to be linked with RFLP alleles at the Shrunken-2 (Sh2) locus, a structural gene encoding the major subunit of the starch synthetic enzyme ADP-glucose pyrophosphorylase. A multiple linear regression model consisting of 6 significant RFLP loci on different chromosomes explained over 64 % of the total variation for kernel protein concentration. Similar results were detected for starch concentration. Thus, several chromosomal regions with large effects may be responsible for a significant portion of the changes in kernel protein and starch concentration in the Illinois Long Term Selection Experiment.     

Storage-protein variation in wild emmer (Triticum turgidum ssp.dicoccoides) from Jordan and Turkey.

Genetic diversity in the seed storage-proteins encoded at theGlu-A1,Glu-B1 andGli-B1/Glu-B3 loci was studied electrophoretically in 315 individuals belonging to nine populations ofT. dicoccoides from Jordan and three from Turkey. The inter- and intra-population distribution of seed storage-protein alleles at the considered loci and its link with geographical factors were investigated. Population differentiation in seed storage-proteins was in some cases very high with very weak correlations with geographic distance. Greater gene differentiation was found within and between populations which were geographically very close in Jordan than between those from Jordan and Turkey. However the distribution of alleles appeared to be non random. Samples collected from populations at locations over 900 m above sea level were less polymorphic than those collected at lower altitudes (500–700 m), whereas the relative genetic differentiation between populations was greater between those collected at higher altitudes. Seed storage-protein differentiation was significantly correlated with the altitude of the collecting sites. Although it is difficult to point out the selective pressure of altitude per se, altitude can reflect an integration of several environmental parameters. The possible adaptive value of seed storage-proteins is discussed.     

Restriction fragment length polymorphism and molecular taxonomy in Vitis vinifera L.

Forty-six accessions of grapevine (V. vinifera L.) were compared by restriction fragment length polmorphism (RFLP) analysis, and 111 informative or unique restriction fragments were found that revealed an important level of polymorphism. RFLP patterns were compared in two ways: by calculating electrophoretic similarity degree values further analyzed by principal component analysis and by studying the distribution of rare restriction fragments. Six taxonomic groups could be defined, which partially confirmed relationships derived from ampelographical data. Our data support the existence of ecogeographical groups.