Utilization of SSR and AFLP markers for the assessment of distinctness in durum wheat

Molecular techniques provide new possibilities to characterize advanced genetic materials for registration purposes and for the protection of breeders’ rights. The objective of this work was to compare the simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers with morphological descriptors, currently in use, for the assessment of variety distinctness in durum wheat. Fifty-six F8 or F9 lines or sublines at different levels of relatedness derived from four crosses, two BC1- and 11 BC3-derived lines, were characterized with 27 morphological traits, including 17 official Community Plant Variety Office (CPVO) descriptors, seven AFLP primer combinations, and 98 SSR primer pairs. The similarities based on all three marker classes reflected, on average, the degree of relatedness of the materials. However, molecular markers (MMs) and in particular SSRs produced classifications more closely representing the relationships among lines, allowing us to discriminate even tightly related genotypes that morphological descriptors failed to distinguish. The moderate correlations between similarities based on morphological and molecular data, and the wide range of MM differences corresponding to few or no morphological differences, imply that at present MMs should only be used as a complementary tool to assess distinctness. Based on these results, it seems that a set of 28 SSRs (one per chromosome arm) represents a useful prescreening tool to identify the entry pairs sufficiently different at MM level (≥13 polymorphisms) for which a field evaluation could be avoided, with relevant savings in resources and optimization of the field trial design.