Multiomic Explorations of Fruit Texture and Postharvest Quality in Blackberry and Muscadine Grape

For most fresh-market fruit crops, texture is an important trait that strongly affects both shipping potential and consumer opinion. Efficient, scalable phenotyping methods are required by breeding programs to effectively select for improvements to fruit texture quality. In muscadine, we have developed a recommendation for characterizing complex muscadine grape texture profiles by comparing the results of breeders’ ratings, descriptive sensory panel results, and an array of instrumental protocols. Regression models were constructed to predict awareness of skins, crispness, hardness, and visual separation explaining 85%, 91%, 82%, and 83% of variance respectively. Genotypes that scored most highly in breeders’ ratings of overall texture had soft skins and firm flesh, suggesting that both qualities are important targets for texture improvement in muscadine. We have also developed an R shiny based web-application, called ShinyFruit, for image-based analysis of fruit morphology and color quality. ShinyFruit was tested against manual methods of size and red drupelet reversion (RDR) estimation in a diverse population of blackberry cultivars and breeding selections. ShinyFruit results shared a strong positive correlation with manual measurements for blackberry length (r = 0.96) and significant, albeit weaker, correlations with manual RDR estimation methods (r = 0.62 - 0.70). Further validation of ShinyFruit’s potential was provided when it was used to generate phenotypic datasets across a genome wide association study (GWAS) panel of 300 diverse blackberry genotypes. This GWAS panel is the first reported in autotetraploid blackberry, and numerous quantitative trait loci (QTL) for blackberry texture and RDR were identified, spanning chromosomes Ra01, Ra02, Ra03, and Ra06. All QTL associated with RDR were located on Ra02 and most of these 212 single nucleotide polymorphisms (SNPs) were in high linkage disequilibrium. Three variants on homologs of polygalcturonase (PG), pectin methylesterase (PME), and β-glucosidase explained 27% of variance in fruit firmness and were located on chromosomes Ra06, Ra01, and Ra02 respectively. Both fruit firmness and RDR appear to be complex, moderately heritable traits, which may be most effectively incorporated into a genomic selection model. Expression-level evidence suggests that an inhibitor of PME may be associated with the fruit firmness QTL identified on Ra01. The expression of this PME inhibitor was negatively correlated with PME activity through fruit development in the ‘crispy’ fruited A-2453T. Expansin-like proteins were also expressed more highly in A-2453T compared to the soft-fruited ‘Black GemTM’, suggesting that this protein family could play a unique role in the ‘crispy’ texture phenotype. By combining newly developed phenotyping methods with informative genomic and transcriptomic datasets, we provide a strong foundation for continued research. Future improvement of texture in blackberry should prioritize training genomic selection models which could be trained on our accumulated datasets and supported by ShinyFruit phenotyping

Multiomic Explorations of Fruit Texture and Postharvest Quality in Blackberry and Muscadine Grape

For most fresh-market fruit crops, texture is an important trait that strongly affects both shipping potential and consumer opinion. Efficient, scalable phenotyping methods are required by breeding programs to effectively select for improvements to fruit texture quality. In muscadine, we have developed a recommendation for characterizing complex muscadine grape texture profiles by comparing the results of breeders’ ratings, descriptive sensory panel results, and an array of instrumental protocols. Regression models were constructed to predict awareness of skins, crispness, hardness, and visual separation explaining 85%, 91%, 82%, and 83% of variance respectively. Genotypes that scored most highly in breeders’ ratings of overall texture had soft skins and firm flesh, suggesting that both qualities are important targets for texture improvement in muscadine. We have also developed an R shiny based web-application, called ShinyFruit, for image-based analysis of fruit morphology and color quality. ShinyFruit was tested against manual methods of size and red drupelet reversion (RDR) estimation in a diverse population of blackberry cultivars and breeding selections. ShinyFruit results shared a strong positive correlation with manual measurements for blackberry length (r = 0.96) and significant, albeit weaker, correlations with manual RDR estimation methods (r = 0.62 - 0.70). Further validation of ShinyFruit’s potential was provided when it was used to generate phenotypic datasets across a genome wide association study (GWAS) panel of 300 diverse blackberry genotypes. This GWAS panel is the first reported in autotetraploid blackberry, and numerous quantitative trait loci (QTL) for blackberry texture and RDR were identified, spanning chromosomes Ra01, Ra02, Ra03, and Ra06. All QTL associated with RDR were located on Ra02 and most of these 212 single nucleotide polymorphisms (SNPs) were in high linkage disequilibrium. Three variants on homologs of polygalcturonase (PG), pectin methylesterase (PME), and β-glucosidase explained 27% of variance in fruit firmness and were located on chromosomes Ra06, Ra01, and Ra02 respectively. Both fruit firmness and RDR appear to be complex, moderately heritable traits, which may be most effectively incorporated into a genomic selection model. Expression-level evidence suggests that an inhibitor of PME may be associated with the fruit firmness QTL identified on Ra01. The expression of this PME inhibitor was negatively correlated with PME activity through fruit development in the ‘crispy’ fruited A-2453T. Expansin-like proteins were also expressed more highly in A-2453T compared to the soft-fruited ‘Black GemTM’, suggesting that this protein family could play a unique role in the ‘crispy’ texture phenotype. By combining newly developed phenotyping methods with informative genomic and transcriptomic datasets, we provide a strong foundation for continued research. Future improvement of texture in blackberry should prioritize training genomic selection models which could be trained on our accumulated datasets and supported by ShinyFruit phenotyping

Strategic irrigation against apple scab

Proceedings to the 15th International Conference on Organic Fruit Growing

Variations arising through tissue culture in soft fruits

The study mainly concerns the potential of the tissue culture for mass propagation and to evaluate the trueness to type of regenerated plants from tissue culture using appropriate molecular markers. Three soft fruits species Ribes, Fragaria and Rubus were used in this study. The study has three main sections dealing with an evaluation of appropriate molecular marker systems to study the plants regenerated via micropropagation, callus culture and regeneration and tissue culture and regeneration.The first section evaluates the potential of SDS-PAGE protein electrophoresis and RAPD-PCR as markers to distinguish among clonally propagated cultivars of R. nigrum. SDS-PAGE was able to distinguish only four out of ten cultivars tested. RAPD-PCR was able to distinguish all the cultivars studied using only two primers. The data generated by RAPD-PCR and from pedigree information was used to examine the relatedness among the cultivars studied. RAPD-PCR was further used to examine the purity of the cultivar Baldwin collected at various locations in the UK. Polymorphism was detected and differences were found between the sub-samples of a single cultivar.The second section deals with the multiplication of Rubus, Ribes and Fragaria by micropropagation. The effect of culture cycle on the plants regenerated was evaluated using RAPD-PCR. Ribes did not show any variation until the 14th generation cycle but in the 15th and 16th cycles variation was detected from 6.2% and 13.4% respectively. Considerable variation was detected in Rubus starting with the 4th sub-culture and was at a maximum in the 7th sub-culture. In Fragaria. all plants at sub-culture 3 were evaluated and variation was detected between them. The relevance of such variation on the release of material of all three species is discussed in relation to certification scheme requirements.The third experimental section evaluates the potential of callus as explant source for the multiplication and regeneration of plants in Ribes and Fragaria species. The study also describes investigations in the optimum growth regulators concentrations for callus culture and subsequent plant regeneration. Both the explant type leaf disc and leaf petiole showed successful callus induction in Ribes cultivars. However, plant regeneration was not successful in the cultivars and explant sources studied. In Fragaria regeneration was easily achieved from leaf disc callus and the plants were evaluated for trueness to type using RAPD-PCR This indicated variation ranges from 0.68 to 22.80%.The final discussion reviews micropropagation, callus culture and regeneration and their application to mass propagation. The use of molecular marker systems to evaluate multiplication methodology is discussed both in terms of the needs of the soft fruits industry and as the general approach to the evaluation of progeny of clonally propagated species

Ornamental plants: a summary of research, 1993-1994

Aesthetic evaluation of crabapples at the Secrest Arboretum in Wooster, Ohio: 1993-1994 / Erik A. Draper and James A. Chatfield -- Evaluation of crabapples for apple scab at the Secrest Arboretum in Wooster, Ohio: 1993-1994 / James A. Chatfield and Erik A. Draper -- The Ohio State University Water Quality Assessment Program / Mary Ann Rose, John Peterson and Laura Kramer -- Root rot of Taxus spp in Ohio caused by Phytophthora cinnamomi / Michael A. Ellis, Sally A. Miller, August F. Schmitthenner and Kenneth D. Cochran -- Winter injury on woody ornamental plants in Ohio: the winter of 1993-1994 / T. Davis Sydnor, James A. Chatfield, Randall H. Zondag, Pamela J. Bennett, Joseph F. Boggs, Kenneth D. Cochran -- Ornamental plant problems in Ohio: 1994 / James A. Chatfield, David J. Shetlar, Nancy Taylor, Joseph F. Boggs, Pamela J. Bennett, Randall H. Zondag, Michael A. Ellis, Allen Baumgard -- Ornamental plant problems in Ohio: 1993 / James A. Chatfield, Joseph F. Boggs, Paul Kauffman, David J. Shetlar, Nancy Taylor, Randall H. Zonda

Dissecting the impact of environment, season and genotype on blackcurrant fruit quality traits.

This work aims to determine the effect of genotype x environment (GxE) interaction that influence blackcurrant (Ribes nigrum) fruit quality. We applied metabolomics-driven analysis on fruits from four cultivars grown in contrasting European-locations over two seasons. By integrating metabolomics and sensory analysis, we also defined specific metabolic signatures associated with consumer acceptance. Our results showed that rainfall is a crucial factor associated with accumulation of delphinidin- and cyanidin-3-O-glucoside, the two mayor blackcurrant pigments meanwhile temperature affects the main organic acid levels which can be decisive for fruit taste. Sensorial analysis showed that increases in terpenoid and acetate ester volatiles were strongly associated with higher appreciation score, while proacacipetalin, a cyanogenic-glycoside, was positively associated to bitter taste. Our results pave the way for the selection of high-quality cultivars and suitable production sites for blackcurrant cultivation.publishedVersio

A review on metabolomics for quality improvement of fruit crops

The field of metabolomics is gaining ground in plant biology, and its potential uses in agricultural biotechnology are expanding. Metabolomics is the study of metabolites, which are extremely small molecules. The phenotype correlates more strongly with the metabolomic profile than with the genomic, transcriptomic, or proteomic profiles. Plant metabolic profiling is another application of metabolomics that has been used to identify previously uncharacterized genes and their roles. The use of metabolomics to evaluate mutants and transgenic plants, track fruit development, determine quality, detect disease resistance, determine abiotic stress tolerance, etc., has become increasingly important. Metabolomics has also been applied to plant studies, which have become increasingly important in efforts to improve fruit quality. We first assess the profound influence metabolomics has had over the past decade, then provide an introduction to the field, its current contribution, and the hope it holds for enhancing fruit production