Relationship between esterase gene frequencies and length in juvenile snapper Chrysophrys auratus Forster

Samples of 0-group snapper Chrysophrys auratus were collected in the Hauraki Gulf of New Zealand in 1979,1980 and 1981. Each fish was measured and the liver examined for an esterase polymorphism. A similar change in allele frequency with length was observed in each year class. In the total data set there is a significant relationship between allele frequency and length. The relationships between allele frequencies and temperature and growth, along with implications for genetic-stock separation studies are discussed.     

Evidence of a genomic insertion in intron 2 of SOD1 causing allelic drop‐out during routine diagnostic testing for canine degenerative myelopathy

Degenerative myelopathy is a severe and progressive neurodegenerative disease and, in the majority of breeds, is associated with the c.118G>A substitution in exon 2 of the canine superoxide dismutase 1 (SOD1) gene. Our laboratories have been engaged in determining the cause of many discordant findings between the parental and the offspring genotypes found by different laboratories. In both cases, the discordant findings refer to actual heterozygous dogs that had been typed as homozygous for the variant allele. To that aim, the genomic context of the causative variant was investigated in two Hovawart dogs. An insertion of 54 nucleotides composed of a poly‐T stretch and 15 nucleotides containing the duplication of the exon 2–intron 2 junction was found. The insertion was responsible for the partial mismatch of the reverse primer used for a direct sequencing assay. The mismatch hampered the amplification of the corresponding allele and caused an evident drop‐out effect. The insertion is in complete linkage disequilibrium with the c.118G allele. The allele containing the insertion was highly prevalent in Hovawart dogs, accounting for the 26.6% of allele frequency. The insertion was also found in other unrelated breeds such as Rough Collies and Standard Poodles. In conclusion, the study illustrates the importance of correctly designing the primers to avoid inaccurate genotyping of the degenerative myelopathy causative variant in exon 2 of the SOD1 gene.     

Nucleotide composition-based prediction of gene expression efficacy

A correlation between efficacy of gene expression and nucleotide composition of its protein-coding sequences was studied. It was found that measures based exclusively on codon frequencies are analogous to codon adaptation index [1] and do not adequately reveal this correlation. A more general measure is suggested, i.e., elongation efficacy index, which takes into account both the codon frequencies and the level of local mRNA complementarity. Utilization of this measure facilitated adequate recognition of highly expressed genes in 18 unicellular organisms, i.e., 14 eubacteria, three archaebacteria, and yeast.     

Isoelectric focusing of horse serum esterase isozymes and detection of new phenotypes

A new method for separating the isozymes of horse serum esterase is described. The improved resolution has enabled us to detect several previously undescribed phenotypes. This method has also been used to detect two different apparently 'silent' alleles.     

Genetic differences among language families in Europe

We investigated whether 59 allele frequencies and 10 cranial variables differed among speakers of the 12 modern language families in Europe. Although this is a classical analysis of variance design, special techniques had to be developed for the analysis because of spatial autocorrelation of both biological and language data. The method examines pooled sums of squares within language families. These are compared with the same quantities obtained by randomly partitioning the available data points in Europe into internally cohesive subsets representing the same sample sizes for each language family as in the originally observed data. Our results suggest that for numerous genetic systems, population samples differ more among language families than they do within families. These findings are considered in relation to two contrasting models: a model of random spatial differentiation of gene frequencies unrelated to language and a model of aboriginal genetic differences among speakers of different language groups. Our observed findings suggest partial validity of both models.     

Breed demarcation and potential for breed allocation of horses assessed by microsatellite markers

Population demarcation of eight horse breeds was investigated using genotype information of 306 horses from 26 microsatellite loci. The breeds include the indigenous Norwegian breeds Fjord Horse, Nordland/Lyngen Horse, Døle Horse and Coldblooded Trotter together with Icelandic Horse, Shetland Pony, Standardbred and Thoroughbred. Both phylogenetic analysis and a maximum likelihood method were applied to examine the potential for breed allocation of individual animals. The phylogenetic analysis utilizing simple allele sharing statistics revealed clear demarcation among the breeds; 95% of the individuals clustered together with animals of the same breed in the phylogenetic tree. Even breeds with a short history of divergence like Døle Horse and Coldblooded Trotter formed distinct clusters. Implementing the maximum likelihood method allocated 96% of the individuals to their source population, applying an assignment stringency of a log of the odds ratio larger than 2. Lower allocation stringency assigned nearly all the horses. Only three individuals were wrongly allocated a breed by both methods. In conclusion, the study demonstrates clear distinction among horse breeds, and by combining the two assignment methods breed allocation could be determined for more than 99% of the individuals.     

Frequencies of plasma protease inhibitor alleles in Australian horse breeds and the recognition of two new alleles

Investigation of the plasma protease inhibitor system (Pi) in the Arabian and quarter horse breeds and re-examination of the standardbred breed resulted in the recognition of two new Pi alleles, designated E and L2. PiE is rare and has been found in only three quarter horses. In contrast, PiL2 is relatively common in the standardbred (0.107) and allowed subdivision of PiL into PiL and PiL2. Splitting of PiL resulted in an exclusion probability (PE) of 0.649 for the standardbred Pi system. Frequencies of the Pi genes have now been determined for four breeds (thoroughbred, standardbred, quarter horse and Arabian) of horses in Australia.