Genetic diversity of Niger onions (Allium cepa L.) assessed by simple sequence repeat markers (SSR)

Onion is the most important vegetable crop in Niger in terms of crop value. Niger has an enormous potential for production of onions and is also an important exporter. The principle type of grown onion is the pungent landrace 'Violet de Galmi', but farmers cultivate several onion landraces that have a brown, red, violet, white and yellow color in separate production areas. However the organization of genetic variation within and among landraces is poorly characterized. In this study, we analyzed variation among Niger onion landraces using simple sequence repeat (SSR) markers. The mean observed heterozygosity (H-o) within onion landraces from Niger is 0.400, while the expected heterozygosity (H-s) is 0.452. This apparent heterozygosity deficit was however due to the presence of null alleles, rather than to non-random mating within population. Among the 16 onion landraces, within population diversity was greater (90%) than between population diversity (10%). Bayesian clustering analyses fail to detect differentiated genetic clusters, indicating a globally weak level of differentiation. Nevertheless, Principal Coordinate analysis (PCoA) shows that genetic diversity was organized in a way consistent both with morphological traits and geography. Assignment tests also show that most of the onion landraces from Niger are original in terms of genetic composition. Our results highlight which landraces are most original genetically. These landraces deserve particular attention for ex situ and in situ conservation, which should contribute to the improvement of local onion in Niger.