Comparison of morphological traits and molecular markers to analyse diversity and structure of alfalfa (Medicago sativa L.) cultivars

Diversity and structure of populations may differ substantially between morphological traits and molecular markers. Explanations of such discrepancies are crucial for further progress in breeding as well as for the maintenance of genetic resources. Our objective was to compare indices of among-cultivars differentiation for morphological traits (QST) and molecular markers (FST) in alfalfa (Medicago sativa), a legume forage species. Ten cultivars representing the Northern and Southern types commonly grown in Europe were investigated. For each cultivar, 40 genotypes were analysed with 16 SSR markers and four morphological traits measured in two locations and several cuts. QST values were in general high (0.02–0.39) compared to the differentiation observed with molecular markers (FST = 0.01), especially for growth habit, indicating that morphological traits were more efficient to structure the diversity than molecular markers. For morphological traits, a clear separation of Northern and Southern cultivars was observed, whereas for molecular markers, no clear structure was detected. Nevertheless, the grazing type cultivar Luzelle was separated from the rest of the cultivars for both morphological traits and molecular markers. Although pairwise differences between cultivars were significant for both morphological traits and molecular markers, the main part of the variation was found within cultivars. This large within-cultivar variation may be explained, besides the outcrossing reproductive mode and autotetraploid genetics, by the recent history of M. sativa domestication in Europe and the frequent seed exchanges. Selection for morphological traits (QST > FST) was achieved without modification of within-cultivar neutral diversity