Inheritance of fruit-coat colours in Trichosanthes anguina Linn.

Summary In Trichosanthes anguina Linn. (Cucurbitaceae), reciprocal crosses among three naturally occurring fruit-coat colour varieties (deep green, green and white) and two yellow fruit-coat colour mutants isolated in the M₁ generation showed that a multiple allelic series control the fruit-coat colours. In the F₂ generation the fruit-coat colours segregated in a monohybrid ratio with deep green dominant over green, yellow and white, green dominant over yellow and white, and yellow dominant over white. Two yellow fruit-coat colour mutants used in this study were isolated from X-ray- and EMS-treated populations of a white fruit-coat colour variety.     

Equine plasminogen polymorphism: allelic frequencies in 23 breeds

A modified procedure for detection of the two alleles of equine plasminogen using Western blotting methods following polyacrylamide gel isoelectric focusing is described. Gene frequencies in 23 breeds and Equus przewalskii are provided.     

Genetic differentiation of a primitive teleost,the African bonytongue Heterotis niloticus,among river basins and within a floodplain river system in Benin,West Africa

Examination of eight microsatellite DNA loci revealed high levels of genetic differentiation among populations of the African bonytongue Heterotis niloticus from three river basins that constitute important fishing areas in Benin. Low levels of population genetic differentiation were detected within the Ouemé–Sô River floodplain system. These results have important implications for conservation and management of stocks supporting important inland fisheries in West Africa.     

The evolutionary significance of genetic variation at enzyme synthesizing loci in the teleost Fundulus heteroclitus

Using the teleost Fundulus heteroclitus as an experimental model, we demonstrate how a multi-disciplinary approach to problems of intraspecies genetic variation can provide a better understanding of complex biodiversity problems than can be addressed by a more monolithic approach. We emphasize the importance of starting with simple molecular systems and making predictions that can be tested by experimentation at a higher level of biological complexity-leading from molecules to cells to organ systems to organisms and eventually laboratory and field selection experiments. Using this interdisciplinary approach, we address the classical 'selectionisti neutralist' controversy.     

Auxin influences symptom expression and phytoplasma colonisation in periwinkle infected with periwinkle leaf yellowing phytoplasma

Auxin imbalance was suggested as a key factor in phytoplasma symptom development. Furthermore, remission of the symptoms of phytoplasma‐infected shoots can be promoted by culturing them in vitro in high‐auxin‐containing media. Therefore, effect of spraying 1‐naphthaleneacetic acid (NAA) on infected periwinkle (Catharanthus roseus) with periwinkle leaf yellowing (PLY) phytoplasma was examined. 1‐Naphthaleneacetic acid stimulated symptom development in phytoplasma‐inoculated shoots. Accelerated symptom development was associated with early accumulation of phytoplasmas. Two PATHOGENESIS‐RELATED (PR) genes, CrPR1a and CrPR1b, were induced by PLY phytoplasma infection, and the induction was suppressed by NAA. Therefore, the accelerated symptom development may be due to the suppression effect of NAA on PR‐related defence. However, while NAA promoted symptom development on shoots inoculated with phytoplasma, more non‐symptomatic shoots containing no phytoplasma were observed, suggesting that NAA prevents phytoplasma colonisation in non‐symptomatic shoots. The expression of two genes encoding jasmonic acid (JA) biosynthesis key enzymes, lipoxygenase and allene oxide cyclase, was downregulated in non‐symptomatic shoots of infected plants, and remained downregulated after auxin treatment. Therefore, the auxin‐promoted resistance should be JA independent. Because auxin may promote symptom development of PLY phytoplasma‐infected periwinkles, it may not link to plant resistance to phytoplasma infection.     

Kappa-casein polymorphisms among cattle breeds and bison herds

Summary
We identified the Hind III restriction site polymorphism of K-casein in cattle reported by Pinder et al. ( Animal Genetics 22, 11, 1991) and found an additonal polymorphism ( Rsa I) in cattle and bison. The Hin dIII and Rsa I restriction sites were mapped and three haplotypes (alleles) were identified. Preliminary screening of 39 cattle and 71 bison revealed one allele restricted to cattle, one restricted to bison, and one shared by the species. No fixed allelic differences were observed among cattle breeds or among bison herds or subspecies.     

Noninvasive population genetics: a review of sample source,diet, fragment length and microsatellite motif effects on amplification success and genotyping error rates

Noninvasive population genetics has found many applications in ecology and conservation biology. However, the technical difficulties inherent to the analysis of low quantities of DNA generally tend to limit the efficiency of this approach. The nature of samples and loci used in noninvasive population genetics are important factors that may help increasing the potential success of case studies. Here we reviewed the effects of the source of DNA (hair vs. faeces), the diet of focal species, the length of mitochondrial DNA fragments, and the length and repeat motif of nuclear microsatellite loci on genotyping success (amplification success and rate of allelic dropout). Locus-specific effects appeared to have the greatest impact, amplification success decreasing with both mitochondrial and microsatellite fragments’ length, while error rates increase with amplicons’ length. Dinucleotides showed best amplification success and lower error rates compared to longer repeat units. Genotyping success did not differ between hair- versus faeces-extracted DNA, and success in faeces-based analyses was not consistently influenced by the diet of focal species. While the great remaining variability among studies implies that other unidentified parameters are acting, results show that the careful choice of genetic markers may allow optimizing the success of noninvasive approaches.     

ARES: software to compare allelic richness between uneven samples

Allelic richness is one of the most basic measures of genetic diversity. Its calculation is, however, still problematic because estimates depend on sample size. This paper describes an r library that calculates mean allelic richness with confidence bounds for a range of sample sizes. It takes a file in genepop format as input, or alternatively a binary data matrix with columns representing different individuals and rows representing different alleles. The output is tabular as well as graphical. Unlike existing tools, ares does extrapolate beyond the sample size and provides confidence bounds for these predictions.     

Linkage disequilibrium analysis of allelic heterogeneity in DNA methylation

Heterogeneity of DNA methylation status among alleles is observed in various cell types and is involved in epigenetic gene regulation and cancer biology. However, the individual methylation profile within each allele has not yet been examined at the whole-genome level. In the present study, we applied linkage disequilibrium analysis to the DNA methylation data obtained from whole-genome bisulfite sequencing studies in mouse germline and other types of cells. We found that the methylation status of 2 consecutive CpG sites showed deviation from equilibrium frequency toward concordant linkage (both methylated or both unmethylated) in germline cells. In the imprinting loci where methylation of constituent alleles is known, our analysis detected the deviation toward the concordant linkage as expected. In addition, we applied this analysis to the transitional zone between methylated and unmethylated regions and to the cells undergoing epigenetic reprogramming. In both cases, deviation to the concordant-linked alleles was conspicuous, indicating that the methylation pattern is not random but rather concordant within each allele. These results will provide the key to understanding the mechanism underlying allelic heterogeneity.