Population structure and long-range linkage disequilibrium in a durum wheat elite collection.

A collection of 134 durum wheat accessions comprising worldwide modern varieties and a number of founders was assembled and characterised with 70 SSRs for genetic diversity and level of background linkage disequilibrium (LD). Results of both a distance-based and a Bayesian model-based cluster analysis highlighted the high level of subdivision (stratification) present in the elite durum wheat germplasm. In the model-based analysis, high probabilities of data were obtained setting from six to eight hypothetical subpopulations. AMOVA was used to test for significance of the molecular variance component explained by the origin of materials and for evaluating the level of differentiation present among and within the six main durum gene pools represented. Considering the germplasm as a whole, LD statistics indicated the presence of a very high average level of background LD, both in syntenic and nonsyntenic locus pairs: D’ (an LD measure) averaged 0.67 for marker pairs less than 10 cM apart and 0.43 for pairs with a 10-20 cM distance; in the whole germplasm set, LD between independent markers still remained high, with significant LD found in 54% and 38% of the SSR pairs at P 0.01 and 0.001 levels, respectively. The effect of germplasm structure on LD was accounted for by re-evaluating LD within each of the three main subgroups identified by structure analysis. In such case, the LD level remained high for tightly to moderately linked locus pairs (0-20 cM), but was greatly reduced in the independent locus pairs.