Genetic diversity structure of western-type carrots

Abstract

Background: Carrot is a crop with a wide range of phenotypic and molecular diversity. Within cultivated carrots, the western gene pool comprises types characterized by different storage root morphology. First western carrot cultivars originated from broad-based populations. It was followed by intercrosses among plants representing early open-pollinated cultivars, combined with mass phenotypic selection for traits of interest. Selective breeding improved root uniformity and led to the development of a range of cultivars differing in root shape and size. Based on the root shape and the market use of cultivars, a dozen of market types have been distinguished. Despite their apparent phenotypic variability, several studies have suggested that western cultivated carrot germplasm was genetically non-structured.

Results: Ninety-three DcS-ILP markers and 2354 SNP markers were used to evaluate the structure of genetic diversity in the collection of 78 western type open-pollinated carrot cultivars, each represented by five plants. The mean percentage of polymorphic loci segregating within a cultivar varied from 31.18 to 89.25% for DcS-ILP markers and from 45.11 to 91.29% for SNP markers, revealing high levels of intra-cultivar heterogeneity, in contrast to its apparent phenotypic stability. Average inbreeding coefficient for all cultivars was negative for both DcS-ILP and SNP, whereas the overall genetic differentiation across all market classes, as measured by F_ST, was comparable for both marker systems. For DcS-ILPs 90-92% of total genetic variation could be attributed to the differences within the inferred clusters, whereas for SNPs the values ranged between 91 to 93%. Discriminant Analysis of Principal Components enabled the separation of eight groups cultivars depending mostly on their market type affiliation. Three groups of cultivars, i.e. Amsterdam, Chantenay and Imperator, were characterized by high homogeneity regardless of the marker system used for genotyping.

Conclusions: Both marker systems used in the study enabled detection of substantial variation among carrot plants of different market types, therefore can be used in germplasm characterization and analysis of genome relationships. The presented results likely reveal the actual genetic diversity structure within the western carrot gene pool and point at possible discrepancies within the cultivars' passport data.

Keywords: DAPC; Daucus carota; DcSto; Genetic diversity; Market classes; Population structure; Root shape; SNP.

Fig. 1

Typical shapes of carrot storage roots representing some of the most popular market types. A - Nantes, B - Berlikum, C - Autumn King (=Flakkee), D – Long Orange, E - Imperator, F – St. Valery, G - Amsterdam, H - Danvers, I - Chantenay, J – Paris Market, K - Guérande (=Oxheart). Bar length – 20 cm

Fig. 2

Comparison of the distribution of estimated pairwise F_ST between the 78 studied OP carrot cultivars

Fig. 3

Estimated genetic structure of the 390 carrot plants representing 78 cultivars. A – genetic structure inferred using 93 DcS-ILP markers for K = 3–5 and K = 7; B – genetic structure inferred using 2354 SNP markers for K = 3–5 and K = 7. Each plant is represented by vertical line divided into colored segments representing the membership fractions in the K clusters

Fig. 4

Percentage of cultivars assigned to the assumed clusters. Assignment is based on different thresholds (Q ≥ 0.5 and Q ≥ 0.7) of the membership coefficients using SNP and DcS-ILP markers for the most probable numbers of K: K = 3–5 and K = 7. Q < 0.5 indicates a high level of admixture within a cultivar

Fig. 5

Estimated genetic structure of 78 carrot cultivars based on SNPs, inferred for K = 3–5 and K = 7. Two-letter abbreviations are used for indication of carrot market types: AM – Amsterdam, AU – Autumn King (Flakkee), BE – Berlikum, PA – Paris Market, IM – Imperator, NA – Nantes, DA – Danvers, GU – Guerande (Oxheart), CH – Chantenay, FO – fodder carrot. Three-letter abbreviations are corresponding to the cultivar symbols listed in Additional file 11: Table S10

Fig. 6

Estimated genetic structure of 78 carrot cultivars based on DcS-ILP markers, inferred for K = 3–5 and K = 7. Two-letter abbreviations are used for indication of carrot market types: AM – Amsterdam, AU – Autumn King (Flakkee), BE – Berlikum, PA – Paris Market, IM – Imperator, NA – Nantes, DA – Danvers, GU – Guerande (Oxheart), CH – Chantenay, FO – fodder carrot. Three-letter abbreviations are corresponding to cultivar symbols listed in Additional file 11: Table S10

Fig. 7

Discriminant analysis of principal components (DAPC) for 78 carrot cultivars. Analysis was carried out on DcS-ILP (a, b) and SNP (c, d) datasets. The axes represent Linear Discriminants (LD): 1st vs. 2nd (A, C) and 1st vs. 3rd (b, d). Each dot represents a cultivar. Two-letter abbreviations are used for indication of carrot market types prevailing in specific groups: AM – Amsterdam, AU – Autumn King (Flakkee), BE – Berlikum, PA – Paris Market, IM – Imperator, NA – Nantes, DA – Danvers, GU – Guerande (Oxheart), CH – Chantenay, FO – fodder carrot

Fig. 8

Schematic representation of the origin of main types of Western carrot as proposed by Banga [14]. Solid arrows show direction of the development of new cultivar types. Punctuated arrows indicate possible origin of the particular type. Underlined names indicate the types of cultivars investigated in the present study. Colours of the boxes represent particular market types or groups of market types clustered using DAPC method for both DcS-ILP and SNP data (see Fig. 7)