Genetic diversity and population structure in Ethiopian mustard (Brassica carinata A. Braun) revealed by high-density DArTSeq SNP genotyping.

Abstract

Background: Ethiopian mustard (Brassica carinata (A) Braun) is a promising oilseed crop with the potential for sustainable biofuel and bio-industrial applications. Despite the presence of diverse germplasms in Ethiopia, their genetic diversity remains largely unexplored. This study evaluated the genetic diversity and population structure of 188 B. carinata genotypes using high-density Single Nucleotide Polymorphism (SNP) markers generated though DArTseq™ Genotyping-by-Sequencing (GBS). Of the 15,515 identified DArTSeq SNPs, 3,793 high-quality markers were retained and used to analyze the genetic diversity and population structure.

Results: The results from STRUCTURE, principal coordinate analysis (PCoA), and neighbor-joining tree analyses revealed two slightly distinct subpopulations, with Pop1 predominantly comprising genotypes from the Oromia and Amhara regions (86.17%), whereas Pop2 primarily consisted of released varieties, suggests the influence of targeted selection. Despite the presence of subpopulations, PCoA indicated a relatively limited overall genetic diversity among the genotypes. Analysis of Molecular Variance (AMOVA) revealed higher genetic variation within populations (65.19%) than between populations (34.81%), resulting in low genetic differentiation (PhiPT = 0.02) and high gene flow (Nm = 5.74). Notably, subpopulation formation was not strongly correlated with geographical origin, highlights that factors beyond geography, such as gene flow and selection pressure, may have played a significant role in shaping the observed genetic diversity. Genetic diversity indices revealed a slightly low-to-moderate variation within the B. carinata populations, as evidenced by the slightly low expected heterozygosity (He = 0.21) and moderate polymorphic information content (PIC = 0.36).

Conclusion: Overall, this study revealed a moderate level of genetic diversity within the evaluated B. carinata genotypes. The results offer valuable insights into the genetic structure of this species and highlight the need for targeted strategies to enhance genetic diversity in future breeding initiatives and conservation efforts.