Abstract
Garlic (Allium sativum) is used worldwide in cooking and industry, including pharmacology/medicine and cosmetics, for its interesting properties. Identifying redundancies in germplasm blanks to generate core collections is a major concern, mostly in large stocks, in order to reduce space and maintenance costs. Yet, similar appearance and phenotypic plasticity of garlic varieties hinder their morphological classification. Molecular studies are challenging, due to the large and expected complex genome of this species, with asexual reproduction. Classical molecular markers, like isozymes, RAPD, SSR, or AFLP, are not convenient to generate germplasm core-collections for this species. The recent emergence of high-throughput genotyping-by-sequencing (GBS) approaches, like DArTseq, allow to overcome such limitations to characterize and protect genetic diversity. Therefore, such technology was used in this work to: (i) assess genetic diversity and structure of a large garlic-germplasm bank (417 accessions); (ii) create a core collection; (iii) relate genotype to agronomical features; and (iv) describe a cost-effective method to manage genetic diversity in garlic-germplasm banks. Hierarchical-cluster analysis, principal-coordinates analysis and STRUCTURE showed general consistency, generating three main garlic-groups, mostly determined by variety and geographical origin. In addition, high-resolution genotyping identified 286 unique and 131 redundant accessions, used to select a reduced size germplasm-bank core collection. This demonstrates that DArTseq is a cost-effective method to analyze species with large and expected complex genomes, like garlic. To the best of our knowledge, this is the first report of high-throughput genotyping of a large garlic germplasm. This is particularly interesting for garlic adaptation and improvement, to fight biotic and abiotic stresses, in the current context of climate change and global warming.
Highlights
Garlic (Allium sativum) is a plant producing an edible bulb, made of storage leaves known as cloves
DArTseq is a cost-effective genotyping tool for creating and maintaining germplasm banks, allowing to properly ascertain, manage and maintain available biodiversity
We have significantly reduced the analyzed garlic germplasmbank size, identifying redundant accessions and generating a unique core collection, with the consequent reduction in space and maintenance expenses
Summary
Garlic (Allium sativum) is a plant producing an edible bulb, made of storage leaves known as cloves. It is of Asian origin, being Allium longicuspis considered its wild ancestor. Cloves must be reproduced every year, since they cannot be stored for longer periods and germinated, as happens with standard botanical seeds. Such peculiarity adds extra cost and inconvenience to its maintenance, mainly for large germplasm collections. The peculiar garlic reproduction could lead to low genome diversity, since meiosis is not involved in its clonal reproduction by vegetative propagation (Kamenetsky et al, 2015). Transposable elements are involved in the evolution of this species
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