M. D. Gale

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.

RFLP-based genetic maps of wheat homoeologous group 7 chromosomes

SummaryRestriction fragment length polymorphism (RFLP) mapping was attempted using 18 cDNA clones, 14 anonymous and 4 of known function, which had been shown to have homologous DNA sequences on the group 7 chromosomes of wheat. The loci identified by these probes have been mapped on one or more chromosomes in this homoeologous group using linkage data derived from various F2, random inbred, doubled haploid and single chromosome recombinant populations. The maps also include three isozyme loci, five disease resistance loci, two anthocyanin pigment loci and a vernalisation response locus. The mapping data have been used to determine the extent of map co-linearity over the A, B and D genomes, the degree of RFLP variability in the three genomes and the relative efficiency of various restriction enzymes in detecting RFLPs in wheat. The strategy for future mapping in wheat, particularly the use of “alien” genomes or segments, such as that from Aegilops ventricosa used here, is discussed.

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

Isolation and characterisation of microsatellites from hexaploid bread wheat

Abstract The development of large panels of simple-to-analyse genetic markers for tagging agronomically important genes and diversity studies in hexaploid bread wheat is an important goal in applied cereal genetic research. We have isolated and sequenced over 200 clones containing microsatellites from the wheat genome and have tested 153 primer pairs for genetic polymorphism using a panel of ten wheat varieties, including the parents of our main mapping cross. A subset comprising 49 primer pairs detects 76 loci, of which 74 can be unequivocably allocated to one of the wheat chromosomes. A relatively low frequency of the loci detected are from the D genome, and these loci show less polymorphism than those from the A and B genomes. Generally, the microsatellites show high levels of genetic polymorphism and an average of 3.5 alleles per locus with an average polymorphism information content (PIC), value of 0.51. The observed levels of polymorphism are positively correlated with the length of the microsatellite repeats. A high proportion, approximately two-thirds, of primer pairs designed to detect simple sequence repeat (SSR) variation in wheat do not generate the expected amplification products and, more significantly, often generate unresolvable PCR products. In general, our results agree closely with those obtained from other recent studies using microsatellites in plants.

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.

Optimizing wheat grain yield: effects of Rht (gibberellin-insensitive) dwarfing genes

Four sets of near-isogenic lines carrying different combinations of the alleles Rht-B1b , Rht-D1b and Rht-B1c for gibberellin-insensitive dwarfism in hexaploid wheat ( Triticum aestivum L. ) were compared with tall controls in a series of yield trials in eastern England and central Germany. In all four varietal backgrounds the effects of Rht-B1b and Rht-D1b were similar (plant height ≈ 86 and 83% of tall controls respectively) and in combination reduced plant height to c. 58%. The Rht-B1c allele caused more severe dwarfism ( c. 50%) and, when combined with Rht-D1b , reduced plant height still further to c. 41%. Data from the trials were consistent with a model for height/yield relationships in which the pleiotropic effects of the Rht alleles on yield can be inferred from their primary function: insensitivity to gibberellin limits stem extension growth, decreasing assimilate demand for this organ and diverting it to the developing ear (which is not itself dwarfed). The net balance between the resulting increase in harvest index and the curvilinear relationship observed between plant height and total shoot yield results in optimum grain yields at intermediate plant heights. Yield advantages of shorter plants over tall controls were evident over several trials with mean grain yields ranging from 200 to 760 g m −2 . The optimum plant height for yield improvement in different genetic backgrounds was achieved by different Rht alleles according to the background varietal height, such that intrinsically taller genotypes required more potent Rht alleles to achieve maximum potential grain yield. Ear yield components showed increases in grain number due to Rht pleiotropy, from which it is inferred that the number of grains per ear is limited by supply of assimilates pre-anthesis. Increases in grain number were associated with decreases in mean weight per grain which varied according to severity of dwarfism and varietal background, so that the net effect on grain yield per ear was sometimes positive, sometimes negative, and sometimes neutral in different Rht /variety combinations.

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.

Simple sequence repeat (SSR) markers survey of the cassava (Manihot esculenta Crantz) genome: towards an SSR-based molecular genetic map of cassava

Abstract The development of PCR-based, easily automated molecular genetic markers, such as SSR markers, are required for realistic cost-effective marker-assisted selection schemes. This paper describes the development and characterization of 172 new SSR markers for the cassava genome. The placement of 36 of these markers on the existing RFLP framework map of cassava is also reported. Two similar enrichment methods were employed. The first method yielded 35 SSR loci, for which primers could be designed, out of 148 putative DNA clones. A total of 137 primer pairs could be designed from 544 putative clones sequenced for the second enrichment. Most of the SSRs (95%) were di-nucleotide repeats, and 21% were compound repeats. A major drawback of these methods of SSR discovery is the redundancy – 20% duplication; in addition, primers could not be designed for many SSR loci that were too close to the cloning site – 45% of the total. All 172 SSRs amplified the corresponding loci in the parents of the mapping progeny, with 66% of them revealing a unique allele in at least one of the parents, and 26% having unique alleles in both of the parents. Of the 36 SSRs that have been mapped, at least 1 was placed on 16 out of the 18 linkage groups of the framework map, indicating a broad coverage of the cassava genome. This preliminary mapping of the 36 markers has led to the joining of a few small groups and the creation of one new group. The abundance of allelic bridges as shown by these markers will lead to the development of a consensus map of the male- and female-derived linkage groups. In addition, the relatively higher number of these allelic bridges, 30% as against 10% for RFLPs in cassava, underscores SSR as the marker of choice for cassava. The 100% primer amplification obtained for this set of primers also confirms the appropriateness of SSR markers for use in cassava genome analysis and the transferability of the technology as a low-cost approach to increasing the efficiency of cassava breeding. Current efforts are geared towards the generation of more SSR markers to attain a goal of 200 SSR markers, or 1 SSR marker every 10 cM.

Fifty new microsatellite loci for the wheat genetic map

Abstract Hexaploid bread wheat (Triticum aestivum) has low levels of RFLP. Simple sequence repeats, however, show high levels of polymorphism and are therefore especially useful in intervarietal breeding applications. We present 53 newly mapped microsatellite loci for the wheat genetic map, 41 primary loci and 12 additional loci from these same primer pairs. Markers have been accredited with a quality score on a scale of 1–5 which describes the complexity of the amplification product profile from each primer pair.

AFLP markers for the study of rice biodiversity

Abstract AFLP was used as a DNA fingerprinting technique in rice (Oryza sativa L.) germplasm analysis. The high efficiency and random coverage of AFLP markers were established. With only five combinations of primers and RFLP anchors, a framework linkage map was constructed. This map demonstrated that the AFLP markers from a limited number of primers were not confined to any particular regions or chromosomes in the rice genome. To analyse the biodiversity of 57 rice germplasm accessions, we examined 179 polymorphic AFLP markers generated from four primer combinations. Both principal component analysis and cluster analysis were used, and three groups were clearly identified which corresponded to genotypes of Isozyme Groups I, II and VI. The number of markers needed for robust classification of rice germplasm and the diversity between/within the groups was established.