Inter-Primer Binding Site (IPBS) Retrotransposon Markers Provide Insights Into the Genetic Diversity and Population Structure of Carrots (Daucus, Apiaceae)

Abstract

Studies of genetic diversity and population structure are essential as an initial step in conservation and breeding programs\rfor modern crops. Carrot (Daucus spp.) is among the ten most important vegetables worldwide, however, its genetic structure and\rphylogenetic relationships are not totally deciphered. Here, we explored the utility of 21 inter-primer binding site (iPBS) retrotransposon\rmarkers to determine the genetic diversity and population structure of 38 accessions of Daucus and one accession of a related genus. The\rmanual scoring revealed 309 bands based on their presence/absence. The dendrogram based on the UPGMA clustering algorithm and\ra principal coordinate analysis (PCoA) indicated the presence of four clusters. The Daucus species with 2n=18 chromosome (subclade\rA´) separated from the other two species D. pusillus and D. muricatus, which were positioned into two individual clusters. The other\rclade includes the Daucus from the B group. It was also noticed that few accessions were intermixed amongst clusters. Different genetic\rdiversity parameters were estimated based on the four clusters (populations) defined by STRUCTURE software, demonstrating that\rclusters 3 and 4 possessed the lowest and highest diversity values, respectively. AMOVA showed variation between and within clusters\rof 41.85% and 58.15%, respectively. The highest population divergence (Fst) was observed between clusters 2 and 3 (0.579), on the other\rhand, clusters 1 and 4 depicted the lowest Fst with 0.160. Our research highlighted that iPBS markers were successful and effective to study\rDaucus genetic diversity. These results will contribute to the genetic improvement of carrots and sustainable management of its diversity