Multi-scale models can facilitate whole plant simulations by linking gene networks, protein synthesis, metabolic pathways, physiology, and growth. Whole plant models can be further integrated with ecosystem, weather, and climate models to predict how various interactions respond to environmental perturbations. These models have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts. Outcomes will potentially accelerate improvement of crop yield, sustainability, and increase future food security. It is time for a paradigm shift in plant modeling, from largely isolated efforts to a connected community that takes advantage of advances in high performance computing and mechanistic understanding of plant processes. Tools for guiding future crop breeding and engineering, understanding the implications of discoveries at the molecular level for whole plant behavior, and improved prediction of plant and ecosystem responses to the environment are urgently needed. The purpose of this perspective is to introduce Crops in silico (cropsinsilico.org), an integrative and multi-scale modeling platform, as one solution that combines isolated modeling efforts toward the generation of virtual crops, which is open and accessible to the entire plant biology community. The major challenges involved both in the development and deployment of a shared, multi-scale modeling platform, which are summarized in this prospectus, were recently identified during the first Crops in silico Symposium and Workshop.

Fruit size regulation was studied in the apple cultivar ‘Gala’ and a large fruit size spontaneous mutant of ‘Gala’, ‘Grand Gala’ (GG). GG fruits were 15% larger in diameter and 38% heavier than ‘Gala’ fruits, largely due to an increase in size of the fruit cortex. The mutation in GG altered growth prior to fruit set and during fruit development. Prior to fruit set, the carpel/floral-tube size was enhanced in GG and was associated with higher cell number, larger cell size, and increased ploidy through endoreduplication, an altered form of the cell cycle normally absent in apple. The data suggest that the mutation in GG promotes either cell production or endoreduplication in the carpel/floral-tube cells depending on their competence for division. Ploidy was not altered in GG leaves. During fruit growth, GG fruit cells exited cell production earlier, and with a DNA content of 4C suggesting G2 arrest. Cell size was higher in GG fruits during exit from cell production and at later stages of fruit growth. Final cell diameter in GG fruit cortex cells was 15% higher than that in ‘Gala’ indicating that enhanced fruit size in GG was facilitated by increased cell size. The normal progression of cell expansion in cells arrested in G2 may account for the increase in cell size. Quantitative RT-PCR analysis indicated higher MdCDKA1 expression and reduced MdCYCA2 expression during early fruit development in GG fruits. Together, the data indicate an important role for cell expansion in regulating apple fruit size.

Floral development was studied in buds of `Starkspur Supreme Delicious' apple trees growing on B.9, M.26 EMLA, M.7 EMLA, P.18, and seedling rootstocks. In each of 3 years, buds were sampled from the previous years growth at intervals throughout the growing season and dissected to determine whether the apex was domed, indicating the start of floral development. Number of bud scales and true leaves increased during the early part of the growing season, but remained fairly constant beyond 70 days after full bloom. The type of rootstock did not affect the number of bud scales or transition leaves, and effects on true leaf numbers were small and inconsistent. Final bract number per floral bud was similarly unaffected by rootstock. The proportion of buds in which flowers were formed was influenced by rootstock in only one year of the study, which was characterized by high temperatures and low rainfall over the period of flower formation. Bracts were observed only in floral buds, and became visible after doming of bud apices had occurred. Flowers were formed during the first 20 days in August, regardless of rootstock or year. The appendage number of vegetative buds was constant from 70 days after full bloom until the end of the growing season, but the number of appendages in floral buds increased due to the continued production of bracts. The critical bud appendage number for `Starkspur Supreme Delicious' before flower formation was 20, and was stable among rootstocks and years. Buds with diameters above 3.1 mm were generally floral, but on this basis only 65% of buds could be correctly classified. Spur leaf number, spur leaf area, and spur leaf dry weight were not good predictors of floral formation within the spur bud.

Microwave-assisted extraction (MAE) of phenolic antioxidants from the pomace of Red Delicious and Jonathan apple varieties was optimized using response surface methodology. Optimization parameters included solvent type, microwave power, solvent volume to sample ratio and extraction time. Optimum conditions were based on the total polyphenol content (TPC) of extracts. Antioxidant activities of optimized extracts were also measured by inhibition percentage (IP) of the DPPH (2,2-diphenyl-1-picrylhydrazyl) free radical. High-performance liquid chromatography was used to identify and quantify some of the major phenolics extracted. Red Delicious pomace had the highest TPC (15.8 mg GAE/g) obtained under the optimum extraction conditions of 735 W power and 149 s extraction time with 10.3 mL of ethanol per gram dry sample. The DPPH IP of this extract was 77.1%. Phloridzin, caffeic acid, chlorogenic acid and quercetrin were some of the major polyphenols identified in the extracts. MAE was found to be an effective method of extracting antioxidant compounds from apple pomace. PRACTICAL APPLICATIONSExtraction of phenolics from apple pomace using microwave-assisted extraction (MAE) has significant potential compared with traditional extraction methods, as it significantly reduces extraction time and solvent consumption while generating higher extraction yields. The optimized extraction conditions obtained in this study resulted in extracts with high concentrations of polyphenols and high DPPH (2,2-diphenyl-1-picrylhydrazyl) radical-scavenging activity. Optimized extraction conditions were found to be independent of apple variety and therefore can be extended to extraction of phenolics from the pomace of other apple cultivars. This work opens the door for further research on the feasibility of an industrial-scale continuous MAE process for the recovery of these valuable compounds from apple pomace. In addition, there is promise for these value-added extracts to be used in a number of applications, including the extension of product shelf life (as an alternative to synthetic antioxidants), functional food ingredients and dietary supplements.

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Fifteen sequences of sunlight exposure and exclusion were imposed on fruit of 'Granny Smith' apple (Malus domestica BorIch.) by covering individual fruit with opaque paper bags. Fruit were harvested at commercial maturity and fruit background colour, blush, soluble solids concentration, flesh fIrmness, and starch pattern index were measured. The following year, seven of the same sequences were repeated and fruit colour was measured at lO-day intervals beginning from fruit drop until commercial harvest. A strong linear relationship between fruit colour lightness and hue (visually perceived colour) was evident in both years. Fruit became lighter as greenness decreased while an increasing yellowness only slightly increased lightness. Longer durations oflight exclusion resulted in lighter coloured fruit, but for a given duration of shading, fruit exposed 1 month before harvest were lighter than fruit which remained shaded until harvest. All fruit became lighter in colour with time, although the rate at which fruit became paler was increased by profound shading. The incidence and severity of blush was highest on fruit from which light had been excluded for more than 2 months and then re-exposed 1 to 2 months before harvest. Exclusion of light depressed the soluble solids concentration slightly, although flesh firmness and starch index were unaffected.

Two-year-old branch sections of `Starkspur Supreme Delicious' apple (Malus domestics Borkh.) trees growing on 17 rootstock were studied over 6 years to determine the effects of rootstock on shoot morphology and spur quality and describe how these factors may be related to precocity and productivity. Shoot length was affected by rootstock and was positively related to trunk cross-sectional area within each year, but the slope of the regression line decreased as trees matured. The number of spurs on a shoot was largely a product of shoot length. Spur density was inversely related to shoot length, where rootstock with longer shoots had lower spur densities. Flower density was not related to spur density, and shoot length only accounted for a minor part of the variation in flower density. The proportion of spurs that produced flowers was closely related to flower density, indicating that rootstock influence flower density by affecting the development of individual buds rather than by the production of more buds. More vigorous rootstock generally had spurs with larger individual leaves and higher total leaf area per spur, but fewer spur leaves with lower specific leaf weights. More precocious rootstock were also more productive over a 10-year period when yields were standardized for tree size. Tree size was the best indicator of precocity and productivity, which could be predicted with a high degree of certainty as early as the 4th year.

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