Using carrot centromeric repeats to study karyotype relationships in the genus Daucus (Apiaceae)

Dariusz Kadluczka,Ewa Grzebelus

doi:10.1186/s12864-021-07853-2

Abstract

BackgroundIn the course of evolution, chromosomes undergo evolutionary changes; thus, karyotypes may differ considerably among groups of organisms, even within closely related taxa. The genus Daucus seems to be a promising model for exploring the dynamics of karyotype evolution. It comprises some 40 wild species and the cultivated carrot, a crop of great economic significance. However, Daucus species are very diverse morphologically and genetically, and despite extensive research, the taxonomic and phylogenetic relationships between them have still not been fully resolved. Although several molecular cytogenetic studies have been conducted to investigate the chromosomal structure and karyotype evolution of carrot and other Daucus species, detailed karyomorphological research has been limited to carrot and only a few wild species. Therefore, to better understand the karyotype relationships within Daucus, we (1) explored the chromosomal distribution of carrot centromeric repeats (CentDc) in 34 accessions of Daucus and related species by means of fluorescence in situ hybridization (FISH) and (2) performed detailed karyomorphological analysis in 16 of them.ResultsWe determined the genomic organization of CentDc in 26 accessions of Daucus (belonging to both Daucus I and II subclades) and one accession of closely related species. The CentDc repeats were present in the centromeric regions of all chromosomes of 20 accessions (representing 11 taxa). In the other Daucus taxa, the number of chromosome pairs with CentDc signals varied depending on the species, yet their centromeric localization was conserved. In addition, precise chromosome measurements performed in 16 accessions showed the inter- and intraspecific karyological relationships among them.ConclusionsThe presence of the CentDc repeats in the genomes of taxa belonging to both Daucus subclades and one outgroup species indicated the ancestral status of the repeat. The results of our study provide useful information for further evolutionary, cytotaxonomic, and phylogenetic research on the genus Daucus and may contribute to a better understanding of the dynamic evolution of centromeric satellites in plants.

Highlights

In the course of evolution, chromosomes undergo evolutionary changes; karyotypes may differ considerably among groups of organisms, even within closely related taxa
Daucus species, indicating the presence of CentDc-like sequences in three of them, whereas the two remaining ones were further analyzed by fluorescence in situ hybridization (FISH) to confirm the absence of these repeats [33]. These findings suggest the hypothesis that carrot centromeric repeats are widespread in the genus Daucus and that their chromosomal distribution can be examined by molecular cytogenetics
FISH on metaphase chromosome spreads with CentDc were used as a probe and displayed a clear hybridization pattern in 27 out of 34 accessions examined in this study (Fig. 1 and 2a–h)

Summary

Introduction

In the course of evolution, chromosomes undergo evolutionary changes; karyotypes may differ considerably among groups of organisms, even within closely related taxa. To better understand the karyotype relationships within Daucus, we (1) explored the chromosomal distribution of carrot centromeric repeats (CentDc) in 34 accessions of Daucus and related species by means of fluorescence in situ hybridization (FISH) and (2) performed detailed karyomorphological analysis in 16 of them. Unlike low-copy-number sequences, repetitive elements are highly variable and evolve more rapidly, leading to changes in the abundance and chromosomal distribution of their copies Due to their high copy number and tendency to cluster, they are excellent probes for fluorescence in situ hybridization (FISH), a powerful molecular cytogenetic technique, providing valuable information on their physical localization, making them advantageous for comparative studies concerning evolutionary relationships between species [6, 7]. FISH with satellite DNAbased probes has been successfully applied for the understanding of chromosomal evolution in several agronomically important plant species, including sugar beet [8], maize [15], radish [16], common bean [17], spinach [18], and quinoa [19]

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