Inheritance and linkage of isozyme loci in almond

The segregation of seven isozyme marker genes was investigated using eight controlled crosses in almond. The cultivar Nonpareil was the maternal parent in all crosses. Pollination was achieved using eight different cultivars, and a total of 3200 individual kernels were assessed. For each isozyme the goodness-of-fit test was used to test for departure from the expected frequencies assuming Mendelian inheritance. Given a higher than expected number of significant results for individual isozymes, independent segregation between pairs of isozymes was tested using the chi-square statistic on the resulting two-way contingency tables. In all crosses a highly significant association (P value< 0.001) was observed between (1) the AAT- 1 and IDH isozymes loci and (2) the LAP-1 and PGM-2 isozymes loci, which leads to the conclusion that the respective isozyme pairs are linked.In addition, a significant association (P value < 0.001) was observed between LAP-1 and GPI-2 when the pollen sources were Fritz, Mission, or Price, but this could not be tested for the remaining five pollen sources, Carmel, Grant, Keane, Ne plus Ultra, Peerless, because they are homozygous at these loci. If LAP-1 is linked with GPI-2 and PGM-2, it might be expected that we should find evidence of linkage between GPI-2 and PGM-2. The lack of a significant association between these two isozymes suggests that LAP-1 is located centrally on the chromosome. These three pairs of linked loci are the first to be reported in almond.     

DNA typing of grapevines: A universal methodology and database for describing cultivars and evaluating genetic relatedness

With established ampelographic techniques for grapevine identification it is often difficult to achieve a satisfactory, objective result. We have developed a DNA typing system using sequence-tagged microsatellite site markers as a means of differentiating cultivars of grapevine. A semi-automated analysis procedure was linked to an electronic database and found to be an objective and reliable system for cultivar identification using this simple marker type. The accumulated DNA typing data from over eighty cultivars demonstrated that cultivars that are difficult to differentiate phenotypically using ampelographic techniques can be distinguished by DNA typing. Parentage analysis uncovered errors in parent assignment of cultivar identification in specific cases. The electronic database has a conservative format to take into account the occurrence of null alleles and the possibility of missed alleles. Computer-assisted comparisons of cultivars in the database can be performed and various approaches for estimating the match probability that two unrelated cultivars have the same genotype simply due to chance are discused. We suggest that further development of the database through international co-operation using standardised sequence-tagged site markers offers the possibility of achieving a universal grapevine identification system.     

Overexpression and characterization of two human salivary proline rich proteins

Proline rich proteins (PRP) are among major human saliva constituents and are known to interact with wine tannins that are involved in astringency. To characterize these interactions, a human salivary proline rich pro-protein, PRB4S, was overexpressed in Pichia pastoris. Six recombinant proteins resulting from maturation in bioreactor were detected by SDS-PAGE analysis between 15 and 45 kDa (apparent molecular weight). Two of them, the 45 and the 15 kDa ones, were isolated from culture supernatant by adsorption and permeation chromatography. They were characterized by N-terminal sequencing and MALDI-TOF analysis after trypsic digestion. The 45 kDa protein is glycosylated while the 15 kDa one was obtained after a furin-like proteolysis. Both of them are similar to human whole saliva PRP resulting from proteolysis of PRB4S pro-protein in Golgi network and known as II-1 and IB-5. Because of their sensitivity to proteolysis or their unusual mobility on SDS-PAGE gel, these recombinant proteins seem to be intrinsically unstructured proteins.     

Stigma proteins of the two loci self-incompatible grass Phalaris coerulescens

Summary Protein extracts from four self-incompatible genotypes of Phalaris coerulescens were subjected to analysis by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and ultra-thin isoelectric focusing. A comparison between stigma, root and leaf extracts showed that there was no significant difference in electrophoretic or isoelectric focusing patterns between the genotypes for both root and leaf proteins. However, stigma protein patterns did vary between genotypes especially within the molecular weight region of 43 000–97 000 and within the pI range 5–7. The stigma-specific changes strongly suggest a link between the self-incompatible genotype and these stigma proteins. However, because there are two loci involved, it is not yet possible to precisely assign particular proteins to each S- or Z-allele.     

Inheritance of two endosperm protein loci in rice (Oryza sativa L.)

Summary Previous studies indicated two types of phenotypic protein markers as two minor bands of SDS-PAGE for rice storage protein. A variant derived from a Pakistani variety, Dular, was found to show a mobility variant with Band 11, a relatively faster-moving band as compared to Band 10, while most of the other cultivated rices exhibited Band 10 at a molecular weight of around 100–110 K. Band 11 was also observed in several wild rice species. How this variant occurred is not known. Another marker is characterized by the presence of either Band 56 (slower-migrating band) or Band 57 (faster-migrating band) in most cultivars at a molecular weight of about 28–27 K. Most indica varieties developed in Taiwan have Band 57 and japonica varieties have Band 56. Genetic analysis of F₁, F₂ and F₃ seeds from interstrain crosses indicated that Band 10 versus Band 11 and Band 56 versus Band 57 are due to codominant alleles at two loci. Tests of independent inheritance between these two loci (Band 10/11 versus Band 56/57) indicated that there is no linkage between them. Both of these two protein loci encode for endosperm proteins and mostly belong to the minor polypeptide subunits of the glutelin fraction of rice seed proteins. Studies on reciprocal crosses indicate dosage effects as exhibited in band patterns. Variations in band intensity were frequently observed when the maternal genotype was different.     

Genes encoding the small subunit of RUBISCO belong to two highly conserved subfamilies in Nicotianeae

Summary The sequences of seven complementary DNAs or genes encoding the small subunit (SSU) of ribulose-1,5-bisphosphate carboxylase oxygenase (RUBISCO) in several Nicotianeae were examined. Two new SSU genes isolated fromNicotiana sylvestris were included. Both sequence comparisons and Southern analyses with specific probes reveal that SSU genes fall into two homogeneous subfamilies that are highly conserved in Nicotianeae and are also present in other Solanaceae. Additional criteria such as number of introns and level of expression fitted to this classification. Homogeneity must have been maintained by gene conversion and/or an unusually high fidelity of DNA replication, whereas traces of slippage-stranded DNA mispairing and/or transposition probably explain local changes. Taken as a whole, these results show that the divergence between the two subfamilies predated the divergence between genera inside the Solanaceae, but that Nicotianeae retained the most simple SSU gene family structure.     

Two distinct P element subfamilies in the genome of Drosophila bifasciata

The genome of Drosophila bifasciata harbours two distinct subfamilies of P-homologous sequences, designated M-type and O-type elements based on similarities to P element sequences from other species. Both subfamilies have some general features in common: they are of similar length (M-type: 2935 bp, O-type: 2986 bp), are flanked by direct repeats of 8 by (the presumptive target sequence), contain terminal inverted repeats, and have a coding region consisting of four exons. The splice sites are at homologous positions and the exons have the coding capacity for proteins of 753 amino acids (M-type) and 757 amino acids (O-type). It seems likely that both types of element represent functional transposons. The nucleotide divergence of the two P element subfamilies is high (31%). The main structural difference is observed in the terminal inverted repeats. Whereas the termini of M-type elements consist of 31 by inverted repeats, the inverted repeats of the O-type elements are interrupted by non-complementary stretches of DNA, 12 by at the 5 end and 14 by at the 3 end. This peculiarity is shared by all members of the O-type subfamily. Comparison with other P element sequences indicates incongruities between the phylogenies of the species and the P transposons. M-type and O-type elements apparently have no common origin in the D. bifasciata lineage. The M-type sequence seems to be most closely related to the P element from Scaptomyza pallida and thus could be considered as a more recent invader of the D. bifasciata gene pool. The origin of the O-type elements cannot be unequivocally deduced from the present data. The sequence comparison also provides new insights into conserved domains with possible implications for the function of P transposons.     

A proposal for standardization in forensic bovine DNA typing: allele nomenclature of 16 cattle-specific short tandem repeat loci

In this study, a proposal is presented for the allele nomenclature of 16 polymorphic short tandem repeat (STR) loci ( BM1824 , BM2113 , ETH10 , ETH225 , INRA023 , SPS115 , TGLA122 , TGLA126 , TGLA227 , ETH3 , TGLA53 , BM1818 , CSRM60 , CSSM66 , HAUT27 and ILSTS006 ) for bovine genotyping ( Bos taurus ). The nomenclature is based on sequence data of the polymorphic region(s) of the STR loci as recommended by the DNA commission of the International Society of Forensic Genetics for human DNA typing. To cover commonly and rarely occurring alleles, a selection of animals homozygous for the alleles at these STR loci were analysed and subjected to sequence studies. The alleles of the STR loci consisted either of simple or compound dinucleotide repeat patterns. Only a limited number of alleles with the same fragment size showed different repeat structures. The allele designation described here was based on the number of repeats including all variable regions within the amplified fragment. The set of 16 STR markers should be propagated for the use in all bovine applications including forensic analysis.     

Inheritance of RFLP loci in a loblolly pine three-generation pedigree

Summary A high-density restriction fragment length polymorphism (RFLP) linkage map is being constructed for loblolly pine (Pinus taeda L.). Loblolly pine cDNA and genomic DNA clones were used as probes in hybridizations to genomic DNAs prepared from grandparents, parents, and progeny of a three-generation outbred pedigree. Approximately 200 probes were evaluated for their ability to detect polymorphic loci between DNAs prepared from the two parent trees, 20–1010 and 11–1060, and cut with four different restriction enzymes: BamHI, DraI, EcoRI, and HindIII. More than half of the probes detecting single- or low-copy number sequences (56%) revealed polymorphisms between the two parents with at least one restriction enzyme. If necessary, an additional hybridization to DNAs prepared from the four grandparent trees was conducted to determine the zygosity of parent trees. Ten of these probes were hybridized to progeny DNAs from this cross and, as expected, the markers were inherited as simple codominant Mendelian alleles. Four of the ten probes detected segregation of three alleles at one locus, and four probes detected more than one independently segregating locus. RFLPs can be used immediately to assess genetic diversity in conifer populations and to efingerprint genotypes in tree improvement programs.     

Anther-specific,developmentally regulated expression of genes encoding a new class of proline-rich proteins in sunflower

We have used RNA gel blot analysis to demonstrate the anther-specific expression of three genes in sunflower. Expression of these genes was first detected shortly before flower opening, which occurs sequentially on the sunflower inflorescence, and continues during pollination. In contrast, these genes are not expressed (or only weakly expressed) in a male-sterile line in which anther development aborts. In situ hybridization experiments showed that these genes are only expressed in the single cell layer of the sunflower anther epidermis. In the case of one of these genes, which codes for an abundant mRNA, we report the peptide sequences deduced from the sequence of two similar but non identical cDNAs. These proteins contain a potential signal peptide and are characterized by the presence of a proline-rich region which reads KPSTPAPPPPPP(PP)K. Our results also suggest that several proline-rich proteins of unknown functions are specifically synthesized during the maturation of anthers in sunflower.     

A proposal for standardization in forensic equine DNA typing: allele nomenclature for 17 equine‐specific STR loci

In this study, a proposal is presented for the allele nomenclature of 17 polymorphic STR loci (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, HTG10, LEX3 and VHL20) for equine genotyping (Equus caballus). The nomenclature is based on sequence data of the polymorphic region of the STR loci as recommended by the DNA commission of the International Society for Forensic Genetics for human DNA typing. For each STR locus, several alleles were selected and animals homozygous for those alleles were subjected to sequence analysis. The alleles of the 17 STR loci consisted either of simple (10), compound (6) or complex repeat patterns (1). Only a limited number of alleles with the same fragment size showed different repeat structures. The allele designation described here was based on the number of repeats, including all variable regions within the amplified fragment.     

Concordant divergence in proteins and mitochondrial DNA between two vole species in the genusClethrionomys

The bank vole (Clethrionomys glareolus) and the northern red-backed vole (C. rutilus) are two closely related species where interspecific crosses result in fertile female but sterile male offspring. Mitochondrial DNA (mtDNA) fromC. rutilus has passed the species barrier and is found inC. glareolus from northern Fennoscandia. The present report shows that the genetic distance between the two species, calculated from enzyme data (Nei'sD), is 0.64. Isoelectric focusing of muscle proteins resolved around 55 bands, of which each species had 6 or 7 bands not present in the other species. Sequence divergence of mtDNA from the two species is 13.9%. A comparison between protein and mtDNA distances in other species pairs reveals a high correlation between the two measures, indicating that differences in mtDNA between taxa are not random when compared to divergence in protein-coding nuclear genes. The relationship between genetic divergence in proteins and that in mtDNA betweenClethrionomys glareolus andC. rutilus is similar to that found in other species pairs. It is also shown that despite large differences on the protein level it is still, in some cases, possible for species pairs to produce fertile hybrid females.This study was sponsored by the Swedish Natural Science Research Council, the Erik Philip-Sörensen Foundation, and the Nilsson-Ehle Foundation.     

A phylogeny of Anisophylleaceae based on six nuclear and plastid loci: ancient disjunctions and recent dispersal between South America, Africa, and Asia

The Anisophylleaceae comprise 29-34 species of shrubs and trees occurring in lowland forests and swamps in tropical Africa, Asia, and South America. These species are placed in four genera with disjunct geographic distributions; Anisophyllea has 25-30 species in South America, Africa, and Malesia; Combretocarpus has one species in Sumatra and Borneo; Poga one species in equatorial Africa; and Polygonanthus two in the Amazon Basin. Here we use a phylogeny based on six nuclear and plastid loci sequenced for 15 species representing the four genera to infer their relationships and the relative and absolute ages of the range disjunctions. Combretocarpus is sister to the other three genera, and Polygonanthus then sister to Poga and Anisophyllea. Ansiophyllea, represented by 12 species from all three continents, is monophyletic. A relaxed Bayesian clock calibrated with the oldest fossils from a relevant outgroup, Tetramelaceae, suggests that the disjunctions between Combretocarpus, Poga, and Polygonanthus date back to the Cretaceous, Mid-, and Upper Eocene, whereas the intercontinental disjunctions within Anisophyllea appear to date back only some 22-23 million years and thus probably result from long-distance dispersal.     

Accumulation of extracellular proteins bearing unique proline-rich motifs in intercellular spaces of the legume nodule parenchyma

Summary. Nodulins encoding repetitive proline-rich cell wall proteins (PRPs) are induced during early interactions with rhizobia, suggesting a massive restructuring of the plant extracellular matrix during infection and nodulation. However, the proteins corresponding to these gene products have not been isolated or characterized, nor have cell wall localizations been confirmed. Posttranslational modifications, conformation, and interactions with other wall polymers are difficult to predict on the basis of only the deduced amino acid sequence of PRPs. PsENOD2 is expressed in nodule parenchyma tissue during nodule organogenesis and encodes a protein with distinctive PRP motifs that are rich in glutamate and basic amino acids. A database search for the ENOD2 signature motifs indicates that similar proteins may have a limited phylogenetic distribution, as they are presently only known from legumes. To determine the ultrastructural location of the proteins, antibodies were raised against unique motifs from the predicted ENOD2 sequence. The antibodies recognized nodule-specific proteins in pea (Pisum sativum), with a major band detected at 110 kDa, representing a subset of PRPs from nodules. The protein was detected specifically in organelles of the secretory pathway and intercellular spaces in the nodule parenchyma, but it was not abundant in primary walls. Similar proteins with an analogous distribution were detected in soybean (Glycine max). The use of polyclonal antibodies raised against signature motifs of extracellular matrix proteins thus appears to be an effective strategy to identify and isolate specific structural proteins for functional analysis. Correspondence and reprints: Delaware Biotechnology Institute, Newark, DE 19711, U.S.A.     

A high amount of satellite DNA in the genome of Lupinus angustifolius L.

Embryo DNA, isolated from ungerminated seeds of Lupinus angustifolius L., contains an exceptionally high amount of guanine-cytosine-rich satellite DNA. The thermal denaturation curve of total embryo DNA is biphasic with an inflexion point at 62% denaturation, indicating the presence of satellite DNA. The satellite fraction could be separated from the mainband DNA by three successive preparative CsCl-gradient centrifugations. The densities of the DNA fractions are 1.7045 g cm^-3 and 1.6925 g cm^-3, respectively. The percentages of guanine-cytosine calculated from these densities are comparable to the percentages of GC calculated from the melting temperatures. Finally, ressociation studies prove that foldback DNA and highly repeated sequences are much more frequent in the satellite DNA fraction than in the mainband DNA.Abbreviation C _o t the product of the DNA concentration (mol nucleotides l^-1) and the time (s) of incubation in a DNA reassociation reaction - GC guanine-cytosine - np nucleotide parirs - T temperature interval between 16 and 84% denaturation     

Experimental verification of microsatellite null alleles in Norway spruce (Picea abies [L.] Karst.): Implications for population genetic studies

Three stands ofPicea abies [L.] Karst. with different density in the Harz Mountains (Lower Saxony, Germany) were characterized at 4 microsatellite loci. An excess of homozygotes was observed in all 3 stands at 1 simple sequence repeat (SSR) locus, suggesting the presence of null alleles. To test for the segregation of a null allele, 24 openpollinated seeds (haploid megagametophytes and embryos) from apparently homozygous mother trees were analyzed. For 1 of 3 trees that could be identified as heterozygous for a null allele, no significant deviation from the expected 1∶1 segregation into marker absence (null allele) and marker presence of the second maternal allele could be observed in the haploid megagametophyte. Concordantly, the numbers of embryos heterozygous for the null allele and for the other maternal allele were not significantly different from each other. Inheritance analyses in seedlings and corresponding megagametophytes of gymnosperms were used as a direct experimental verification of microsatellite null alleles in single-tree progeny. Microsatellites with an abundance of null alleles should be discarded from further analysis because inclusion of these loci results in incorrect estimation of allele frequencies.     

Genetic diversity of six isozyme loci in cultivated barley of Tibet

Summary A random sample of 463 accessions of cultivated barley from the Tibet Hordeum germplasm collection was assayed electorphoretically for genetic diversity at six isozyme loci. Two loci (Acp-1 and Got-1) were found to be monomorphic and extensive variation was detected at the remaining four loci (Est-1, Est-2, Est-3 and Est-4). The allelic composition of Tibetan barley appeared to be distinct as compared to the results of previous studies of barleys from other parts of the world. Partitioning of genetic diversity showed that approximately 96% of the total variation was maintained at the within-subregion level and only about 4% was accounted for by differentiation among the eight subregions. Analysis of multilocus genotypes revealed non-random association of the alleles at the four loci, both in the entire sample and in all the subregions, although the four major multilocus genotypes did not show significant departure from the expectation based on complete random association. The possible causes for the establishment of these multilocus associations were discussed.     

RFLP patterns of gliadin alleles in Triticum aestivum L.: implications for analysis of the organization and evolution of complex loci

A correspondence between RFLP patterns and gliadin alleles at the Gli-1 and Gli-2 loci was established in a set of 70 common wheat (T.aestivum L.) cultivars using -gliadin (K32) and -gliadin (pTU1) specific probes. All Gli-B1 and Gli-D1 alleles which differed in encoded -gliadins showed definite RFLP patterns after hybridization with the K32 probe. Two groups of Gli-B1 alleles, Gli-B1b-like and Gli-B1e-like, were identified, and these could originate from distinct genotypes of the presumptive donor of the B-genome. Intralocus recombination and/or gene conversion as well as small deletions, gene silencing and gene amplification were assumed to be responsible for the origin of new gliadin alleles. Silent -gliadin sequences were shown to exist in all of the genotypes studied. K32 also differentiated Gli-A1a from all other Gli-A1 alleles as well as the Gli-B11 allele in cultivars carrying the 1B/1R (wheat/rye) translocation. PTU1 was shown to recognize several Gli-A2 alleles, but not the Gli-B2 or Gli-D2 alleles. Moreover, this probe hybridized to chromosome 1R sequences suggesting the existence of rye gene(s), probably silent, for -gliadin-like proteins on chromosome 1R.     

Use of a promoter-specific probe to identify two loci from the Rhizobium meliloti nodulation regulon

The nodulation regulon of Rhizobium meliloti AK631 includes several operons (nodABC, hsnABC, hsnD, efn locus) which have in common a consensus promoter sequence called the nod box. A synthetic nod box probe was used to identify two additional nod boxes, n4 and n5, which were subcloned for study. By constructing lac fusions, we show that n4 and n5 sponsor induction of downstream regions as previously shown for n1-nodABC and n2-hsnABC. Using site-directed Tn5 mutagenesis, we find that the n5 locus plays a significant role in nodulation of alfalfa and sweetclover, whereas the n4 locus is important for alfalfa, but not for sweetclover. Hybridization data suggest that the n5 locus is conserved among Rhizobium species. In contrast, the n4 locus seems to be unique to Rhizobium meliloti strains, in agreement with the host-specific phenotype of n4 locus mutants. Thus, the use of a promoter probe allows us to identify nodulation genes which may be overlooked by standard methods such as random Tn5 mutagenesis.     

Non-random distribution of Alu-family repeats in human chromosomes

A phage lambda recombinant clone containing at least 8 Alu-family repeats (AFRs) has been isolated from a human genomic library, and DNA from the phage was used as a probe for in situ hybridization on G-banded human metaphase chromosomes of healthy donors and leukemic patients. Some chromosome bands show prominent clusters of silver grains in all individuals examined: 1p34, 1q23, 2q21–22, 10p14, 11p14, 10q21 and 11q14. The data suggest non-random distribution of AFRs in the human genome.