Characterization and application of soybean YACs to molecular cytogenetics

Yeast artificial chromosomes (YACs) are widely used in the physical analysis of complex genomes. In addition to their value in chromosome walking for map-based cloning, YACs represent excellent probes for chromosome mapping using fluorescence in situ hybridization (FISH). We have screened such a library for low-copy-number clones by hybridization to total genomic DNA. Four clones were chosen for chromosome tagging based upon their low or moderate signal. By using degenerate oligonucleotide-primed PCR (DOP-PCR), we were able to use relatively small amounts of soybean YAC DNA, isolated directly by preparative pulsed-field gel electrophoresis, as FISH probes for both metaphase chromosome spreads and interphase nuclei. FISH chromosomal analysis using the three of the clones as probes resulted in relatively simple hybridization patterns consistent with a single homologous locus or two homoeologous loci. The fourth YAC probe resulted in a diffuse hybridization pattern with signal on all metaphase chromosomes. We conclude that YACs represent a valuable source of probes for chromosomal analysis in soybean.     

Analysis of the genes encoding the largest subunit of RNA polymerase II in Arabidopsis and soybean

We have cloned and sequenced the gene encoding the largest subunit of RNA polymerase II (RPB1) from Arabidopsis thaliana and partially sequenced genes from soybean (Glycine max). We have also determined the nucleotide sequence for a number of cDNA clones which encode the carboxyl terminal domains (CTDs) of RNA polymerase II from both soybean and Arabidopsis. The Arabidopsis RPB1 gene encodes a polypeptide of approximately 205 kDa, consists of 12 exons, and encompasses more than 8 kb. Predicted amino acid sequence shows eight regions of similarity with the largest subunit of other prokaryotic and eukaryotic RNA polymerases, as well as a highly conserved CTD unique to RNA polymerase II.The CTDs in plants, like those in most other eukaryotes, consist of tandem heptapeptide repeats with the consensus amino acid sequence PTSPSYS. The portion of RPB1 which encodes the CTD in plants differs from that of RPB1 of animals and lower eukaryotes. All the plant genes examined contain 2–3 introns within the CTD encoding regions, and at least two plant genes contain an alternatively spliced intron in the 3 untranslated region. Several clustered amino acid substitutions in the CTD are conserved in the two plant species examined, but are not found in other eukaryotes. RPB1 is encoded by a multigene family in soybean, but a single gene encodes this subunit in Arabidopsis and most other eukaryotes.     

Variability in giant fennel (Ferula communis,Umbelliferae): Ribosomal RNA nuclear genes

The rDNA of five accessions of the giant fennel (Ferula communis, Umbelliferae) was analyzed. The restriction map of Bam H 1, Eco R 1 and Hind III sites was established for one of them. Variation between the five accessions was observed at several levels. Three have a homogeneous repeat size, whereas the two others are heterogeneous, one presenting an additional site heterogeneity. However, the general pattern of organization is very similar and there is much greater similarity between theFerula accessions than with the pattern observed for carrot, a plant from the same family. Variation was also observed in the copy number of the rDNA repeats, which ranges from 900 to 3 500. The results demonstrate that the five accessions can be clearly differentiated by molecular analysis of their DNA although they belong to the same species or subspecies. They also demonstrate that different isolated populations of a species evolve independently, thus shedding light on the molecular mechanisms of speciation.     

5S rRNA genes in Pisum: sequence, long range and chromosomal organization

Summary We have employed a combination of techniques to examine the organization of pea 5S rRNA genes. These include the analysis of length variant interspersion patterns in cosmid clones, sequence analysis, Southern analysis of both conventional gels and field inversion gels and in situ hybridization. From these analyses we conclude that the 5S rRNA genes of pea are arranged in three major tandem arrays which are represented by three large EcoRI fragments and that these correspond to the three sites of in situ hybridization in the haploid pea complement     

The myrosinase gene family in Arabidopsis thaliana: gene organization,expression and evolution

Myrosinase (thioglucoside glucohydrolase, EC 3.2.3.1.) is in Brassicaceae species such as Brassica napus and Sinapis alba encoded by two differentially expressed gene families, MA and MB, consisting of about 4 and 10 genes, respectively. Southern blot analysis showed that Arabidopsis thaliana contains three myrosinase genes. These genes were isolated from a genomic library and two of them, TGG1 and TGG2, were sequenced. They were found to be located in an inverted mode with their 3 ends 4.4 kb apart. Their organization was highly conserved with 12 exons and 11 short introns. Comparison of nucleotide sequences of TGG1 and TGG2 exons revealed an overall 75% similarity. In contrast, the overall nucleotide sequence similarity in introns was only 42%. In intron 1 the unusual 5 splice border GC was used. Phylogenetic analyses using both distance matrix and parsimony programs suggested that the Arabidopsis genes could not be grouped with either MA or MB genes. Consequently, these two gene families arose only after Arabidopsis had diverged from the other Brassicaceae species. In situ hybridization experiments showed that TGG1 and TGG2 expressing cells are present in leaf, sepal, petal, and gynoecium. In developing seeds, a few cells reacting with the TGG1 probe, but not with the TGG2 probe, were found indicating a partly different expression of these genes.     

Characterization of soybean vegetative storage proteins and genes

Summary Soybean vegetative storage proteins (VSPs) were purified and characterized. Anion exchange HPLC resolved partially purified VSPs into fractions containing 27-kD/27-kD and 29-kD/29-kD homodimers and 27-kD/29-kD heterodimers. Reversed-phase HPLC resolved partially purified VSPs into three fractions. One fraction contained only 27-kD VSP and the other two contained 29-kD VSP. The two 29-kD VSP fractions differed with respect to their cyanogen bromide cleavage patterns, an observation that indicated the 29-kD VSPs were heterogeneous. Genomic clones that contained 29-kD VSP genes were also isolated and characterized. One genomic clone contained a complete 29-kD VSP gene and was sequenced. The coding region in the clone contained two introns whose borders had regulatory sequences typical of other eukaryotic genes. Putative polyadenlyation signals were present in the 3-flanking region of the gene, while putative TATA, CAAT, and enhancer core sequences were found in the 5-flanking regions. A second genomic clone that was studied contained the 5 regions of two partial 29-kD VSP genes in an inverted linkage. Genomic DNA gel blots showed that the two genes were organized in the same arrangement in the soybean genome.Cooperative research between USDA/Agricultural Research Service and the Indiana Agricultural Experiment Station. Journal Paper No. 12,192 from the Indiana Agricultural Experiment Station     

Hypomethylated sequences: Characterization of the duplicate soybean genome

Soybean is believed to be a diploidized tetraploid generated from an allotetraploid ancestor. In this study, we used hypomethylated genomic DNA as a source of probes to investigate the genomic structure and methylation patterns of duplicated sequences. Forty-five genomic clones from Phaseolus vulgaris and 664 genomic clones from Glycine max were used to examine the duplicated regions in the soybean genome. Southern analysis of genomic DNA using probes from both sources revealed that greater than 15% of the hypomethylated genomic regions were only present once in the soybean genome. The remaining ca. 85% of the hypomethylated regions comprise duplicated or middle repetitive DNA sequences. If only the ratio of single to duplicate probe patterns is considered, it appears that 25% of the single-copy sequences have been lost. By using a subset of probes that only detected duplicated sequences, we examined the methylation status of the homeologous genomes with the restriction enzymes MspI and HpaII. We found that in all cases both copies of these regions were hypomethylated, although there were examples of low-level methylation. It appears that duplicate sequences are being eliminated in the diploidization process. Our data reveal no evidence that duplicated sequences are being silenced by inactivation correlated with methylation patterns.     

Transient expression of foreign genes in rice,wheat and soybean cells following particle bombardment

The development of an efficient transformation system is a prerequisite for the molecular analysis of gene expression in plants. In crop plants, this development has been hindered by difficulties encountered both in whole plant regeneration from protoplasts and in the general insusceptibility of monocots to Agrobacterium-mediated transformation. We have circumvented these difficulties by transferring foreign genes directly into the intact cells (with cell walls) of three important crop plants including rice, wheat and soybean by a particle bombardment device. Oryza sativa and Triticum monococcum cells were bombarded with accelerated tungsten particles coated with plasmids containing a -glucuronidase gene as the reporter. Blue transformed cells were detected in an in situ enzyme assay. The number of blue cells was next used as a convenient criterion to study several factors affecting gene transfer efficiency. After optimal conditions were defined, gene transfer into intact cells of O. sativa, T. monococcum and Glycine max was successfully carried out with chloramphenicol acetyltransferase (CAT) gene as the reporter.     

Fluorescentin situ hybridization to soybean metaphase chromosomes

Repetitive DNA sequences were detected directly on somatic metaphase chromosome spreads from soybean root tips using fluorescentin situ hybridization. Methods to spread the forty small metaphase chromosomes substantially free of cellular material were developed using protoplasts. The specific DNA probe was a 1.05 kb internal fragment of a soybean gene encoding the 18S ribosomal RNA subunit. Two methods of incorporating biotin residues into the probe were compared and detection was accomplished with fluorescein-labeled avidin. The rDNA probe exhibits distinct yellow fluorescent signals on only two of the forty metaphase chromosomes that have been counterstained with propidium iodide. This result agrees with our previous analyses of soybean pachytene chromosome [27] showing that only chromosome 13 is closely associated with the nucleolus organizer region. Fluorescentin situ hybridization with the rDNA probe was detected on three of the forty-one metaphase chromosomes in plants that are trisomic for chromosome 13.     

Positioning of protein-coding genes on the soybean chloroplast genome

Seven major plastid protein encoding genes were positioned on the soybean chloroplast DNA by heterologous hybridization. These include the genes for the alpha, beta and epsilon subunits of the CF₁ component of ATP synthase (atpA, atpB and atpE respectively), for subunit III of the CF₀ component of ATP synthase (atpH), for the cytochrome f (cytF), for the ‘32 Kd’ thylakoid protein (psbA), and for the large subunit of ribulose-1,5-bisphosphate carboxylase-oxygenase (rbcL), all of which map in the large single copy region. The atpB, atpE and rbcL genes are located in the region adjacent to one of the segments of the inverted repeat. The genetic organization of the soybean chloroplast DNA is compared to that of other plastid genomes.     

Detection byin-situ fluorescence of short,single-copy sequences of chromosomal DNA

Short single-copy probes have been widely used in plant molecular biology. However, they have rarely been effective in plant research usingin situ hybridization techniques, possibly due to limitations imposed by the cell wall. We recently developed two fluorescencein situ hybridization protocols for the single-copy sequence detection in soybean. By enzymatically removing the cell wall, single-copy sequences as short as 1 kb were detected by probes using standard fluorescencein situ hybridization or PCR-primedin situ hybridization (PCR-PRINS). Such technology is useful for genome analysis, in plant molecular, cellular, and biotechnological research.     

Cotransformation frequencies of foreign genes in soybean cell cultures

Summary Through the use of electroporation and a soybean (Glycine max L.) protoplast system, we generated stably transformed cell lines expressing a number of foreign genes (neomycin phosphotransferase,-glucuronidase, chloramphenicol acetyl transferase, and phosphinothricin acetyl transferase). Selected and unselected marker genes were cointroduced either linked on a single plasmid or as separate plasmids. Calli expressing multiple genes were recovered, and Cotransformation frequencies were established for both cases. Our results show a 50% cotransformation frequency in the case of linked genes. In situations in which two genes are introduced on independent plasmids, cotransformation frequencies are 18%–27%. Similar rates of cotransformation were observed among various marker pairs.     

Ribosomal DNAs: an exception to the conservation of gene order in rice genomes

rDNA (18S-5.8S-25S rDNA) and 5S rDNA loci were visualized on the chromosomes of six species of the genus Oryza by fluorescence in situ hybridization (FISH) and the labeled rice chromosomes were identified based on their condensation patterns. As a result, the chromosomes harboring rDNA and/or 5S rDNA loci were determined in the complement for all the known rice genomes. Variation in the location of the rDNA loci indicated the transpositional nature of the rDNAs in the genus Oryza, as also suggested in Triticeae and Allium. Comparative analysis of the locations of rDNA loci among rice, maize and wheat revealed that variability in the physical location of the rDNA loci was characteristic of the genus Oryza and also of the genera of Gramineae. This variability in the location of the rDNA loci between evolutionarily related species is in sharp contrast to the conservation of the general order of genes in their genomes.     

Ribosomal RNA genes of Phaseolus coccineus. I

rDNA fragments, including the whole intergenic spacer (IGS) region of P. coccineus, were cloned into dephosphorylated pUC 13 plasmid. Four clones of different insert size were analysed. Restriction patterns and physical maps of these length variants (pPH1, pPH2, pPH5, pPH6) were performed through complete Eco RI cleavage and partial digestion with Hpa II, Hae III, Sau 3AI, Sma I. Evidence was obtained that the length heterogeneity of the four genes was mainly due to a differing number of about 170 bp sub-repeating elements in the IGS. Indeed, there are 16 of these in pPH1, about 34 in pPH2, 10 in pPH5 and about 60 in pPH6. The sequence analysis of pPH6 sub-repeats revealed that there are two types of sub-repeats: short ones (S) of 162 bp and long ones (L) of 176 bp. The homology between S and L is high (93.8%). S and L elements are present in at least three of the four genes investigated, as shown by a restriction pattern obtained with Hae III digestion to completion. The relative frequency of S and L types, however, differs among the four genes. The possible functional meaning of the subrepeat structure is discussed on the basis of the homology between the S and L sequences on the one hand and on the other the ribosomal sequences of: i) Xenopus promoter(s); ii) wheat block A sub-repeats; iii) presumptive promoter(s) of wheat.     

Restriction fragment length polymorphism diversity in soybean

Summary Fifty-eight soybean accessions from the genus Glycine, subgenus Soja, were surveyed with 17 restriction fragment length polymorphism (RFLP) genetic markers to assess the level of molecular diversity and to evaluate the usefulness of previously identified RFLP markers. In general, only low levels of molecular diversity were observed: 2 of the 17 markers exhibited three alleles per locus, whereas all others had only two alleles. Thirty-five percent of the markers had rare alleles present in only 1 or 2 of the 58 accessions. Molecular diversity was least among cultivated soybeans and greatest between accessions of different soybean species such as Glycine max (L.) Merr. and G. soja Sieb. and Zucc. Principal component analysis was useful in reducing the multidimensional genotype data set and identifying genetic relationships.     

Ribosomal RNA genes in biotypes ofScilla peruviana (Liliaceae)

Scilla peruviana biotypes have different chromosome numbers due to changes in the nucleolar chromosomes and polyploidy. We have examined two diploid (2n = 15 and 2n = 16) and two tetraploid biotypes (2n = 28 and 2n = 32). From the results of rRNA/DNA filter hybridizations it appears that rDNA percentages of the diploid biotypes are, approximately, 2.2-fold higher than those of the tetraploid biotypes. To examine the rRNA gene structure we have utilizedSouthern blot hybridization after DNA digestions with three restriction enzymes: Eco RI, Hind III and Bam HI. From the band analysis of both single and double digestions it has been possible to reveal the presence, in the diploid biotypes, of three gene types, heterogeneous both for length and for nucleotide sequences in the external spacer. The three rRNA genes are 12 600, 12 700, and 12 800 base pairs long and they have a different position of the Hind III sites in the external spacer. On the other hand, a single gene type of 12 600 base pairs, identical to the first type of the diploid biotypes, surprisingly exists in the tetraploid biotypes. Considerations on the rRNA gene regulation and evolution are made.     

Ribosomal RNA genes structure in somePopulus spp. (Salicaceae) and their hybrids

The tandemly repeated multigene families encoding 18S and 25S rRNAs were studied at the restriction enzyme level inPopulus alba L.,Populus deltoides Bartr. exMarsh.,Populus trichocarpa Torr. & Gray and in the hybrids between the last two mentioned species. The analysis of single and double digestion with EcoRI, BamHI, XbaI, and SstI endonucleases showed the presence of single repetitive unit types of 12.25 and 11.75kb inP. alba andP. trichocarpa, respectively.P. deltoides showed two rDNA gene types having the same length (12.25Kb) but different nucleotide sequence in the IGS. The rDNAs genes ofP. deltoides andP. triochocarpa are inherited codominantly in their hybrids.     

Ribosomal RNA genes inQuercus spp. (Fagaceae)

The taxonomy of the genusQuercus is still unclear. In order to elucidate the taxonomy of Mediterranean oaks we have analyzed ribosomal RNA genes ofQuercus cerris, Q. coccifera, Q. trojana, Q. ilex, Q. suber, andQ. macrolepis by means of Southern blot hybridization. Oak nuclear DNA was extracted from root tips of 300 acorns and from catkins of single plants. EcoRI and BamHI restriction endonucleases were used. DNA electrophoresis and rRNA/DNA hybridization were performed usingVicia faba rRNA 18 S and 25 S as probes. The rRNA genes of all the species studied have an identical restriction mapping in the 18 S and 25 S regions, while differences in length are present in the intergenic regions.Q. cerris possesses at least four types of genes of 12.1, 11.5, 8.5, and 8.3 kb;Q. coccifera at least three types of 12.4, 10.4, and 10.1 kb;Q. trojana possesses the same rRNA genes asQ. cerris plus another gene type 12.0 kb long, with EcoRI and BamHI restriction sites in the intergenic spacer;Q. ilex at least three types of 12.4, 10.85, and 9.5 kb;Q. suber at least five types of 11.5, 11.0, 8.6, 8.5, and 8.3 kb;Q. macrolepis, finally, at least seven types of 11.5, 11.0, 10.2, 8.6, 8.5, 8.3, and 8.15 kb.Q. coccifera andQ. ilex rDNA appears quite different respect to other species examined, while high similarity seems to exist betweenQ. cerris, Q. trojana, Q. suber, andQ. macrolepis. These results are in agreement with the taxonomic model proposed bySchwarz for the genusQuercus.     

Identification of molecular markers in soybean comparing RFLP,RAPD and AFLP DNA mapping techniques

Three different DNA mapping techniques—RFLP, RAPD and AFLP—were used on identical soybean germplasm to compare their ability to identify markers in the development of a genetic linkage map. Polymorphisms present in fourteen different soybean cultivars were demonstrated using all three techniques. AFLP, a novel PCR-based technique, was able to identify multiple polymorphic bands in a denaturing gel using 60 of 64 primer pairs tested. AFLP relies on primers designed in part on sequences for endonuclease restriction sites and on three selective nucleotides. The 60 diagnostic primer pairs tested for AFLP analysis each distinguished on average six polymorphic bands. Using specific primers designed for soybean fromEco RI andMse I restriction site sequences and three selective nucleotides, as many as 12 polymorphic bands per primer could be obtained with AFLP techniques. Only 35% of the RAPD reactions identified a polymorphic band using the same soybean cultivars, and in those positive reactions, typically only one or two polymorphic bands per gel were found. Identification of polymorphic bands using RFLP techniques was the most cumbersome, because Southern blotting and probe hybridization were required. Over 50% of the soybean RFLP probes examined failed to distinguish even a single polymorphic band, and the RFLP probes that did distinguish polymorphic bands seldom identified more than one polymorphic band. We conclude that, among the three techniques tested, AFLP is the most useful.     

Direct proof for the presence and expression of two 5% different 16S rRNA genes in individual cells of Haloarcula marismortui

A single-cell-derived pure culture of Haloarcula marismortui was obtained using the optical tweezers technique. Analysis of the 16S rRNA genes unambiguously demonstrated two 5% different 16S rRNA sequences. In addition, expression of both operons in the same cell was shown by fluorescence in situ hybridization with operon-specific probes. Received: September 19, 2000 / Accepted: October 2, 2000