Genetic characterization of a global collection of common buckwheat to harness genetic resources for agricultural diversity

Abstract

Introduction Neglected and underutilized crops have great potential to diversify agroecosystems and human diets but require genetic improvement to make them economically viable alternatives to major crops. Common buckwheat (Fagopyrum esculentum Moench) is valued for its excellent nutritional quality, its ecological importance and its benefits on crop rotation and soil health. However, low and highly variable yields, along with uneven seed ripening, have limited the crop’s usage in farming systems, highlighting the need for improved varieties. The availability of genetic resources and detailed genetic characterization are prerequisites for efficient breeding strategies. Methods In this study, we elucidate the genetic diversity and phylogeography of a global germplasm collection comprising 170 common buckwheat accessions, including nine self-compatible accessions and eleven accessions with determinate growth habit. The collection was genetically characterized using double digest restriction-site associated DNA sequencing to generate accession-specific genome-wide allele frequency fingerprints (GWAFFs). Results Using accurate and repeatable GWAFFs based on 52,182 genome sites, an analysis of genetic admixture revealed seven subclusters within the collection. Our results show that common buckwheat accessions collected in specific regions of the world usually trace back to a single subcluster. Western Europe is an exception, as accessions from several different subcluster have been integrated into local cropping and food systems. Discussion These findings illustrate that most breeding programs for common buckwheat rely on only a fraction of the available genetic diversity. Therefore, the introduction of genetic material from different sources could increase the diversity of many local breeding programs. The precise genetic characterization of the collection with GWAFFs opens opportunities to apply modern breeding strategies such as genomics-assisted selection. True-to-type seed of 81 accessions of the collection were deposited in the Swiss National Gene Bank and are publicly available for cultivation and use in research and breeding.