Biomedical subjects

V Kanazin

Publications and source records attributed to V Kanazin.

6 recordsLinked to original sources

PubMed2000

Electrophoretic detection of single-nucleotide polymorphisms.

Single-nucleotide polymorphisms (SNPs) represent the most prevalent class of genetic markers available for linkage disequilibrium or cladistic analyses. PCR primers may be labeled with fluorescent dyes and used to rapidly and accurately differentiate among alleles that are defined by a single-nucleotide differences. Here, we describe the primer-mediated detection of SNPs based on primer mismatch during allele-specific amplification of preamplified target sequences. Primers are labeled with different fluors at their 5' nucleotides, with their 3' termini at the transition mutation that defines allelic variation at the target locus. Each primer perfectly matches one of the two available alleles for each locus. Electrophoretic detection permits characterization of the product both by size and fluor. This report demonstrates some of the capabilities of this assay, including heterozygote determination and multiplexed analysis.

Alleles↗

PubMed1996

Resistance gene analogs are conserved and clustered in soybean.

Sequences of cloned resistance genes from a wide range of plant taxa reveal significant similarities in sequence homology and structural motifs. This is observed among genes conferring resistance to viral, bacterial, and fungal pathogens. In this study, oligonucleotide primers designed for conserved sequences from coding regions of disease resistance genes N (tobacco), RPS2 (Arabidopsis) and L6 (flax) were used to amplify related sequences from soybean [Glycine max (L.) Merr.]. Sequencing of amplification products indicated that at least nine classes of resistance gene analogs (RGAs) were detected. Genetic mapping of members of these classes located them to eight different linkage groups. Several RGA loci mapped near known resistance genes. A bacterial artificial chromosome library of soybean DNA was screened using primers and probes specific for eight RGA classes and clones were identified containing sequences unique to seven classes. Individual bacterial artificial chromosomes contained 2-10 members of single RGA classes. Clustering and sequence similarity of members of RGA classes suggests a common process in their evolution. Our data indicate that it may be possible to use sequence homologies from conserved motifs of cloned resistance genes to identify candidate resistance loci from widely diverse plant taxa.

Amino Acid Sequence↗

PubMed1996

Organization of the histone H3 genes in soybean, barley and wheat.

Several variants of the replacement histone H3 genes from soybean, barley and wheat have been cloned and sequenced. Analysis of segregating populations in barley and soybean, as well as analysis of clones isolated from a soybean genomic library, suggested that these genes are dispersed throughout the genome. Several genes contains introns located in similar positions, but of different lengths and sequence. Comparison of mRNA levels in different tissues revealed that the intron-containing and intronless genes have different expression patterns. The distribution of the introns in the histone H3 genes across several plant species suggests that some of the introns might have been lost during the evolution of the gene family. Sequence divergence among introns and gene-flanking sequences in cloned gene variants allowed us to use them as specific probes for localizing individual gene copies and analyzing the genomic distribution of these variants across a range of genotypes.

Base Sequence↗

PubMed1996

Phylogenetic utility of histone H3 intron sequences in the perennial relatives of soybean (Glycine: Leguminosae).

Histone H3 loci form a large multigene family in most plant species. In Glycine, some of these loci possess introns, whose sequences can provide characters for assessing phylogenetic relationships among species of the genus. Phylogenetic analyses of two closely related H3-B loci revealed a complex evolutionary pattern, producing trees from which species relationships could not be inferred readily. The single H3-D locus, in contrast, provided data suitable for the construction of gene trees whose topologies were sufficiently similar to other hypotheses of relationships within the subgenus Glycine to give confidence that evolution at this locus is tracking species phylogenies. H3-D topologies identified several of the same groupings found in previous phylogenetic studies using the chloroplast genome. However, histone H3-D and chloroplast genome data sets were in other respects incongruent, as revealed by both topological differences and numerical measures of congruence. The principal difference involved Glycine falcata, whose chloroplast genome belongs to one of the three strongly supported clades in the subgenus, but whose histone H3-D allele was sister to those of the remaining members of the subgenus. The H3-D topology is more in keeping with the morphologically, ecologically, and genetically divergent nature of this species. The H3-D locus appears to be a useful source of phylogenetic characters for interspecific studies in Glycine, providing resolution among taxa whose relationships were unresolved in previous studies.

Chloroplasts↗

PubMed1993

Variability among members of the Hor-2 multigene family.

The hordeins comprise the major prolamin storage proteins of barley. Two major and one minor gene families encode these alcohol-soluble proteins. The Hor-2 gene family encoding the B-hordeins has been estimated to contain 15-30 copies. Although several genes encoding B-hordeins have been cloned and sequenced, little is known about the mechanisms responsible for the generation of the enormous genetic variability at this locus. Polymerase chain reaction sequence amplification provided a simple technique that permitted the amplification of the Hor-2 gene family members from the genomes of several barley genotypes. Sequence analysis of clones permitted the identification of a region within the Hor-2 structural gene that appears to undergo recombinational and slippage-like gene conversion events. In this report we describe variability of the B-hordein genes, possible mechanisms responsible for it, and implications this may have on the evolution of prolamin-encoding gene families.

Base Sequence↗

PubMed1993

The genetics of 5S rRNA encoding multigene families in barley.

Two loci containing genes encoding 5S rRNA were mapped on the second and third chromosomes of barley. The two gene clusters located on different chromosomes differed in the length of the nontranscribed spacer separating the 5S rRNA genes. All nontranscribed spacers contained a variable number of trinucleotide tandem repeats. The distribution of 5S genes between these two clusters and their copy number varied widely between cultivars and doubled haploids derived from a cross between two barley cultivars. However, this variation had no obvious effect on plant phenotype.

Base Sequence↗