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

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.

From landrace to modern hybrid broccoli: the genomic and morphological domestication syndrome within a diverse B. oleracea collection

“…Several key genomic regions bear strong signals of domestication and selection, and warrant further investigation. This terminal chromosome 9 region has been shown to harbor homologs of flowering and chilling requirement genes TLF2 , COL1 , CO , and FLC 32 , 64 – 67 and has been linked to temperature-dependent time to curd initiation in a double-haploid cauliflower 68 , heat-tolerance in a double-haploid italica mapping population 69 , and a head forming and later flowering time phenotype in a double-haploid alboglabra x italica mapping population 27 . We identified a strong F st region (chr9:47.4–48.9) that contained 236 A. thaliana homologs including CO (Bo9g163730) and COL1 (Bo9g163720).…”

“…Approximately 16 biennial or day length sensitive accessions that would normally form heading structures in cooler season Mediterranean climates did not head or flower and were excluded from evaluations. Traits within four trait classes were evaluated: architecture, biomass, head quality, and phenology 27 (Supplementary Table 1 TRAITS). The traits (MT, HE, BR, BS, BU, HC, HU, and OQ) followed standardized protocol employed by the Eastern Broccoli Project 52 using an ordinal scale (1 = worst; 5 = best).…”

“…Linear regression was conducted in R to compare horticultural quality traits with cultivar release year of relevant accessions and principal component axes. Relative importance analysis of horticultural quality was conducted using 1000 bootstrap replications of the "lmg" method in the R package RateRvaR (v. 1.0) 52,99…”

“…In recent years, considerable progress understanding the B. oleracea crop group has been made. Specifically, several key objectives have been accomplished: parsing fundamental genomic architecture [3][4][5] , publication of high-quality reference genomes [6][7][8] , evaluating diversity and domestication processes [9][10][11][12][13][14][15][16][17][18][19][20][21] , and identifying genomic regions or candidate genes associated with horticultural quality [22][23][24][25][26][27] and biotic/abiotic stress resistance [28][29][30][31][32][33][34][35] .…”

Total FLC transcript dynamics from divergent paralogue expression explains flowering diversity in Brassica napus

“…Further evidence for the roles of specific paralogues in generating variation was provided by the demonstration that a combination of BnaFLC.A10 with a defined transposable element together with a functional BnaFLC.A02 is required for winter crop types (Yin et al ., 2020). This is despite the fact that other paralogues are capable of delaying flowering in Arabidopsis, or have been implicated in flowering time control in the closely related B. rapa and B. oleracea species, suggesting that they are largely conserved in flowering‐time control ( BnaFLC.A03a , BraFLC.A02 , BraFLC.A03a , BraFLC.A03b , BraFLC.A10 , BoFLC.C02 , BoFLC.C03b , BoFLC.C09a and BoFLC.C09b ; Tadege et al ., 2001; Schranz et al ., 2002; Pires et al ., 2004; Lin et al ., 2005; Kim et al ., 2007; Razi et al ., 2008; Irwin et al ., 2016; Abuyusuf et al ., 2019; Stansell et al ., 2019).…”