Allan F. Brown

Variation in content of bioactive components in broccoli

The discovery of bioactive components in foods is exciting, suggesting the possibility of improved public health through diet. Yet the content of bioactive components in plant food varies, making quality control and intake recommendations problematic. Variation in content of bioactive components in fruits and vegetables depends upon both genetics and environment, including growing conditions, harvest and storage, processing and meal preparation. Cruciferous vegetables, which contain both anticarcinogenic and antioxidant properties, are excellent examples to illustrate the problem in assessing health benefits of foods that vary in content of bioactive components. In broccoli, the content of both glucosinolates and their bioactive hydrolysis products varies with genotype, environment and processing. Antioxidant vitamins and flavonoid content varies also. Here we review the influences of genetics, environment and post-harvest processing on content of bioactive components in broccoli, an area that is presently only partly understood. Reporting a range for bioactive component content can help the public to make informed choices about diet. For the future, research into the mechanisms behind this variation can lead to an understanding of genetic regulation of these variations, resulting in the generation of a consistent supply of nutritionally enhanced plant foods on the market.

Genomics of Cold Hardiness in Woody Plants

The term cold hardiness or freezing tolerance is used to represent, in a general sense, the ability of plants to adapt to and withstand freezing temperatures. It is a complex, multigenic trait that is too often viewed as a single entity when in fact it is composed of many aspects, all of which can be to some extent viewed as genetically distinct. Advances in molecular biology and genomics have provided significant advances in understanding how plants respond to low temperature and acquire freezing tolerance. Among the most important discoveries has been the identification of the CBF/DREB transcription factor. This transcription factor, along with its regulators such as ICE transcription factors, play a major role in sensing low temperature, initiating the process of cold acclimation, and inducing the expression of a large set of cold-regulated genes. These latter genes are presumed to ameliorate injury to plant cells as a result of freeze-induced desiccation and the presence of extracellular ice. The present review provides a comprehensive overview of CBF and ICE genes in a number of woody plants whose genomes have been sequenced and provides information on the attempts to identify genetic markers for use in marker-assisted selection (MAS) or to improve cold hardiness using genetic transformation technologies. Functional studies of CBF genes in woody plants have indicated that their regulation and impact on abiotic stress resistance are more complex than in herbaceous plants. In particular, the possible relationship of CBF to dormancy is highlighted. Cold hardiness is a complex trait and the challenge in the future will be to use the molecular and genetic tools that are being developed, as well as new developments in bioinformatics, to integrate complex sets of data into a systems view of plant biology. This approach holds the best promise for developing the ability to significantly improve cold hardiness in economically important crops while still maintaining high levels of plant productivity and yield.

Efficient Quantification of the Health-Relevant Anthocyanin and Phenolic Acid Profiles in Commercial Cultivars and Breeding Selections of Blueberries (Vaccinium spp.)

Anthocyanins and phenolic acids are major secondary metabolites in blueberry with important implications for human health maintenance. An improved protocol was developed for the accurate, efficient, and rapid comparative screening for large blueberry sample sets. Triplicates of six commercial cultivars and four breeding selections were analyzed using the new method. The compound recoveries ranged from 94.2 to 97.5 ± 5.3% when samples were spiked with commercial standards prior to extraction. Eighteen anthocyanins and 4 phenolic acids were quantified in frozen and freeze-dried fruits. Large variations for individual and total anthocyanins, ranging from 201.4 to 402.8 mg/100 g, were assayed in frozen fruits. The total phenolic acid content ranged from 23.6 to 61.7 mg/100 g in frozen fruits. Across all genotypes, freeze-drying resulted in minor reductions in anthocyanin concentration (3.9%) compared to anthocyanins in frozen fruits. However, phenolic acids increased by an average of 1.9-fold (±0.3) in the freeze-dried fruit. Different genotypes frequently had comparable overall levels of total anthocyanins and phenolic acids, but differed dramatically in individual profiles of compounds. Three of the genotypes contained markedly higher concentrations of delphinidin 3-O-glucoside, cyanidin 3-O-glucoside, and malvidin 3-O-glucoside, which have previously been implicated as bioactive principles in this fruit. The implications of these findings for human health benefits are discussed.

Simultaneous Extraction and Quantitation of Carotenoids, Chlorophylls, and Tocopherols in Brassica Vegetables

Brassica oleracea vegetables, such as broccoli (B. oleracea L. var. italica) and cauliflower (B. oleracea L. var. botrytis), are known to contain bioactive compounds associated with health, including three classes of photosynthetic lipid-soluble compounds: carotenoids, chlorophylls, and tocopherols. Carotenoids and chlorophylls are photosynthetic pigments. Tocopherols have vitamin E activity. Due to genetic and environmental variables, the amounts present in vegetables are not constant. To aid breeders in the development of Brassica cultivars with higher provitamin A and vitamin E contents and antioxidant activity, a more efficient method was developed to quantitate carotenoids, chlorophylls, and tocopherols in the edible portions of broccoli and cauliflower. The novel UPLC method separated five carotenoids, two chlorophylls, and two tocopherols in a single 30 min run, reducing the run time by half compared to previously published protocols. The objective of the study was to develop a faster, more effective extraction and quantitation methodology to screen large populations of Brassica germplasm, thus aiding breeders in producing superior vegetables with enhanced phytonutrient profiles.

Genetic diversity, population structure and genome-wide marker-trait association analysis emphasizing seed nutrients of the USDA pea (Pisum sativum L.) core collection

Genetic diversity, population structure and genome-wide marker-trait association analysis was conducted for the USDA pea (Pisum sativum L.) core collection. The core collection contained 285 accessions with diverse phenotypes and geographic origins. The 137 DNA markers included 102 polymorphic fragments amplified by 15 microsatellite primer pairs, 36 RAPD loci and one SCAR (sequence characterized amplified region) marker. The 49 phenotypic traits fall into the categories of seed macro- and micro-nutrients, disease resistance, agronomic traits and seed characteristics. Genetic diversity, population structure and marker-trait association were analyzed with the software packages PowerMarker, STUCTURE and TASSEL, respectively. A great amount of variation was revealed by the DNA markers at the molecular level. Identified were three sub-populations that constituted 56.1%, 13.0% and 30.9%, respectively, of the USDA Pisum core collection. The first sub-population is comprised of all cultivated pea varieties and landraces; the second of wild P. sativum ssp. elatius and abyssinicum and the accessions from the Asian highland (Afghanistan, India, Pakistan, China and Nepal); while the third is an admixture containing alleles from the first and second sub-populations. This structure was achieved using a stringent cutoff point of 15% admixture (q-value 85%) of the collection. Significant marker-trait associations were identified among certain markers with eight mineral nutrient concentrations in seed and other important phenotypic traits. Fifteen pairs of associations were at the significant levels of P ≤ 0.01 when tested using the three statistical models. These markers will be useful in marker-assisted selection to breed pea cultivars with desirable agronomic traits and end-user qualities.

RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing.

BackgroundBlueberries are a rich source of antioxidants and other beneficial compounds that can protect against disease. Identifying genes involved in synthesis of bioactive compounds could enable the breeding of berry varieties with enhanced health benefits.ResultsToward this end, we annotated a previously sequenced draft blueberry genome assembly using RNA-Seq data from five stages of berry fruit development and ripening. Genome-guided assembly of RNA-Seq read alignments combined with output from ab initio gene finders produced around 60,000 gene models, of which more than half were similar to proteins from other species, typically the grape Vitis vinifera. Comparison of gene models to the PlantCyc database of metabolic pathway enzymes identified candidate genes involved in synthesis of bioactive compounds, including bixin, an apocarotenoid with potential disease-fighting properties, and defense-related cyanogenic glycosides, which are toxic. Cyanogenic glycoside (CG) biosynthetic enzymes were highly expressed in green fruit, and a candidate CG detoxification enzyme was up-regulated during fruit ripening. Candidate genes for ethylene, anthocyanin, and 400 other biosynthetic pathways were also identified. Homology-based annotation using Blast2GO and InterPro assigned Gene Ontology terms to around 15,000 genes. RNA-Seq expression profiling showed that blueberry growth, maturation, and ripening involve dynamic gene expression changes, including coordinated up- and down-regulation of metabolic pathway enzymes and transcriptional regulators. Analysis of RNA-seq alignments identified developmentally regulated alternative splicing, promoter use, and 3′ end formation.ConclusionsWe report genome sequence, gene models, functional annotations, and RNA-Seq expression data that provide an important new resource enabling high throughput studies in blueberry.

Lycopene Estimation in Tomato Lines Using Infrared Absorbance and Tomato Analyzer

The color of red tomatoes (Solanum lycopersicum L.) is mostly from the carotenoid pigment lycopene, which is of interest to consumers and the tomato industry because of its purported protective effects against diabetes, cardiovascular events, and some cancers. Lycopene content was measured in at least 179 tomato lines with pink, red, and dark red fruit derived from a diverse genetic background to determine the level of variation for lycopene and to develop prediction models. Two methods (Tomato Analyzer or DigiEye) for quantifying total lycopene and to develop prediction models were tested on tomato fruit to find a high throughput lycopene measurement system suitable for screening hundreds of lines in a breeding program. The tomato lycopene content ranged from 28 to 133 mg•kg−1 of tomato sample, indicating a wide variation in the set of tomato lines. Using this variation, lycopene prediction models were developed. Though a single equation could not be developed using data from the DigiEye or Tomato Analyzer to predict lycopene content of tomato fruit, individual equations within color groups proved useful in predicting lycopene content (r = 0.77, P < 0.05). Our data indicate that rapid analysis of tomato fruit, kept relatively intact, can be done to accurately predict lycopene content in a wide range of fruit colors. Current address for Dan Randall: Shaw Industries Inc., 200 Industrial Blvd., Bainbridge, GA 39817.

Trait variation and genetic diversity in a banana genomic selection training population

Banana (Musa spp.) is an important crop in the African Great Lakes region in terms of income and food security, with the highest per capita consumption worldwide. Pests, diseases and climate change hamper sustainable production of bananas. New breeding tools with increased crossbreeding efficiency are being investigated to breed for resistant, high yielding hybrids of East African Highland banana (EAHB). These include genomic selection (GS), which will benefit breeding through increased genetic gain per unit time. Understanding trait variation and the correlation among economically important traits is an essential first step in the development and selection of suitable GS models for banana. In this study, we tested the hypothesis that trait variations in bananas are not affected by cross combination, cycle, field management and their interaction with genotype. A training population created using EAHB breeding material and its progeny was phenotyped in two contrasting conditions. A high level of correlation among vegetative and yield related traits was observed. Therefore, genomic selection models could be developed for traits that are easily measured. It is likely that the predictive ability of traits that are difficult to phenotype will be similar to less difficult traits they are highly correlated with. Genotype response to cycle and field management practices varied greatly with respect to traits. Yield related traits accounted for 31–35% of principal component variation under low and high input field management conditions. Resistance to Black Sigatoka was stable across cycles but varied under different field management depending on the genotype. The best cross combination was 1201K-1xSH3217 based on selection response (R) of hybrids. Genotyping using simple sequence repeat (SSR) markers revealed that the training population was genetically diverse, reflecting a complex pedigree background, which was mostly influenced by the male parents.

Bananas and Plantains (Musa spp.)

Bananas and plantains are one of the most important crops in the world, yet very few hybrids are cultivated. Bananas face considerable pressure from multiple biotic and abiotic stresses, but its genetic improvement is impeded by constraints on seed set due to multiple physiological and reproductive issues. The triploid nature of almost all commercially important bananas requires a complicated breeding scheme involving cross hybridization across ploidy levels and results in poor seed set that reduces the probability of obtaining favorable recombination. The poor seed set is further complicated by issues of parthenocarpy and partial to complete female and male sterility that are not fully understood. While the introduction of genomic resources of this perennial long cycling crop promises to hasten the development of improved cultivars, there is a need to maintain vigorous and committed long-term international breeding programs.

Genomic Prediction in a Multiploid Crop: Genotype by Environment Interaction and Allele Dosage Effects on Predictive Ability in Banana

First empirical evidence of genomic prediction in a multi‐ploidy banana population is presented. The effect of allele dosage single nucleotide polymorphism on prediction accuracy depends on the trait. Use of averaged environmental data improves prediction accuracy. BayesB model can be used across all traits during genomic prediction in banana breeding. The high predictive values show the potential of genomic prediction in banana breeding.