BUILDING A BETTER BROCCOLI: IS BEAUTY REALLY IN THE EYE OF THE BEHOLDER?
Stansell, Zachary James
Internationally, broccoli (Brassica oleracea var. italica) is among the most economically important, nutritionally rich, and widely-grown fresh vegetable crops. Despite the importance of broccoli and other B. oleracea vegetables, a comprehensive investigation comparing its phenomic and genomic diversity across landrace and modern hybrid germplasm has yet to be accomplished. Moreover, improving horticultural quality in regionally adapted broccoli and other B. oleracea crops is challenging due to complex genetic control of traits affecting morphology, development, and yield. This work presents an interdisciplinary approach that evaluates the genomics and phenomics that underpin the diversity, domestication, and horticultural quality of landrace and improved broccoli germplasm. To evaluate domestication and diversity within this crop and its larger crop group, two genotyping-by-sequencing studies were conducted to compare domestication footprints and diversity in diverse collections of italica germplasm. The first study evaluated 85 italica, botrytis, and alboglabra accessions, determining that a greater degree of allelic diversity was present within landrace broccoli and the overwhelming majority (96.1%) of SNPs differentiating improved cauliflower from landrace cauliflower were common to the larger pool of broccoli germplasm, supporting a parallel or later development of cauliflower, and clarifying the population structure, phylogeny, and domestication footprintsof landrace and improved broccoli. A second study builds upon the prior work by evaluating 109 italica or italica/botrytis intermediate accessions, including 54 commercial F 1 hybrids and 55 landrace accessions for 24 horticultural quality traits within four trait classes (architecture, biomass, head quality, and phenology). Four inferred subpopulations within the pool of italica germplasm were readily distinguished by principal component analysis, phylogeny reconstruction, population structure, and identity-by-state analysis. Moreover, 13 reduction-in-diversity genomic regions, 53 selective sweeps, and 30 runs of homozygosity associated with domestication processes were identified within modern F1 hybrid germplasm. One diverse sprouting broccoli subpopulation collected in the Southern Italian Peninsula and Sicily contained 4.7 fold greater unique alleles per accessions compared to Calabrese broccoli hybrids, providing a valuable resource in broccoli improvement efforts. Mapping horticultural quality traits to genomic loci is an essential step in understanding and improving horticultural quality in broccoli germplasm. To accomplish this, a study was conducted using a double-haploid mapping population (BolTBDH; Chinese kale × broccoli; N = 175) that 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 markers. This work provides a framework for B. oleracea improvement efforts by targeting key genomic loci contributing to high horticultural quality broccoli. For example, four head quality QTL (OQ C03@57.0, OQ C04@33.3, OQ C08@25.5, and OQ C09@49.7) explain a cumulative 81.9% of phenotypic variance in the broccoli heading phenotype, and contain the key flowering related candidate genes, including homologs of FLOWERING LOCUS C (FLC; Bo9g173400 and Bo9g173370), and exhibit epistatic effects. To select improved and locally adapted broccoli hybrids, multiple head quality traits must be optimized concurrently. To assist this selection process, we conducted a study assessing five candidate indices generated from linear combinations of quality traits such as head color, head smoothness, bead size, bead uniformity, and others. These indices were tested for an ability to reduce interobserver variability and to select specific attributes most associated with the overall horticultural quality of heads. Head smoothness, bead uniformity, head color, and holding ability accounted for 78% of variation in overall head quality. Intraclass correlation coefficients, which measure the degree of concordance among raters, were increased from 0.71 to 0.88 (p < 0.05) and from 0.67 to 0.80 (p < 0.05) in two trials when comparing the simple overall quality assessment with an index weighted by the most important individual head attributes. A quality index accounting for the relative importance of individual traits can enhance identification of optimal hybrids adapted to target conditions. This method can be used to improve concordance for subjective ratings and has been prepared as an R package for general work with horticultural quality crops.
Brassica oleracea; Broccoli; Diversity; Domestication; Italica; Quality Traits
Hua, Jian; Roeder, Adrienne
Ph. D., Horticulture
Doctor of Philosophy
Attribution 4.0 International
dissertation or thesis
Except where otherwise noted, this item's license is described as Attribution 4.0 International