Genetic Diversity of Field Pennycress (Thlaspi arvense) Reveals Untapped Variability and Paths Toward Selection for Domestication

• Published in: Agronomy (Basel) Vol. 9; no. 6; p. 302
• Main Authors: Frels, Katherine, Chopra, Ratan, Dorn, Kevin M., Wyse, Donald L., Marks, M. David, Anderson, James A.
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 01.06.2019
• Subjects: Agricultural practices; Bayesian analysis; Breeding; Cluster analysis; Cold weather; Collections; Cover crops; Domestication; Fatty acids; Genetic diversity; Genetic markers; genetic variation; Genomes; Genomics; Germplasm; Linkage disequilibrium; Microthlaspi; Nucleotides; pennycress; Plant breeding; Plant introductions; Population; Population genetics; Population structure; Principal components analysis; Pruning; Seeds; Single-nucleotide polymorphism; Thlaspi arvense; United States > US
• ISSN: 2073-4395; 2073-4395
• DOI: 10.3390/agronomy9060302

Evaluation of genetic diversity within wild populations is an essential process for improvement and domestication of new crop species. This process involves evaluation of population structure and individual accessions based on genetic markers, growth habits, and geographic collection area. In this study, accessions of field pennycress were analyzed to identify population structure and variation in germplasm available for breeding. A total of 9157 genome-wide single nucleotide polymorphisms (SNPs) were identified among the 121 accessions analyzed, and linkage disequilibrium based pruning resulted in 3497 SNPs. Bayesian cluster analysis was implemented in STRUCTURE v2.3.4 to identify four population groups. These groups were confirmed based on principal components analysis and geographic origins. Pairwise diversity among accessions was evaluated and revealed considerable genetic variation. Notably, a subset of accessions from Armenia with exceptional genetic variation was identified. This survey is the first to report significant genetic diversity among pennycress accessions and explain some of the phenotypic differences previously observed in the germplasm. Understanding variation in pennycress accessions will be a crucial step for selection, breeding, and domestication of a new cash cover crop for cold climates.