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.
Highlights
Improvement of broccoli and other Brassica oleracea vegetables is constrained by complex interactions of many genes affecting plant architecture, developmental processes, and yield
Genotype-by-sequencing of all initial lines (N = 202) resulted in 168,722,056 quality barcoded reads distributed across 2,529,429 unique tags of which 670,347 were mapped, producing 263,998 SNPs
Lines identified as hybrids indicated by heterozygous calls, twinned lines, and crossover event outliers were removed, resulting in 175 lines included in multiple quantitative trait locus (QTL) mapping (Supplementary Data S1–S3)
Summary
Improvement of broccoli and other Brassica oleracea vegetables (cauliflower, cabbage, kale, Gai lan, Brussels sprouts, kohlrabi, and collard) is constrained by complex interactions of many genes affecting plant architecture, developmental processes, and yield. A current limitation in B. oleracea vegetable crop improvement is a lack of publicly available mapping populations, constraining information integration across research programs. Attempts to unify existing maps have been limited due to variable germplasm, different marker types, and linkage group nomenclature (Hu et al, 1998). These populations are often difficult to maintain due to self-incompatibility (Farnham, 1998; Bohuon et al, 1998; Sebastian et al, 2000; Pink et al, 2008; Walley et al, 2012)
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