Genomic diversity of a world collection of proso millet (Panicum miliaceum L.) and genome wide association study for field and seed traits

The climate crisis threatens sustainability of crop production worldwide. Crop diversification may contribute to support food security while reducing the negative impacts of climate change. Proso millet (Panicum milaceum L.) is a minor cereal crop which holds potential for diversification and adaption to different environmental conditions. In this study, we assembled a world collection of proso millet consisting of 88 varieties and landraces to investigate its genomic and phenotypic diversity for seed traits, and to identify marker-trait associations (MTA).Sequencing of restriction-site associated DNA yielded 494 Million reads, deriving 2,412 high quality single nucleotide polymorphisms (SNPs) that were used to study the diversity in the collection and perform a genome wide association study (GWAS). SNP diversity revealed two main clusters separating accessions originating in Western Europe, Eastern Asia and Americas from accessions sampled in Southern Asia, Western Asia, and Africa. A Bayesian structure analysis reported four cryptic genetic groups, showing that landraces accessions had a significant level of admixture and that most of the improved proso millet materials clustered separately from landraces. The collection was highly diverse for seed traits, with color varying from white to dark brown and width spanning from 1.82 mm to 2.55 mm. A GWAS study considering seed traits and previously measured agronomic traits identified 13 MTAs.Using genomics and automated seed phenotyping, we elucidated phylogenetic relationships and phenotypic diversity in global millet. We identified MTAs for important plant and seed traits indicating the presence of alleles with potential for application in proso breeding programs.