The Sec-1 locus on the short arm of chromosome 1R of rye (Secale cereale)

This paper describes a detailed sequence analysis of the omega-secalin gene array at the Sec-1 locus on the short arm of chromosome 1 of rye. The analysis shows that the genes are separated by 8 kb of spacer sequence and that the gene/spacer units are arranged in a head to tail fashion. The boundaries of the array are identified, and a fragment containing the majority of the genes in the array is separated by PFG analysis. The sequence data of one 9.2 kb gene unit have been determined, and because of the similarity of the gene units within the array these data provide a detailed sequence analysis of 140 kb of the Sec-1 locus. Fluorescence in situ hybridization, using lambda clones isolated for the structural analysis, identifies the position of the array on the rye chromosomes relative to the 5S rRNA genes.

Intraspecific and interspecific variation in 5S RNA genes are decoupled in diploid wheat relatives

5S RNAs form part of the ribosome in most organisms. In some, e.g., prokaryotes and some fungi, the genes are part of the ribosomal operon, but in most eukaryotes they are in tandem arrays of hundreds to thousands of copies separate from the main ribosomal array. 5S RNA genes can be aligned across kingdoms. We were therefore surprised to find that, for 28 diploid species of the wheat tribe (Triticeae), nucleotide diversity within an array is up to 6.2% in the genes, not significantly different from that of the nontranscribed spacers. Rates of concerted evolution must therefore be insufficient to homogenize the entire array. Between species, there are significantly fewer fixed differences in the gene than would be expected, given the high within-species variation. In contrast, the amount of variation between species in the spacer is the same as or greater than that within individuals. This leads to a paradox. High variation within an individual suggests that there is little selection on any particular gene within an array. But conservation of the gene across species implies that polymorphisms are periodically eliminated at a rate approximately equal to or greater than that of speciation. Levels of intraspecific polymorphism and interspecific divergence are thus decoupled. This implies that selective mechanisms exist to eliminate mutations in the gene without also affecting the spacer.

Disomic Thinopyrum intermedium addition lines in wheat with barley yellow dwarf virus resistance and with rust resistances

Zhong 5 is a partial amphiploid (2n = 56) between Triticum aestivum (2n = 42) and Thinopyrum intermedium (2n = 42) carrying all the chromosomes of wheat and seven pairs of chromosomes from Th. intermedium. Following further backcrossing to wheat, six independent stable 2n = 44 lines were obtained representing 4 disomic chromosome addition lines. One chromosome confers barley yellow dwarf virus (BYDV) resistance, whereas two other chromosomes carry leaf and stem rust resistance; one of the latter also confers stripe rust resistance. Using RFLP and isozyme markers we have shown that the extra chromosome in the Zhong 5-derived BYDV resistant disomic addition lines (Z1, Z2, or Z6) belongs to the homoeologous group 2. It therefore carries a different locus to the BYDV resistant group 7 addition, L1, described previously. The leaf, stem, and stripe rust resistant line (Z4) carries an added group 7 chromosome. The line Z3 has neither BYDV nor rust resistance, is not a group 2 or group 7 addition, and is probably a group 1 addition. The line Z5 is leaf and stem rust resistant, is not stripe rust resistant, and its homoeology remains unknown.Key words: Agropyron, intermediate wheatgrass, leaf rust, stem rust, stripe rust, luteovirus.

DNA profiling techniques for plant variety identification

The unambiguous identification of plant varieties is important in many areas of agriculture and plant biology research. New techniques based on DNA profiling provide novel approaches to varietal identification which offer advantages over traditional morphological comparisons. These advantages include great potential resolving power, data that can be analysed objectively, testing at all stages of development, and cost effectiveness. In this review, the advantages of recently introduced polymerase chain reaction (PCR) based methods are compared with the well-established restriction fragment length polymorphism technique. Two approaches to PCR-based DNA profiling (random amplification of polymorphic DNA, sequence-tagged sites analysis) are compared and contrasted, and statistical methods for the analysis of data are described. The potential use of these techniques for Plant Breeders Rights registration in Australia is outlined.

Amplification of DNA sequences in wheat and its relatives: the Dgas44 and R350 families of repetitive sequences

The sequence of a Triticum tauschii genomic clone representing a family of D-genome amplified DNA sequences, designated Dgas44, is reported. The Dgas44 sequence occurs on all chromosomes of the D genome of wheat, Triticum aestivum, and in situ hybridization revealed it to be evenly dispersed on all seven chromosome pairs. An internal HindIII fragment of Dgas44, designated Dgas44-3, defines the highly amplified region that is specific to the D genome. The polymerase chain reaction was used to amplify a 236-bp fragment within Dgas44-3 from chromosomes 1D, 2D, 3D, 4D, 5D, and 7D, and identical copies of this region of the Dgas44-3 sequence were found among the isolates from each of the chromosomes. The Dgas44-3 sequence population from specific chromosomes differed on average by 0.22% from the original Dgas44 sequence. The Dgas44 sequence was found to differentiate between the D genome present in T. aestivum, T. tauschii, hexaploid T. crassum, T. cylindricum, T. ventricosum, in which the sequence was present in a highly amplified form and T. juvenale, T. syriacum, and tetraploid T. crassum where the sequence family was difficult to detect. Another class of amplified sequences previously considered to be rye "specific." R350, was isolated from tetraploid wheat and its dispersed distribution on chromosomes was similar to the Dgas44 family in T. tauschii. In contrast with the Dgas44 sequence family, genome specificity for the remnant R350 sequence family was not evident since it was present on all wheat chromosomes.

A directed search for DNA sequences tightly linked to cereal cyst nematode resistance genes in Triticum tauschii

An improved system for identifying DNA sequences linked to a targeted region was developed by fractionating DNA sequences prior to polymerase chain reaction (PCR) analysis. In an attempt to identify DNA markers linked to a strong CCN resistance gene, Ccn-D1, in Triticum tauschii, DNA samples from individuals homozygous for resistance and susceptibility at the Ccn-D1 locus in a segregating progeny were bulked separately to produce "near isogenic" DNA pools. The polymerase chain reaction was employed to generate several DNA amplification products from each of the bulked DNA segregants using 240 random (RAPD) and 4 semirandom (consensus sequences of intron–splice junctions) primers. A DNA polymorphic fragment was apparent between the resistant and susceptible bulks using one of the semirandom primers. Hydroxylapatite chromatography of reannealed DNA (to Cot values > 100) was used to enrich low copy DNA sequences in the bulk DNA segregants (resistant and susceptible DNA pools). PCR analysis on the low copy enriched DNA pool increased the level of polymorphism detected between bulked segregants. One of the RAPD fragments present in only the resistant low copy DNA pool was cloned and mapped to the distal region of the long arm of chromosome 2D. By using the cloned RAPD fragment, csE20-2, to assay an RFLP locus in three independent F2 progenies, complete cosegregation was obtained with the Ccn-D1 locus. Joint segregation analysis from a genome-wide mapping of RFLP markers and a second CCN resistance in T. tauschii, Ccn-D2, showed this locus to be loosely linked to the proximal region of chromosome 2.Key words: gene targeting, low copy sequences, RAPD, RFLP, bulk segregants.

Analysis of a genomic DNA segment carrying the wheat high-molecular-weight (HMW) glutenin Bx17 subunit and its use as an RFLP marker

A genomic fragment containing the Bx17 high-molecular-weight (HMW) glutenin gene was isolated from a wheat genomic library. The fragment contains a coding region of 2.82kb with 1.98-kb downstream and 12.8-kb upstream flanking regions. The fragment was sequenced and compared with previously published glutenin genes from chromosomes 1A, 1B and 1D using a computer alignment package. The Bx17 gene shows marked similarity to the Bx7 gene sequence. A phenetic tree derived from the alignments is presented. Also shown are restriction fragment length polymorphisms (RFLPs) at the glutenin loci in a set of Australian and international wheat varieties using different regions of the glutenin clone as probes. The RFLPs correlated well with the protein composition in all cultivars analysed.

The cytogenetic and molecular architecture of chromosome 1R--one of the most widely utilized sources of alien chromatin in wheat varieties

Chromosome 1R of rye (Secale cereale) is one of the most intensively used sources of alien chromatin in bread wheat. It provides a source of valuable disease resistance genes and its widespread use has stimulated the development of genetic maps incorporating protein and DNA markers. Published data as well as new mapping data were combined into a consensus map by using common markers in the different mapping studies to orient the various data sets relative to each other. The consensus map provides a tentative order, and relative distances, between the genetic markers. A summary of the dispersed repetitive sequences that are now available for the detection and characterization of chromosome 1R segments in wheat is also provided.

The Nor-D3 locus of Triticum tauschii: natural variation and genetic linkage to markers in chromosome 5

Variation in the intergenic spacer region of the ribosomal RNA genes (located at the Nor locus) was assayed in a collection of 411 accessions of Triticum tauschii from Turkey, USSR, Iran, Afghanisan, Pakistan, and China. Twenty rDNA genotypes were identified and it was demonstrated that T. tauschii accessions from the USSR and Iran have the highest diversity at the Nor locus. At least four of the rDNA genotypes were demonstrated to be alleles of a single major locus, in segregating F2 progeny analyses. The TaqI restriction fragment associated with rDNA genotype 7 was shown to be the same as the Nor-D3a allele present in all bread wheats (based on chromosome location and length of the intergenic spacer region). This genotype was significantly associated with T. t. ssp. strangulata, previously argued to be the donor of the D genome to hexaploid wheat. The Nor locus showed a high level of recombination with the 5SDna-2 locus, which was also located on chromosome 5D. The Nor locus is placed distal to the 5SDna-2 locus but proximal to the grain softness protein gene (XGsp) on the short arm of chromosome 5D.Key words: D genome, Nor-D3, rDNA polymorphism, chromosomal location.

The molecular–genetic analysis of Triticum tauschii, the D-genome donor to hexaploid wheat

DNA from Triticum tauschii (the D-genome donor to hexaploid wheat, Triticum aestivum) has been cloned using the restriction endonuclease PstI to generate fragments for insertion into the plasmid pBR322 or pUC118. A total of 143 clones were studied and demonstrated to contain one of the following sequence types: (i) a D-genome amplified repetitive sequence, (ii) polymorphic repetitive sequences ("fingerprint-type" sequences), (iii) polymorphic low to moderately repetitive sequences (PLR sequences), (iv) polymorphic low copy number sequences (PL sequences), and (v) invariant sequences. The D-genome amplified sequence was found to be located on all seven chromosomes. A genetic linkage map using PL and PLR sequences was produced by analysing F2 segregating progeny from crosses between two different taxa of T. tauschii. In addition to using DNA clones from T. tauschii, clones from other laboratories containing either anonymous sequences or genes coding for known products (e.g., 7S globulin, dehydrin, germin, storage protein) were used in the genetic linkage map. Multiple locations were mapped for the PLR sequences and were often clustered on single chromosomes. The restriction fragment length polymorphism markers and isozymes analysed were generally distributed over all the linkage groups that were identified and, when used in conjunction with published markers, provided the basis for a genetic map of T. tauschii.Key words: D genome, genetic linkage, restriction fragment length polymorphism, isozymes, chromosomal location.

New Secale cereale (rye) DNA derivatives for the detection of rye chromosome segments in wheat

Subcloning of a clone of the 120-bp family of rye, pSc119, has produced two extremely useful probes. pSc119.1 assays rye-specific dispersed repetitive sequence families. It is present on all seven rye chromosomes and hybridizes to the entire length of each chromosome, with the exception of some telomeres and the nucleolar organiser region. pSc119.2, in contrast, hybridizes predominantly to the telomeric regions of rye chromosomes, with some interstitial sites. Unlike pSc119.1, it assays similar repetitive sequence families in both wheat and rye chromosomes.

Phylogenetic relationships of Triticum tauschii, the D-genome donor to hexaploid wheat. 4. Variation and chromosomal location of 5S DNA

The 5S DNA sequences in Triticum tauschii are organised in large clusters containing units that are primarily either 420 ("short") or 490 base pairs (bp) in length ("long"). The main cluster of short units was shown to be located on chromosome 1D in hexaploid wheat and is designated 5SDna-D1, while the cluster of long units was shown to be on chromosome 5D and is designated 5SDna-D2. The chromosomal locations in hexaploid wheat most likely correspond to those in T. tauschii and this could be shown directly for the 5SDna-D2 locus by using a T. tauschii 5D substitution in 'Chinese Spring' wheat. The sequence alignment of units derived from 5SDna-D1 and 5SDna-D2 revealed three apparent deletions in the noncoding spacer region, which were fixed in units from 5SDna-D1, and one deletion, which was fixed in units from 5SDna-D2. A minor size class, 400 bp long and closely related to the units from 5SDna-D1, was found in 2 of 415 accessions surveyed. A continuous range of quantitative changes in the number of 5S DNA units at the two loci was evident with up to a 10-fold relative abundance level of units being found in some accessions. Triticum tauschii var. typica was particularly noteworthy in that many accessions showed more units at 5SDna-D2 relative to 5SDna-D1. Partial thermal dissociation experiments with radioactive probes, synthesized from either the short or long 5S DNA units, hybridized to genomic DNA showed that the population of units at the respective loci were relatively homogeneous and clearly distinct from each other.(ABSTRACT TRUNCATED AT 250 WORDS)

A second locus for the 5S multigene family in Secale L.: sequence divergence in two lineages of the family

The 5S RNA genes in Secale sp. are arranged as tandem arrays of a 460- and 480-bp repeating sequence. These size classes were initially discovered by restriction endonuclease analysis using BamHI and subsequently by DNA sequencing of cloned units. The length variation between short and long units originated from major deletion–insertion events in the noncoding spacer region of the 5S DNA repeat units. In situ hybridization with [3H]cRNA and biotin-labelled probes synthesized from both the short and long 5S DNA units of S. cereale localized the sites on chromosome 1R and a new site on a chromosome identified as 5R. We propose that the chromosome 1R locus, which has been mapped previously, be named 5SDna-R1 and the second locus, reported in the present paper, be referred to as 5SDna-R2. A preferential hybridization of a probe from the long unit to the 5SDna-R2 locus and of a probe from the short unit to the 5SDna-R1 locus is reported. The clustering of long units in the 5SDna-R2 locus was confirmed by restriction endonuclease digestion of DNA from rye chromosome 5R additions to wheat. Nucleotide sequence alignment of 5S DNA repeat units from a number of Secale species, using both phenetic and cladistic computer programmes, demonstrated that two clear lineages corresponding to the long and short units existed in this genus. The different Secale species could not be unambiguously differentiated using the 5S DNA sequences.Key words: Secale, 5S multigene family, restriction mapping, molecular evolution.

A second locus for the 5S multigene family in Secale L.: sequence divergence in two lineages of the family

The 5S RNA genes in Secale sp. are arranged as tandem arrays of a 460- and 480-bp repeating sequence. These size classes were initially discovered by restriction endonuclease analysis using BamHI and subsequently by DNA sequencing of cloned units. The length variation between short and long units originated from major deletion-insertion events in the noncoding spacer region of the 5S DNA repeat units. In situ hybridization with [3H]cRNA and biotin-labelled probes synthesized from both the short and long 5S DNA units of S. cereale localized the sites on chromosome 1R and a new site on a chromosome identified as 5R. We propose that the chromosome 1R locus, which has been mapped previously, be named 5SDna-R1 and the second locus, reported in the present paper, be referred to as 5SDna-R2. A preferential hybridization of a probe from the long unit to the 5SDna-R2 locus and of a probe from the short unit to the 5SDna-R1 locus is reported. The clustering of long units in the 5SDna-R2 locus was confirmed by restriction endonuclease digestion of DNA from rye chromosome 5R additions to wheat. Nucleotide sequence alignment of 5S DNA repeat units from a number of Secale species, using both phenetic and cladistic computer programmes, demonstrated that two clear lineages corresponding to the long and short units existed in this genus. The different Secale species could not be unambiguously differentiated using the 5S DNA sequences.

DNA analyses in wheat breeding

A simplified procedure of sample preparation for the isolation of DNA (accessible to restriction fragment length polymorphism, RFLP, mapping) from wheat leaf material is presented. The procedure utilizes a sap extractor and approximately 500 samples can be processed in 1 week. The ability to handle this number of samples makes it feasible to interact with a plant breeding programme when a particularly valuable DNA marker is available. Three examples of analysing large populations are presented to demonstrate the application of the modified procedure to isolating DNA from wheat leaves.Key words: techniques, restriction fragment length polymorphism, genomic DNA isolation.

The direct measurement of ribosomal RNA gene activity in wheat–rye hybrids

Cloned rDNA segments, from wheat (Triticum aestivum) and rye (Secale cereale), which included the entire spacer region plus parts of the flanking 18S and 26S rRNA genes, were used to assay transcripts formed in the nuclei from wheat–rye hybrids. The tetraploid triticales (× Triticosecale Wittmack) carrying a complete rye chromosome complement and a combination of wheat chromosomes, as well as wheat and rye per se, were studied. Nuclei isolated from young leaves were incubated in the presence of [32P]UTP for 10 min, after which the total RNA was isolated. Hybridization of this radioactive RNA to the cloned rDNA segments showed that the suppression of rye NOR activity, measured cytologically, can be directly related to a major reduction in rRNA synthesis.Key words: NOR suppression, RNA transcripts, isolated nuclei.

The molecular-cytogenetic analysis of grasses and its application to studying relationships among species of the Triticeae

An analysis of four species from the genus Secale, including the study of different accessions, has shown that the properties of DNA clones of monomer units from three repeated sequence loci, namely, Ter, Nor, and 5S DNA, proved to be representative of the entire loci from which they were isolated. This finding in Secale species, including the discovery of a new locus for 5S DNA on chromosome 5R, has been used to interpret information on the Ter, Nor, and 5S DNA loci from 15 species in the Triticeae complex. The evolutionary relationship among species suggested by the DNA sequence data has shown many consistencies with a number of other characters such as those used in classical systematics, as well as geographical distribution data and isozyme and chromosome-pairing studies. Apparent inconsistencies such as a close relationship between the R and P genomes at the Ter loci are interpreted in terms of amplification-deletion phenomena known to occur at repetitive sequence loci. In addition, this study included species endemic to Australia and thus provided a broad time span in which to consider some features of repeated sequence family evolution, such as the conservation of certain parts of 5S DNA spacer regions.

Characterization of a potential source of barley yellow dwarf virus resistance for wheat

Resistance to barley yellow dwarf virus (BYDV) has been described in lines derived from crosses between wheat and Thinopyrum intermedium. The resistance in one such line, Zhong 4, originating in China, was expressed against two different serotypes of BYDV as measured by accumulation of virus in infected seedlings. F1 hybrids between wheat (2n = 42) and Zhong 4 (2n = 56) had 49 chromosomes and intermediate levels of virus when compared to the parent lines. Cytological and molecular hybridization studies suggested that the BYDV resistance in Zhong 4 is carried on a set of seven pairs of nonwheat chromosomes that derived from a combination of the E and X genomes present in Th. intermedium.Key words: Barley yellow dwarf virus, wheat, ribosomal DNA, Agropyron intermedium, Thinopyrum intermedium, virus resistance.