Polymorphic insertions of DcSto miniature inverted-repeat transposable elements reveal genetic diversity structure within the cultivated carrot

Abstract

Miniature inverted-repeat transposable elements (MITEs) are a potent source of polymorphisms in plant genomes. A genotyping system, named DcS-ILP, based on polymorphic insertions of Stowaway MITEs (DcStos) localized in introns and identified in the reference genome DH1, has been developed for carrot. Here, we report an extension of the DcS-ILP genotyping system by incorporation of non-reference insertions identified in resequenced genomes representing the eastern gene pool. We genotyped 52 carrot accessions representing the eastern and western carrot gene pools with 92 markers developed previously (western DcS-ILP panel) together with 84 newly developed markers (eastern DcS-ILP panel). Overall, the DcS-ILP markers revealed a highly structured genetic diversity separating the eastern and the western carrot accessions at K = 2 and differentiating Indian breeding lines from the eastern accessions at K = 3. The eastern DcS-ILP panel proved to be more robust with respect to the eastern carrot gene pool, while it provided little information on the western accessions, as many of the DcSto insertions present in the eastern gene pool were absent in the western gene pool. As the western carrot accessions represent improved cultivars, DcSto insertional polymorphisms allowed detection of a selection-driven bottleneck at the improvement stage. Selection in the course of the improvement stage generally operated on standing variation, as the subset of DcSto insertions present in the western carrot likely originated from transposition events preceding the separation of both gene pools. However, occasional frequency shifts in the opposite direction were also revealed, possibly indicating selection for favorable variants associated with DcSto insertions.

Keywords: Daucus carota; Diversity; Intron length polymorphism; MITE; Mobile DNA.

Fig. 1

Distribution of 169 DcSto copies used to develop the eastern DcS-ILP panel on nine carrot chromosomes. The 84 polymorphic DcSto insertions used for genotyping (constituting the “eastern DcS-ILP panel”) are highlighted in blue

Fig. 2

Genetic diversity structure in a collection of 52 carrot accessions representing eastern (E01-E22), Indian (EI01-EI10), and western (W01-W20) gene pools using the combined information from western and eastern DcS-ILP panels (the total of 176 markers). STRUCTURE results at K = 2 (a) and K = 3 (b) and PCoA results (c) are shown

Fig. 3

Genetic diversity structure in a collection of 52 carrot accessions representing eastern (E01-E22), Indian (EI01-EI10), and western (W01-W20) gene pools genotyped with 84 markers from the eastern DcS-ILP panel. STRUCTURE results at K = 2 ( a) and K = 3 (b) and PCoA results (c)) are shown

Fig. 4

Genetic diversity structure in a collection of 52 carrot accessions representing eastern (E01-E22), Indian (EI01-EI10), and western (W01-W20) gene pools genotyped with 92 markers from the western DcS-ILP panel. STRUCTURE results at K = 2 (a) and K = 3 (b) and PCoA results (c) are shown

Fig. 5

Box plots showing allelic frequencies with respect to the presence of DcSto copies (i.e., the “occupied” alleles), as revealed by DcS-ILP genotyping. WaWp, western accessions/western DcS-ILP panel; EaWp, eastern accessions/western DcS-ILP panel; WaEp, western accessions/eastern DcS-ILP panel; EaEp, eastern accessions/eastern DcS-ILP panel. Y axis shows frequency of the “occupied” allele