Vance M. Whitaker

Strawberry Flavor: Diverse Chemical Compositions, a Seasonal Influence, and Effects on Sensory Perception

Fresh strawberries (Fragaria x ananassa) are valued for their characteristic red color, juicy texture, distinct aroma, and sweet fruity flavor. In this study, genetic and environmentally induced variation is exploited to capture biochemically diverse strawberry fruit for metabolite profiling and consumer rating. Analyses identify fruit attributes influencing hedonics and sensory perception of strawberry fruit using a psychophysics approach. Sweetness intensity, flavor intensity, and texture liking are dependent on sugar concentrations, specific volatile compounds, and fruit firmness, respectively. Overall liking is most greatly influenced by sweetness and strawberry flavor intensity, which are undermined by environmental pressures that reduce sucrose and total volatile content. The volatile profiles among commercial strawberry varieties are complex and distinct, but a list of perceptually impactful compounds from the larger mixture is better defined. Particular esters, terpenes, and furans have the most significant fits to strawberry flavor intensity. In total, thirty-one volatile compounds are found to be significantly correlated to strawberry flavor intensity, only one of them negatively. Further analysis identifies individual volatile compounds that have an enhancing effect on perceived sweetness intensity of fruit independent of sugar content. These findings allow for consumer influence in the breeding of more desirable fruits and vegetables. Also, this approach garners insights into fruit metabolomics, flavor chemistry, and a paradigm for enhancing liking of natural or processed products.

Identification of candidate flavonoid pathway genes using transcriptome correlation network analysis in ripe strawberry (Fragaria × ananassa) fruits

Highlight This work in strawberry fruit predicts new genes relevant to a key metabolic pathway using correlation analysis, and then demonstrates their function in a rapid and effective transient assay.

Applications of molecular markers in strawberry

This review examines current and potential applications of molecular markers in strawberry (Fragaria spp.). The most prevalent uses of markers in strawberry are for analyses of genetic diversity, genetic mapping, and cultivar identification. Cultivar identification is by far the most important use of markers to date for the protection of intellectual property as well as to confirm the identity of nursery stock through multiple cycles of asexual propagation. These applications have been accelerated by continuous discovery of simple sequence repeat markers and the development of multiplexed sets. Mapping studies have confirmed the allopolyploid genome structure of cultivated strawberry and shed light onto genetic events that punctuate its domestication. Though marker-trait associations have been identified for disease resistance, photoperiodic flowering, and sex expression, marker-assisted selection in breeding is currently confined to a few entities in the private sector. Pedigree-based analysis holds promise for identifying additional marker-trait associations and simultaneously mining alleles in multiple genetic backgrounds. Meanwhile, the completion of the diploid strawberry genome sequence promises to accelerate candidate-gene approaches for marker discovery.

A genome-enabled, high-throughput, and multiplexed fingerprinting platform for strawberry (Fragaria L.)

Strawberry (Fragaria L.) genotypes bear remarkable phenotypic similarity, even across ploidy levels. Additionally, breeding programs seek to introgress alleles from wild germplasm, so objective molecular description of genetic variation has great value. In this report, a high-throughput, robust protocol for generating highly-informative simple sequence repeat (SSR) patterns is presented to address these issues. The methods are comparable to SSR use in DNA typing in humans and are based on identification of high-number repeats composed of tetra- through nona-nucleotide repeat units found in the Fragaria vesca genome sequence. Individual SSR-containing regions were examined for variability over a range of 219 strawberry genotypes. A single-fluorophore secondary labeling strategy was devised that allows simultaneous amplification of eight SSR regions in a single PCR reaction. The approach yields reproducible, highly-variable, complex patterns (Shannon-Weaver Index 7.09–13.88). The technique may be applied to detect closely-related individuals across ploidy levels, including full sibling progeny in an inter-related octoploid pedigree. Genetic diversity among various cultivars and progenitor wild species in the United States Department of Agriculture-Agricultural Research Service Fragaria Supercore collection was also evaluated. The results build on known relationships, and also raise questions about accepted relationships between several genotypes.

An experimental validation of genomic selection in octoploid strawberry.

The primary goal of genomic selection is to increase genetic gains for complex traits by predicting performance of individuals for which phenotypic data are not available. The objective of this study was to experimentally evaluate the potential of genomic selection in strawberry breeding and to define a strategy for its implementation. Four clonally replicated field trials, two in each of 2 years comprised of a total of 1628 individuals, were established in 2013–2014 and 2014–2015. Five complex yield and fruit quality traits with moderate to low heritability were assessed in each trial. High-density genotyping was performed with the Affymetrix Axiom IStraw90 single-nucleotide polymorphism array, and 17 479 polymorphic markers were chosen for analysis. Several methods were compared, including Genomic BLUP, Bayes B, Bayes C, Bayesian LASSO Regression, Bayesian Ridge Regression and Reproducing Kernel Hilbert Spaces. Cross-validation within training populations resulted in higher values than for true validations across trials. For true validations, Bayes B gave the highest predictive abilities on average and also the highest selection efficiencies, particularly for yield traits that were the lowest heritability traits. Selection efficiencies using Bayes B for parent selection ranged from 74% for average fruit weight to 34% for early marketable yield. A breeding strategy is proposed in which advanced selection trials are utilized as training populations and in which genomic selection can reduce the breeding cycle from 3 to 2 years for a subset of untested parents based on their predicted genomic breeding values.

Mini Review: Potential Applications of Non-host Resistance for Crop Improvement

Plant breeding for disease resistance is crucial to sustain global crop production. For decades, plant breeders and researchers have extensively used host plant resistance genes (R-genes) to develop disease resistant cultivars. However, the general instability of R-genes in crop cultivars when challenged with diverse pathogen populations emphasizes the need for more stable means of resistance. Alternatively, non-host resistance is recognized as the most durable, broad-spectrum form of resistance against the majority of potential pathogens in plants and has gained great attention as an alternative target for managing resistance. While transgenic approaches have been utilized to transfer non-host resistance to host species, conventional breeding applications have been more elusive. Nevertheless, avenues for discovery and deployment of genetic loci for non-host resistance via hybridization are increasingly abundant, particularly when transferring genes among closely related species. In this mini review, we discuss current and developing applications of non-host resistance for crop improvement with a focus on the overlap between host and non-host mechanisms and the potential impacts of new technology.

Pedigree-based analysis in a multiparental population of octoploid strawberry reveals QTL alleles conferring resistance to phytophthora cactorum

Understanding the genetic architecture of traits in breeding programs can be critical for making genetic progress. Important factors include the number of loci controlling a trait, allele frequencies at those loci, and allele effects in breeding germplasm. To this end, multiparental populations offer many advantages for quantitative trait locus (QTL) analyses compared to biparental populations. These include increased power for QTL detection, the ability to sample a larger number of segregating loci and alleles, and estimation of allele effects across diverse genetic backgrounds. Here, we investigate the genetic architecture of resistance to crown rot disease caused by Phytophthora cactorum in strawberry (Fragaria × ananassa), using connected full-sib families from a breeding population. Clonal replicates of > 1100 seedlings from 139 full-sib families arising from 61 parents were control-inoculated during two consecutive seasons. Subgenome-specific single nucleotide polymorphism (SNP) loci were mapped in allo-octoploid strawberry (2n = 8 × = 56), and FlexQTL software was utilized to perform a Bayesian, pedigree-based QTL analysis. A major locus on linkage group (LG) 7D, which we name FaRPc2, accounts for most of the genetic variation for resistance. Four predominant SNP haplotypes were detected in the FaRPc2 region, two of which are strongly associated with two different levels of resistance, suggesting the presence of multiple resistance alleles. The phenotypic effects of FaRPc2 alleles across trials and across numerous genetic backgrounds make this locus a highly desirable target for genetic improvement of resistance in cultivated strawberry.

Identifying Resistance to Crown Rot Caused by Colletotrichum gloeosporioides in Strawberry

Resistance to Colletotrichum crown rot (CCR, caused by Colletotrichum gloeosporioides) among commercial strawberry cultivars is variable, and increasing host resistance is a goal of the strawberry breeding program at the University of Florida. Twenty-eight accessions of Fragaria virginiana and F. chiloensis, the progenitor species of the cultivated strawberry (F. × ananassa), were evaluated for CCR resistance on artificially inoculated plants in a field trial, along with cultivars and breeding selections. Accessions PI 612320, PI 612323, and PI 551736 and selections FL 10-128 and FL 10-129 had no mortality in either of two seasons. The most susceptible genotypes had mortality between 75 and 100%. In a separate growth-chamber evaluation, seven genotypes were inoculated by spraying a spore suspension onto the crown or by injecting the suspension directly into the crown tissues. Mortality was higher using the injection method but the ranking of the genotypes was similar for both methods, indicating that resistance is expressed within crown tissues. Among the seven genotypes, selections FL 10-128 and FL 10-129 had the lowest mortality regardless of inoculation method, illustrating that a high level of resistance can be found within the cultivated germplasm.

Detection of Strawberry necrotic shock virus using conventional and TaqMan(®) quantitative RT-PCR.

Graft-indexing of an advanced selection from the University of Florida strawberry breeding program produced virus-like symptoms on Fragaria vesca. However; RT-PCR testing of the material did not detect the presence of any of 16 strawberry virus species or members of virus groups for which strawberries are routinely indexed. Large scale sequencing of the material revealed the presence of an isolate of Strawberry necrotic shock virus. The nucleotide sequence of this isolate from Florida shows a significant number of base changes in the annealing sites of the primers compared to the primers currently in use for the detection of SNSV thereby explaining the most probable reason for the inability to detect the virus in the original screening. RT-PCR and Taqman(®) qPCR assays were developed based on conserved virus sequences identified in this isolate from Florida and other sequences for SNSV currently present in GenBank. The two assays were applied successfully on multiple samples collected from several areas across the United States as well as isolates from around the world. Comparison between the RT-PCR and the qPCR assays revealed that the qPCR assay is at least 100 times more sensitive than conventional PCR.

Clarifying sub-genomic positions of QTLs for flowering habit and fruit quality in U.S. strawberry ( Fragaria × ananassa ) breeding populations using pedigree-based QTL analysis

The cultivated strawberry (Fragaria×ananassa) is consumed worldwide for its flavor and nutritional benefits. Genetic analysis of commercially important traits in strawberry are important for the development of breeding methods and tools for this species. Although several quantitative trait loci (QTL) have been previously detected for fruit quality and flowering traits using low-density genetic maps, clarity on the sub-genomic locations of these QTLs was missing. Recent discoveries in allo-octoploid strawberry genomics led to the development of the IStraw90 single-nucleotide polymorphism (SNP) array, enabling high-density genetic maps and finer resolution QTL analysis. In this study, breeder-specified traits were evaluated in the Eastern (Michigan) and Western (Oregon) United States for a common set of breeding populations during 2 years. Several QTLs were validated for soluble solids content (SSC), fruit weight (FWT), pH and titratable acidity (TA) using a pedigree-based QTL analysis approach. For fruit quality, a QTL for SSC on linkage group (LG) 6A, a QTL for FWT on LG 2BII, a QTL for pH on LG 4CII and two QTLs for TA on LGs 2A and 5B were detected. In addition, a large-effect QTL for flowering was detected at the distal end of LG 4A, coinciding with the FaPFRU locus. Marker haplotype analysis in the FaPFRU region indicated that the homozygous recessive genotype was highly predictive of seasonal flowering. SNP probes in the FaPFRU region may help facilitate marker-assisted selection for this trait.