Linkage mapping of root shape traits in two carrot populations

Abstract

This study investigated the genetic basis of carrot root shape traits using composite interval mapping in two biparental populations (n = 119 and n = 128). The roots of carrot F2:3 progenies were grown over 2 years and analyzed using a digital imaging pipeline to extract root phenotypes that compose market class. Broad-sense heritability on an entry-mean basis ranged from 0.46 to 0.80 for root traits. Reproducible quantitative trait loci (QTL) were identified on chromosomes 2 and 6 on both populations. Colocalization of QTLs for phenotypically correlated root traits was also observed and coincided with previously identified QTLs in published association and linkage mapping studies. Individual QTLs explained between 14 and 27% of total phenotypic variance across traits, while four QTLs for length-to-width ratio collectively accounted for up to 73% of variation. Predicted genes associated with the OFP-TRM (OVATE Family Proteins-TONNEAU1 Recruiting Motif) and IQD (IQ67 domain) pathway were identified within QTL support intervals. This observation raises the possibility of extending the current regulon model of fruit shape to include carrot storage roots. Nevertheless, the precise molecular mechanisms through which this pathway operates in roots characterized by secondary growth originating from cambium layers remain unknown.

Keywords: Daucus carota var sativus; OFP-TRM and IQD plant regulon; genetic mapping.

Fig. 1.

Photograph of carrot (D. carota var sativus) founders “L1408”, “W133”, and “W279”. a) Boxplots displaying differences in carrot root shape traits among founders: b) shoulder curvature, c) tip curvature, d) length, e) length-to-width ratio, f) width, and g) biomass. Significance of mean differences is indicated by distinct lowercase letters within each boxplot (α = 0.05). Multiple comparisons were corrected using the Šidák correction.

Fig. 2.

Phenotypic correlations between populations for root shape traits. Scatterplots of best linear unbiased estimates (BLUEs) below the diagonal show the relationship between traits for both populations. Pearson correlations (r) are shown above the diagonal for each population. The diagonal is the distribution of the trait for each population. All correlations were found to be significant at α = 0.05, except for the correlations between biomass and length-to-width ratio, biomass and tip curvature, biomass, and shoulder curvature, as well as length and width. LW, length-to-width.

Fig. 3.

Composite interval mapping (CIM) of root shape traits in the F_2:3 L1408 × W133 (a) and L1408 × W279 mapping populations (b). The y-axis represents the logarithm of odds (LOD). The LOD significance threshold (α = 0.05, 1,000 permutations) for each variable is indicated by the horizontal lines of the same color. The annotated known position of predicted carrot proteins associated with biological shape within the 1.5-LOD support interval, and less than 2 Mb of significant QTLs are represented by black vertical dotted lines in each chromosome and annotated. OFPs are OVATE Family Proteins, TRMs are TONNEAU1 Recruiting Motif, and IQDs are IQ67 domain. The x-axis represents the genetic position (cM) across nine chromosomes.

Fig. 4.

Reproducible QTL peaks identified for length-to-width ratio on chromosome 2 and root width on chromosome 6 in F_2:3 mapping populations L1408 × W133 (a) and L1408 × W279 (b). Dashed black vertical lines indicate annotated positions of predicted regulators of shape in carrots, namely OVATE Family Proteins 5 (OFP5) and TONNEAU1 Recruiting Motif 9 (TRM9). Additionally, dashed red vertical lines mark the approximate locations of previously reported chromosomal regions (QTLs) associated with carrot root shape traits (Macko-Podgórni et al. 2017; Turner et al. 2018; Brainard et al. 2022). The x-axis represents the physical position in mega bases (Mb) across chromosomes 2 and 6.

Fig. 5.

Relationship between genotype at SNP loci of reproducible QTLs for width (mm) and length-to-width ratio in carrot F_2:3 populations L1408 × W133 (n = 119) and L1408 × W279 (n = 128). Effect plots for width (a) and length-to-width ratio (b) in population L1408 × W133. Effect plots for width (c) and length-to-width ratio (d) in validation population L1408 × W279. Genotypes “A” (L1408) and “B” (W133 or W279) represent the two homozygous states, while “H” denotes the heterozygote. Boxplots with different uppercase letters indicate significant differences at α = 0.05. Multiple comparisons were corrected using the Šidák correction.