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. 2019 Sep 18:10:1104.
doi: 10.3389/fpls.2019.01104. eCollection 2019.

Complex Horticultural Quality Traits in Broccoli Are Illuminated by Evaluation of the Immortal BolTBDH Mapping Population

Zachary Stansell  1   2 , Mark Farnham  3 , Thomas Björkman  1   2
Affiliations

Complex Horticultural Quality Traits in Broccoli Are Illuminated by Evaluation of the Immortal BolTBDH Mapping Population

Zachary Stansell et al. Front Plant Sci. .

Abstract

Improving horticultural quality in regionally adapted broccoli (Brassica oleracea var. italica) and other B. oleracea crops is challenging due to complex genetic control of traits affecting morphology, development, and yield. Mapping horticultural quality traits to genomic loci is an essential step in these improvement efforts. Understanding the mechanisms underlying horticultural quality enables multi-trait marker-assisted selection for improved, resilient, and regionally adapted B. oleracea germplasm. The publicly-available biparental double-haploid BolTBDH mapping population (Chinese kale × broccoli; N = 175) was evaluated for 25 horticultural traits in six trait classes (architecture, biomass, phenology, leaf morphology, floral morphology, and head quality) by multiple quantitative trait loci mapping using 1,881 genotype-by-sequencing derived single nucleotide polymorphisms. The physical locations of 56 single and 41 epistatic quantitative trait locus (QTL) were identified. Four head quality QTL (OQ_C03@57.0, OQ_C04@33.3, OQ_CC08@25.5, and OQ_C09@49.7) explain a cumulative 81.9% of phenotypic variance in the broccoli heading phenotype, contain the FLOWERING LOCUS C (FLC) homologs Bo9g173400 and Bo9g173370, and exhibit epistatic effects. Three key genomic hotspots associated with pleiotropic control of the broccoli heading phenotype were identified. One phenology hotspot reduces days to flowering by 7.0 days and includes an additional FLC homolog Bo3g024250 that does not exhibit epistatic effects with the three horticultural quality hotspots. Strong candidates for other horticultural traits were identified: BoLMI1 (Bo3g002560) associated with serrated leaf margins and leaf apex shape, BoCCD4 (Bo3g158650) implicated in flower color, and BoAP2 (Bo1g004960) implicated in the hooked sepal horticultural trait. The BolTBDH population provides a framework for B. oleracea improvement by targeting key genomic loci contributing to high horticultural quality broccoli and enabling de novo mapping of currently unexplored traits.

Keywords: BoFLC; BolTBDH; Brassica olecarea var. italica; QTL mapping; broccoli; complex horticultural traits; genotype-by-sequencing; “TO1000”.

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Figures

Figure 1
Figure 1
Visual scoring scale of selected traits evaluated in BolTBDH trials. See Table 1 and Stansell et al. (2017) for additional information.
Figure 2
Figure 2
BolTBDH phenotypic analysis: (A) Distribution of phenotypic traits evaluated in year 1 and year 2 (Y12) trials. Trait class is indicated by color (architecture = dark green, biomass = orange, leaf morphology = light green, bud morphology = light blue, heading quality = pink, and phenology = yellow). (B) Y12 between-trait (bottom left) and between-year Y1 vs. Y2 (top right) Spearman correlation coefficients, with negative and positive correlations plotted in red and blue. (C) Percentage of Y12 overall quality model explained by relative importance predictors (RIA) by fitting the model [OQ ∼ LT + MH + MS + VG + LA + LM + LC + BS + BU + BR + HC + HD + HE + HS + HU + DF + DM] using the lmg method with the rateRvaR function raterimp() with 95% confidence intervals estimated by 1,000 permutations.
Figure 3
Figure 3
(A) Heatmap of relative recombination fractions (top left) and logarithm of odds scores (bottom right) comparing all pairs of the 1,881 markers (bottom and left axes) and by chromosome (top and right axes) used to construct BolTBDH genetic map. (B) Segregation distortion (Y-axis; f = P1 allele) observed using all markers (X-axis) disaggregatted by chromosomes (C01–C09). Markers exhibiting significant segregation distortion (χ2 [p.adj] < 0.05) plotted in orange (P1) or purple (P2). Non-significant segregation distortion markers are plotted in grey. (C) Genetic map, marker location (cm), and marker density (cm/marker) by chromosome using all 1,881 BolTBDH markers.
Figure 4
Figure 4
MQM QTL mapping results: (A) QTL plots by trait and chromosome using 1881 markers, 175 double haploid lines, and pooled phenotypes across environments (Y12; X-axis = chromosome, Y-axis = LOD). Horizontal, dashed, grey line = genome-wide significance threshold (α = 0.95) determined from 1,000 permutations of scantwo() for individual traits. Trait class is indicated by color (architecture = dark green, biomass = orange, leaf morphology = light green, bud morphology = light blue, heading quality = pink, and phenology = yellow). (B) Summarized MQM results; traits evaluated in BolTBDH printed along the Y-axis and chromosomes scaled by physical distance (Mbp) are arranged on the X-axis. MQM peak apex given by vertical bar and 95% Bayesian confidence intervals indicated by width of horizontal bar. Color schema is recycled from (A).
Figure 5
Figure 5
Two dimensional scans of all traits using 1,881 markers, using simulated genotype probabilities (N = 1000) with genotype probabilities calculated across 1 cm steps. Epistatic LOD scores are calculated the difference in the log-likelihood of the full model and the additive model for a given QTL pair and are printed above and left of trace. The full model LOD values are printed below and right of trace.
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