Katrien M. Devos

‘Green revolution’ genes encode mutant gibberellin response modulators

World wheat grain yields increased substantially in the 1960s and 1970s because farmers rapidly adopted the new varieties and cultivation methods of the so-called ‘green revolution’. The new varieties are shorter, increase grain yield at the expense of straw biomass, and are more resistant to damage by wind and rain,. These wheats are short because they respond abnormally to the plant growth hormone gibberellin. This reduced response to gibberellin is conferred by mutant dwarfing alleles at one of two Reduced height-1 (Rht-B1 and Rht-D1) loci,. Here we show that Rht-B1/Rht-D1 and maize dwarf-8 (d8), are orthologues of the Arabidopsis Gibberellin Insensitive (GAI) gene,. These genes encode proteins that resemble nuclear transcription factors and contain an SH2-like domain, indicating that phosphotyrosine may participate in gibberellin signalling. Six different orthologous dwarfing mutant alleles encode proteins that are altered in a conserved amino-terminal gibberellin signalling domain. Transgenic rice plants containing a mutant GAI allele give reduced responses to gibberellin and are dwarfed, indicating that mutant GAI orthologues could be used to increase yield in a wide range of crop species.

Cereal Genome Evolution: Grasses, line up and form a circle

The genomes of six major grass species can be aligned by dissecting the individual chromosomes into segments and rearranging these linkage blocks into highly similar structures.

Genome Relationships: The Grass Model in Current Research

Ten years ago, with the advent of comparative mapping, a new tool became available to plant geneticists. Comparative genome analyses demonstrated that gene orders among related plant species remained largely conserved over millions of years of evolution. This finding has revolutionized our thinking

Reference Genome Sequence Of The Model Plant Setaria

We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

Chromosomal rearrangements in the rye genome relative to that of wheat

SummaryAn RFLP-based genetic map of Secale Cereale has provided evidence for multiple evolutionary translocations in the rye genome relative to that of hexaploid wheat. DNA clones which have previously been mapped in wheat indicated that chromosome arms 2RS, 3RL, 4RL, 5RL, 6RS, 6RL, 7RS and 7RL have all been involved in at least one translocation. A possible evolutionary pathway, which accounts for the present day R genome relative to the A, B and D genomes of wheat, is presented. The relevance of these results for strategies designed to transfer useful genes from rye, and probably other related species, to wheat is discussed.

The use of random amplified polymorphic DNA markers in wheat.

SummaryAn evaluation was made of the use of random amplified polymorphic DNA (RAPD) as a genetic marker system in wheat. Reproducible amplification products were obtained from varietal, homozygous single chromosome recombinant line and wheat/alien addition line genomic DNA with selected primers and rigorously optimized reaction conditions. Factors influencing the RAPD patterns are DNA concentration, Mg2+ concentration, polymerase concentration and denaturing temperature. In wheat, the non-homoeologous, non-dose responsive and dominant behaviour of RAPD products devalues their use as genetic markers for the construction of linkage maps, and the high probability that the amplified fragments derive from repetitive DNA limits their use as a source of conventional RFLP probes. However, RAPD markers will most certainly find many applications in the analysis of genotypes where single chromosomes or chromosome segments are to be manipulated.

Structural evolution of wheat chromosomes 4A, 5A, and 7B and its impact on recombination

The construction of comparative genetic maps of chromosomes 4Am and 5Am of Triticum monococcum and chromosomes of homoeologous groups 4, 5 and 7 of T. aestivum has provided insight into the evolution of these chromosomes. The structures of chromosomes 4A, 5A and 7B of modern-day hexaploid bread wheat can be explained by a 4AL/5AL translocation that occurred at the diploid level and is present both in T. monococcum and T. aestivum. Three further rearrangements, a 4AL/7BS translocation, a pericentric inversion and a paracentric inversion, have taken place in the tetraploid progenitor of hexaploid wheat. These structural rearrangements and the evolution of chromosomes 4A, 5A and 7B of bread wheat are discussed. The presence of the 4AL/5AL translocation in several Triticeae genomes raises two questions — which state is the more primitive, and is the translocation of mono- or poly-phylogenetic origin?The rearrangements that have occurred in chromosome 4A resulted in segments of both arms having different positions relative to the telomere, compared to 4Am and to 4B and 4D. Comparisons of map length in these regions indicate that genetic length is a function of distance from the telomere, with the distal regions showing the highest recombination.

RFLP-based genetic map of the homoeologous group 3 chromosomes of wheat and rye

SummaryGenetic maps of chromosomes 3A, 3B and 3D of wheat and 3R of rye were developed using 22 DNA probes and two isozyme marker systems. Analysis of the 49 loci mapped showed extreme clustering around the centromere in all four maps, with large ‘gaps’ in the distal chromosome regions, which is interpreted as being due to strong localisation of recombination towards the ends of the wheat and rye chromosomes. In the centromeric regions gene orders are highly conserved between the three wheat genomes and the rye genome. However, the unpredictable behaviour of the DNA clones that map in distal chromosome locations may indicate that the genomes are diverging most rapidly in the regions of higher recombination. A comparison of cDNA and genomic probes showed the latter to be much more efficient for revealing RFLP. Some classes of gDNA clones, i.e. chromosome-specific sequences and those hybridizing in a non-homoeologous manner, were seen to be most polymorphic. Correlations between map locations and RFLP levels showed no clear relationship. In addition to anonymous DNA clones, the locations of known function clones, sedoheptulose-1,7-bisphosphatase (XSbp), carboxypeptidase I (XCxp1) and a bZIP protein (XEmbp), were ascertained along with those for two isozyme loci, Mal-1 and Est-5.

Comparative RFLP maps of the homoeologous group-2 chromosomes of wheat, rye and barley

SummaryGenetic maps of the homoeologous group-2 chromosomes were constructed, comprising 114 loci in wheat and 34 loci in rye. These include the genes coding for sucrose synthase, sedoheptulose-1,7-bisphosphatase, a bZIP protein (EmBP-1), a peroxidase and an abscisic acid-induced protein (#7). Overall, gene orders are highly conserved in the genomes of wheat, barley and rye, except for the distal ends of chromosome arms 2BS and 2RS, which are involved in interchromosomal, probably evolutionary, translocations. Clustering of loci in the centromeric regions of the maps, resulting from the concentration of recombination events in the distal chromosomal regions, is observed in wheat and rye, but not in barley. Furthermore, loci for which homoeoloci can be detected in rye and barley tend to lie in the centromeric regions of the maps, while non-homoeologous and wheat-specific loci tend to be more evenly distributed over the genetic maps. Mapping of the group-2 chromosomes in the intervarietal ‘Timgalen’ x ‘RL4137’ cross revealed that the T. timopheevi chromosome segment introgressed into chromosome 2B in ‘Timgalen’ is preferentially transmitted. Recombination is also greatly reduced in that segment.

Application of two microsatellite sequences in wheat storage proteins as molecular markers

In eukaryotes, tandem arrays of simple-sequence repeat sequences can find applications as highly variable and multi-allelic PCR-based genetic markers. In hexaploid bread wheat, a large-genome inbreeding species with low levels of RFLP, di- and trinucleotide tandem repeats were found in 22 published gene sequences, two of which were converted to PCR-based markers. These were shown to be genome-specific and displayed high levels of variation. These characteristics make them especially suitable for intervarietal breeding applications.