Genetic drift, historic migration, and limited gene flow contributing to the subpopulation divergence in wild sea beet (Beta vulgaris ssp. maritima (L.) Arcang)

• Published in: PloS one 2024, Vol.19 (9), p.e0308626
• Main Authors: Tehseen, Muhammad Massub, Wyatt, Nathan A, Bolton, Melvin D, Fugate, Karen K, Preister, Lisa S, Yang, Shengming, Ramachandran, Vanitharani, Li, Xuehui, Chu, Chenggen
• Format: Article
• Language: English
• Subjects: Atlantic Ocean; Beta vulgaris; Beta vulgaris - genetics; Cluster analysis; Coasts; Crops; Cultivars; Diversity indices; Domestication; Drift estimation; Evolution; Force distribution; Gene Flow; Genetic diversity; Genetic Drift; Genetic testing; Genetic Variation; Genomes; Genotype & phenotype; Germplasm; Information processing; Mediterranean Sea; Missing data; Nucleotides; Oceans; Phylogenetics; Polymorphism, Single Nucleotide; Sea currents; Single-nucleotide polymorphism; Subpopulations; Sugar beets
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0308626

Cultivated beet (Beta vulgaris L. ssp. vulgaris) originated from sea beet (B. vulgaris ssp. maritima (L.) Arcang), a wild beet species widely distributed along the coasts of the Mediterranean Sea and Atlantic Ocean, as well as northern Africa. Understanding the evolution of sea beet will facilitate its efficient use in sugarbeet improvement. We used SNPs (single nucleotide polymorphisms) covering the whole genome to analyze 599 sea beet accessions collected from the north Atlantic Ocean and Mediterranean Sea coasts. All B. maritima accessions can be grouped into eight clusters with each corresponding to a specific geographic region. Clusters 2, 3 and 4 with accessions mainly collected from Mediterranean coasts are genetically close to each other as well as to Cluster 6 that contained mainly cultivated beet. Other clusters were relatively distinct from cultivated beets with Clusters 1 and 5 containing accessions from north Atlantic Ocean coasts, Clusters 7 and Cluster 8 mainly have accessions from northern Egypt and southern Europe, and northwest Morocco, respectively. Distribution of B. maritima subpopulations aligns well with the direction of marine currents that was considered a main dynamic force in spreading B. maritima during evolution. Estimation of genetic diversity indices supported the formation of B. maritima subpopulations due to local genetic drift, historic migration, and limited gene flow. Our results indicated that B. maritima originated from southern Europe and then spread to other regions through marine currents to form subpopulations. This research provides vital information for conserving, collecting, and utilizing wild sea beet to sustain sugarbeet improvement.