A set of 41 wheat microsatellite markers (WMS), giving 42 polymorphic loci (two loci on each chromosome), was used to describe genetic diversity in a sample of 559 French bread wheat accessions (landraces and registered varieties) cultivated between 1800 and 2000. A total of 609 alleles were detected. Allele number per locus ranged from 3 to 28, with a mean allele number of 14.5. On the average, about 72% of the total number of alleles were observed with a frequency of less than 5% and were considered to be rare alleles. WMS markers used showed different levels of gene diversity: the highest PIC value occurred in the B genome (0.686) compared to 0.641 and 0.659 for the A and D genomes, respectively. When comparing landraces with registered varieties gathered in seven temporal groups, a cluster analysis based on an F(st) matrix provided a clear separation of landraces from the seven variety groups, while a shift was observed between varieties registered before and after 1970. There was a decrease of about 25% in allelic richness between landraces and varieties. In contrast, when considering only registered varieties, changes in diversity related to temporal trends appeared more qualitative than quantitative, except at the end of the 1960s, when a bottleneck might have occurred. New varieties appear to be increasingly similar to each other in relation to allelic composition, while differences between landraces are more and more pronounced over time. Finally, considering a sub-sample of 193 varieties representative of breeding material selected during the twentieth century by the six most important plant breeding companies, few differences in diversity were observed between the different breeding programmes. The observed structure of diversity in French bread wheat collections is discussed in terms of consequences, both for plant breeders and for managers of crop genetic resources.

Bread wheat (Triticum aestivum), one of the world's major crops, is genetically very diverse. In order to select a representative sample of the worldwide wheat diversity, 3,942 accessions originating from 73 countries were analysed with a set of 38 genomic simple sequence repeat (SSR) markers. The number of alleles at each locus ranged from 7 to 45 with an average of 23.9 alleles per locus. The 908 alleles detected were used together with passport data to select increasingly large sub-samples that maximised both the number of observed alleles at SSR loci and the number of geographical origins. A final core of 372 accessions (372CC) was selected with this M strategy. All the different geographical areas and more than 98% of the allelic diversity at the 38 polymorphic loci were represented in this core. The method used to build the core was validated, by using a second set of independent markers [44 expressed sequence tag (EST)-SSR markers] on a larger sample of 744 accessions: 96.74% of the alleles observed at these loci had already been captured in the 372CC. So maximizing the diversity with a first set of markers also maximised the diversity at a second independent set of locus. To relate the genetic structure of wheat germplasm to its geographical origins, the two sets of markers were used to compute a dissimilarity matrix between geographical groups. Current worldwide wheat diversity is clearly divided according to wheat's European and Asian origins, whereas the diversity within each geographical group might be the result of the combined effects of adaptation of an initial germplasm to different environmental conditions and specific breeding practices. Seeds from each accession of the 372CC were multiplied and are now available to the scientific community. The genomic DNA of the 372CC, which can be entirely contained in a 384-deep-well storage plate, will be a useful tool for future studies of wheat genetic diversity.

A highly polymorphic core collection of bread wheat and a more narrow-based breeding material, gathered from pedigrees of seven modern cultivars, was analysed in order to compare genetic diversity indices and linkage disequilibrium (LD) patterns along the chromosome 3B with microsatellite (SSR) and Diversity Arrays Technology markers. Five ancestral gene pools could be identified within the core collection, indicating a strong geographical structure (Northwest Europe, Southeast Europe, CIMMYT-ICARDA group, Asia, Nepal). The breeding material showed a temporal structure, corresponding to different periods of breeding programmes [old varieties (from old landraces to 1919), semi-modern varieties (1920-1959), modern varieties (1960-2006)]. Basic statistics showed a higher genetic diversity in the core collection than in the breeding material, indicating a stronger selection pressure in this latter material. More generally, the chromosome 3B had a lower diversity than the whole B-genome. LD was weak in all studied materials. Amongst geographical groups, the CIMMYT-ICARDA pool presented the longest ranged LD in contrast to Asian accessions. In the breeding material, LD increased from old cultivars to modern varieties. Genitors of seven modern cultivars were found to be different; most marker pairs in significant LD were observed amongst genitors of Alexandre and Koreli varieties, indicating an important inbreeding effect. At low genetic distances (0-5 cM), the breeding material had higher LD than the core collection, but globally the two materials had similar values in all classes. Marker pairs in significant LD are generally observed around the centromere in both arms and at distal position on the short arm of the chromosome 3B.

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Seven Triticum aestivum (cv. Moisson)-Aegilops ventricosa addition lines and four VPM-1 lines were studied by C-banding, and compared with the parental common wheat cultivars Marne-Desprez (hereafter Marne), Moisson, and A. ventricosa lines 10 and 11. All of the VPM-1 lines had similar C-banding patterns and carried the same major 5B:7B translocation as the parental Marne cultivar. According to the C-banding analysis, the VPM-1 lines carry a complete 7D(7D(v)) chromosome substitution and a translocation involving the 5D and 5D(v) chromosomes. However, the translocation of the 2N(v)/6N(v) chromosome of A. ventricosa to the short arm of the 2A chromosome of wheat that had been identified in an earlier study using molecular analysis (Bonhomme A, Gale MD, Koebner RMD, Nicolas P, Jahier J, Bernard M in Theor Appl Genet 90:1042-1048, 1995; Jahier J, Abelard P, Tanguy AM, Dedryver F, Rivoal R, Khatkar S, Bariana HS Plant Breed 120:125-128, 2001) was not detected in our study. However, the appearance of a small pAs1 site at the tip of the chromosome 2A short arm in VPM-1 could be indicative of a minor translocation of the A. ventricosa chromosome. The 5B:7B translocation was also found in all seven T. aestivum-A. ventricosa addition lines, although it was not present in the parental common wheat cultivar Moisson. These lines showed different introgression patterns; besides the addition of the five N(v)-genome chromosomes, they also possessed different D(D(v)) genome substitutions or translocations. A whole arm translocation between chromosome 1N(v) and 3D(v) was identified in lines v86 and v137, and also in the A. ventricosa line 10. This observation lends further support to the idea that A. ventricosa line 10, rather than line 11, was used to develop a set of wheat A. ventricosa addition lines.