The barley Genome and its Relationship with the Wheat Genomes. A Survey with an Internationally Agreed Recommendation for Barley Chromosome Nomenclature

Molecular cloning of three homoeologous cDNAs encoding orthologs of the maize KNOTTED1 homeobox protein from young spikes of hexaploid wheat

The plant knotted1 (kn1)-like homeobox genes are known to play important roles in the maintenance of shoot apical meristem (SAM), determination of cell fate and differentiation of vegetative tissues. To study structural diversity of the three homologous loci encoding a KN1-like homeobox protein in the hexaploid wheat genome, we isolated clones from a cDNA library of young spikes of Japanese common wheat cultivar 'Norin 26'. Three different but highly homologous cDNAs were isolated and their sequences were determined. The mean homology of the deduced amino acid sequences was 96% as compared to the barley ortholog KNOX3. The wheat kn1-like homeobox proteins named WKNOX1 are encoded by a single set of homologous genes on the homologous group 4 chromosomes in the three component genomes of common wheat, i.e. 4A, 4B and 4D. The nucleotide sequence data and the Southern blot pattern suggested that the three homologous loci of wknox1 genes are highly conserved through polyploid evolution of wheat. They were expressed in SAM-containing shoots and young spikes but not in developed leaves, glumes and lemmas and callus tissues. The ectopic expression of the wknox1 was observed in lemma of wheat Hooded (Hd) mutants. The result suggested that the Hd gene is a dominant allele of the wknox1 locus on chromosome 4A.

The 5S rRNA gene diversity in Kengyilia rigidula (Keng and S.L. Chen) J.L. Yang, Yen, and Baum (Poaceae: Triticeae): possible contribution of the H genome to the origin of Kengyilia

Fifty-three units of 5S rDNA sequences from five accessions of Kengyilia rigidula, a member of the tribe Triticeae that also includes wheat, barley, rye, and their wild relatives, have been amplified by the polymerase chain reaction (PCR), cloned, and sequenced. The genome of K. rigidula consists of three haplomes, St, P, and Y. An evaluation of the aligned sequences of the diverse 53 different 5S DNA units yielded three 5S-unit classes. One unit class, Long S1, was assignable to the St haplome, one unit class, the Long P1, was assignable to the P haplome, and a third unit class, Long H1, was assignable to the H haplome. The last was expected to be assignable to the Y haplome, based on previous knowledge. Evolutionary scenarios are put forward to explain this finding. Among those possibilities is that the number of copies of units assignable to the Y haplome is very small and difficult to detect. Short units, reported earlier in K. alatavica, were not found in K. rigidula.

Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints

We have developed a new technique for the physical mapping of barley chromosomes using microdissected translocation chromosomes for PCR with sequence-tagged site primers derived from >300 genetically mapped RFLP probes. The positions of 240 translocation breakpoints were integrated as physical landmarks into linkage maps of the seven barley chromosomes. This strategy proved to be highly efficient in relating physical to genetic distances. A very heterogeneous distribution of recombination rates was found along individual chromosomes. Recombination is mainly confined to a few relatively small areas spaced by large segments in which recombination is severely suppressed. The regions of highest recombination frequency (</=1 Mb/cM) correspond to only 4.9% of the total barley genome and harbor 47.3% of the 429 markers of the studied RFLP map. The results for barley correspond well with those obtained by deletion mapping in wheat. This indicates that chromosomal regions characterized by similar recombination frequencies and marker densities are highly conserved between the genomes of barley and wheat. The findings for barley support the conclusions drawn from deletion mapping in wheat that for all plant genomes, notwithstanding their size, the marker-rich regions are all of similar gene density and recombination activity and, therefore, should be equally accessible to map-based cloning.

The 5S rRNA gene in wall barley (Hordeum murinum L. sensu lato): sequence variation among repeat units and relationship to the Y haplome in the genus Hordeum (Poaceae: Triticeae)

The molecular diversity of the 5S rDNA units in 13 accessions of wall barley, which include Hordeum murinum, H. leporinum, and H. glaucum, is reported. Our analyses, based on 54 sequenced clones, indicate the presence of two sequence classes not previously seen in other barley species; namely, the long Y1 unit class and the short Y1 unit class. In addition, the accumulation of new sequence information has allowed us to refine previous groups. Using these new results, along with previously published work, we present a summary of all the unit classes described to date and potential correspondences between 5S rDNA unit classes and haplomes identified previously. In H. murinum, we found the long H1 and long X2 unit classes, and in one of six accessions referable to H. glaucum we found the unique short Y1 unit class. Our cladistic analyses, using orthologous sequences, provide support for the current model for the relationships among several species within the Triticeae.

Mutants and duplication in chromosome 7 (syn. 5H) in the barley line HA21: duplications may enhance QTLs and serve to make constant linear cis-heterozygosity

Cytological and linkage data indicate a duplication in the short arm of chromosome 7 (syn. 5H) in the mutant line HA21 (barley, Hordeum vulgare, cv. 'Pirkka'). The associated mutant (ha21) shows a weighted average linkage of 22.1 cM with pld, hitherto an ignored anthocyaninless gene, of cv. Pirkka. Some crosses produce F2 segregants with an exaggerated ha21 phenotype which may represent position effect or increased dosage of the mutant gene through recombination. Compared with cv. Pirkka, HA21 has changes in grain chemistry (alpha- and beta-amylase, beta-glucanase), which may be caused by changed QTL dosage or QTL position effect due to duplication. The use of duplication in creating constant +m/+ m or m+/m+ linear cis-heterozygotes is suggested. Linear cis-heterozygotes may produce stable heterosis or attenuate the undesired effects of drastic mutants.

Identification of individual barley chromosomes based on repetitive sequences: conservative distribution of Afa-family repetitive sequences on the chromosomes of barley and wheat

The Afa-family repetitive sequences were isolated from barley (Hordeum vulgare, 2n = 14) and cloned as pHvA14. This sequence distinguished each barely chromosome by in situ hybridization. Double color fluorescence in situ hybridization using pHvA14 and 5S rDNA or HvRT-family sequence (subtelomeric sequence of barley) allocated individual barley chromosomes showing a specific pattern of pHvA14 to chromosome 1H to 7H. As the case of the D genome chromosomes of Aegilops squarrosa and common wheat (Triticum aestivum) hybridized by its Afa-family sequences, the signals of pHvA14 in barley chromosomes tended to appear in the distal regions that do not carry many chromosome band markers. In the telomeric regions these signals always placed in more proximal portions than those of HvRT-family. Based on the distribution patterns of Afa-family sequences in the chromosomes of barley and D genome chromosomes of wheat, we discuss a possible mechanism of amplification of the repetitive sequences during the evolution of Triticeae. In addition, we show here that HvRT-family also could be used to distinguish individual barley chromosomes from the patterns of in situ hybridization.