Assessment of the genetic structure and diversity of arracacha (Arracacia xanthorrhiza) using genotyping-by-sequencing

Abstract

Arracacha, also known as “Peruvian carrot”, is a native crop from the Andean region, and is considered an unexplored root. To date, studies on this crop were mainly focused at the morphological and agronomic level. However, its genetics remains unclear. Today it is feasible to study the genetic composition of this Andean root by next-generation sequencing techniques such as genotyping-by-sequencing (GBS). We here for the first time employed 183 accessions of arracacha from six Andean localities of Peru and identified 8976 SNP markers. STRUCTURE analysis revealed this Andean crop is clustered into four populations, and with few accessions intermingled. A dendrogram was generated using the UPGMA clustering algorithm, and, similar to the principal coordinate analysis (PCoA), it showed four groups. Genetic diversity estimation was conducted considering the four populations identified, revealing very high expected heterozygosity (0.432). AMOVA revealed the greatest variation within populations (89.66%) and indicated that variability between populations is 10.34%. Population divergence (Fst) ranged from 0.02 (cluster 1 vs. cluster 3) to 0.036 (cluster 1 vs. cluster 4). Negative Fis values were also detected for all populations of arracacha, indicating it depends on cross-pollination. We hope this work stimulates the development of additional molecular tools for this orphan crop in order to establish a modern breeding program and conservation strategies of this important Andean crop.