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Realizing the potential of agricultural genomics into practical applications requires quantitative predictions for complex traits and different genotypes and environmental conditions. The objective of this study was to develop and test a procedure for quantitative prediction of phenotypes as a function of environment and specific genetic loci in soybean [Glycine max (L.) Merrill]. We combined the ecophysiological model CROPGRO-Soybean with linear models that predict cultivar-specific parameters as functions of E loci. The procedure involved three steps: (i) a field experiment was conducted in Florida in 2001 to obtain phenotypic data for a set of near-isogenic lines (NILs) with known genotypes at six E loci; (ii) we used these data to estimate cultivar-specific parameters for CROPGRO-Soybean, minimizing root mean square error (RMSE) between observed and simulated values; (iii) these parameters were then expressed as linear functions of the (known) E loci. CROPGRO-Soybean predicted various phenological stages for the same NILs grown in 2002 in Florida with a RMSE of about 5 d using the E loci-derived parameters. A second evaluation of the approach used phenotypic data from cultivar trials conducted in Illinois. Cultivars were genotyped at the E loci using microsatellites. The model predicted time to maturity in the Illinois variety trials with RMSE around 7.5 d; it also explained 75% of the time-to-maturity variance and 54% of the yield variance. Our results suggest that gene-based approaches can effectively use agricultural genomics data for cultivar performance prediction. This technology may have multiple uses in plant breeding.

Climate change due to increased [CO2] and elevated temperature may impact the composition of crop seed. This study was conducted to determine the potential effects of climate change on composition and gene expression of soybean [Glycine max (L.) Merr. cv. ‘Bragg’] seed. Soybean plants were grown in sunlit, controlled environment chambers under diel, sinusoidal temperatures of 28/18, 32/22, 36/26, 40/30, and 44/34°C (day/night, maximum/minimum), and two levels of [CO2], 350 and 700 μmol mol−1, imposed during the entire life cycle. The effect of temperature on mature seed composition and transcripts in developing seed was pronounced, but there was no effect of [CO2]. Total oil concentration was highest at 32/22°C and decreased with further increase in temperature. Oleic acid concentration increased with increasing temperature whereas linolenic acid decreased. Concentrations of N and P increased with temperature to 40/30°C, then decreased. Total nonstructural carbohydrates (TNC) decreased as temperatures increased, and the proportion of soluble sugars to starch decreased. Transcripts of a gene that is downregulated by auxin (ADR12) were dramatically downregulated by elevated temperature, possibly reflecting the altered course of seed development under environmental stress. Transcripts of β‐glucosidase, a gene expressed during normal soybean seed development, were detected in seed grown at 28/18°C but not in seed grown at 40/30°C, which also suggests that normal programs affecting seed composition were perturbed by elevated temperature. These results confirm previous studies indicating that high temperature alters soybean seed composition, and suggest possible mechanisms by which climate change may affect soybean seed development and composition.

Here we present the results from an intercomparison of multiple global gridded crop models (GGCMs) within the framework of the Agricultural Model Intercomparison and Improvement Project and the Inter-Sectoral Impacts Model Intercomparison Project. Results indicate strong negative effects of climate change, especially at higher levels of warming and at low latitudes; models that include explicit nitrogen stress project more severe impacts. Across seven GGCMs, five global climate models, and four representative concentration pathways, model agreement on direction of yield changes is found in many major agricultural regions at both low and high latitudes; however, reducing uncertainty in sign of response in mid-latitude regions remains a challenge. Uncertainties related to the representation of carbon dioxide, nitrogen, and high temperature effects demonstrated here show that further research is urgently needed to better understand effects of climate change on agricultural production and to devise targeted adaptation strategies.

Changes in temperature, CO2, and precipitation under the scenarios of climate change for the next 30 yr present a challenge to crop production. This review focuses on the impact of temperature, CO2, and ozone on agronomic crops and the implications for crop production. Understanding these implications for agricultural crops is critical for developing cropping systems resilient to stresses induced by climate change. There is variation among crops in their response to CO2, temperature, and precipitation changes and, with the regional differences in predicted climate, a situation is created in which the responses will be further complicated. For example, the temperature effects on soybean [Glycine max (L.) Merr.] could potentially cause yield reductions of 2.4% in the South but an increase of 1.7% in the Midwest. The frequency of years when temperatures exceed thresholds for damage during critical growth stages is likely to increase for some crops and regions. The increase in CO2 contributes significantly to enhanced plant growth and improved water use efficiency (WUE); however, there may be a downscaling of these positive impacts due to higher temperatures plants will experience during their growth cycle. A challenge is to understand the interactions of the changing climatic parameters because of the interactions among temperature, CO2, and precipitation on plant growth and development and also on the biotic stresses of weeds, insects, and diseases. Agronomists will have to consider the variations in temperature and precipitation as part of the production system if they are to ensure the food security required by an ever increasing population.

Unique capabilities of various systems for studying the impacts of rising atmospheric CO2 concentration and other environmental factors on growth and yield of plants are presented. These systems include soil–plant–atmosphere research (SPAR) chambers, free‐air carbon dioxide enrichment (FACE) facilities, temperature‐gradient greenhouses (TGG), and open top chambers (OTC). The SPAR chambers have several advantages compared to FACE and other facilities, including: (a) constant CO2 concentration and stabile setpoints; (b) CO2 concentration controlled to any range of sub‐ambient through supra‐ambient levels, providing comparison of plant responses to past and future climates; (c) precise air and dewpoint temperature setpoints; (d) calculation of whole‐canopy photosynthesis and evapotranspiration rates at short time intervals; (e) calculation of whole‐canopy respiration rates during the night; (f) determination of plant responses to temperature alone or including other factors; (g) multiple chambers for simultaneous comparison of plant responses to varying environments, providing data for plant growth modeling; (h) low operating expense for CO2 concentration; and (i) capability of measuring N2 fixation rates in the rooting zone of legumes or methane emissions from rice (Oryza sativa L.). SPAR systems were better suited than FACE systems for more than half of the attributes of enrichment systems identified in this paper. Limitations of plant responses due to fluctuating elevated CO2 concentration and limitations of range of elevated CO2 concentration exist for FACE systems. Controlled environments are needed for developing mathematical growth response functions under a wide range of conditions. Finally, we identified a use of portable SPAR chambers within FACE experiments for confirmation of diminished plant photosynthesis in fluctuating CO2 concentration.

Studies assessing the impact of climate change have focused on plant production, but forage nutritive value, especially of legumes, has often been overlooked. The objective of this study was to determine the effect of increasing temperature and atmospheric CO2 concentration on chemical composition and digestibility of rhizoma peanut (RP, Arachis glabrata Benth.) leaf and stem. In vitro digestible organic matter (IVDOM), neutral and acid detergent fiber (NDF and ADF), and lignin concentrations were determined for plants grown in all combinations of two CO2 (360 and 700 micromol mol(-1)) and four temperature environments (baseline, or ambient temperature in the greenhouse, B; B + 1.5; B + 3.0; and B + 4.5 degrees C). Forage was sampled every 6 to 8 wk during two growing seasons. Neither increasing CO2 nor temperature affected leaf IVDOM, but stem IVDOM declined from 562 (B) to 552 g kg(-1) (B + 4.5) with increasing temperature in Year 1 and from 577 to 511 g kg(-1) in Year 2. Stem NDF increased with increasing temperature from 556 to 561 g kg(-1) in Year 1 and from 519 to 526 g kg(-1) in Year 2. Stem ADF (412 to 418 g kg(-1)) and lignin (80 to 93 g kg(-1)) increased linearly as temperature increased in 1 of 2 yr. Lignin as a proportion of NDF or ADF (lignin/NDF or lignin/ADF) accounted for a large proportion of the variation in stem IVDOM. The RP nutritive value decreases with increasing air temperature, but it is relatively unaffected by atmospheric CO2 concentrations in the range studied.

‘Tifton 85’ bermudagrass (Cynodon spp.) has been widely adopted as a forage and hay crop and is being considered as a cellulosic ethanol feedstock. The objective of this study was to evaluate the effects of N fertilization rate on Tifton 85 regrowth dynamics. A field study was conducted near Gainesville, FL, on established Tifton 85 in 2006 and 2007. The treatments were N rates of 0, 45, 90, and 135 kg N ha−1 regrowth period−1. Tissue mass, leaf:stem ratio, and tiller number and mass were measured weekly during 28-d regrowth periods. Leaf mass followed logistic time trends with the upper asymptote varying between 50 and 225 g m−2 depending on N rate and season (summer and autumn). Stem mass lagged behind leaf mass for 7 to 14 d, subsequently following linear or quadratic time trends to reach between 75 and 300 g m−2 by 28 d. Increasing N rate from 0 to 135 kg ha−1 period−1 increased tiller mass at 28 d from 1.5 to 3 g tiller−1 in summer and 1 to 1.5 g tiller−1 in autumn. Leaf:stem ratio increased to 1.0 within 14 to 21 d, followed by a subsequent decrease. Rhizome and root mass were not affected by N fertilization. Increasing N rate primarily affected mass and proportion of above-ground plant parts, with little effect on mass of below-ground parts. Nitrogen nutrition index values were similar whether calculated from samples taken to a 10-cm stubble height or from samples taken to the soil surface. Regrowth was not enhanced by N rate beyond 90 kg N ha−1 regrowth period−1.

The development of functional root nodules resulting in N2 fixation in soybean [Glycine max (L.) Merr.] can be induced by two strains of rhizobia, Bradyrhizobium japonicum (B. japonicum) and Bradyrhizobium spp. (cowpea-type). Genetic control of response to each type has been recognized in soybeans with two categories identified after inoculation with cowpea-type rhizobial strains: (i) promiscuous, which produces functional nodules, N2 fixation, and green leaves; and (ii) nonpromiscuous, which forms no or nonfunctional nodules and yellow leaves. Using leaf color, segregation patterns indicated that nonpromiscuity was dominant with two alleles segregating at each of two independent loci. With this genetic model, the expression of promiscuity requires the presence of both recessive alleles at each locus. Since the cowpea strain is indigenous to the soils in many tropical areas, especially Africa, the development of promiscuous soybean cultivars would greatly increase soybean production without commercial seed inoculation.

A field study was conducted to determine the fate of atrazine (6‐chloro‐N2‐ethyl‐N4‐isopropyl‐1,3,5‐triazine‐2,4‐diamine) within the root zone (0 to 90 cm) of a sandy soil cropped with sorghum [Sorghum bicolor (L.) Moench] in Gainesville, Florida. Atrazine was uniformly applied at a rate of 1.12 kg a.i. ha−1 to a sorghum crop under moderate irrigation, optimum irrigation, and no irrigation (rainfed), 2 d after crop emergence. Bromide as a tracer for water movement was applied to the soil as NaBr at a rate of 45 kg Br− ha−1, 3 d before atrazine application. Soil water content, atrazine, and Br− concentrations were determined as a function of time using soil samples taken from the root zone. Atrazine sorption coefficients and degradation rates were determined by depth for the entire root zone in the laboratory. Atrazine was strongly adsorbed within the upper 30 cm of soil and most of the atrazine recovered from the soil during the growing season was in that depth. The estimated half‐life for atrazine was 32 d in topsoil to 83 d in subsoil. Atrazine concentration within the root zone decreased from 0.44 kg a.i. ha−1 2 days after application (DAA) to 0.1 kg a.i. ha−1 26 DAA. Negligible amounts of atrazine (≈5 μg kg−1) were detected below the 60‐cm soil depth by 64 DAA. Most of the decrease in atrazine concentration in the root zone over time was attributed to degradation. In contrast, all applied bromide had leached past the 60‐cm soil depth during the same time interval.

Carbohydrate and N reserves are important for perennial grass regrowth after defoliation. The objective of this study was to quantify the effects of N fertilization on dynamics of reserve accumulation and utilization for regrowth of a C4 perennial grass. A field study was conducted at Gainesville, FL, on established ‘Tifton 85’ bermudagrass (Cynodon spp.) in 2006 and 2007. Treatments were N rates of 0, 45, 90, and 135 kg N ha−1 regrowth period−1. Total nonstructural carbohydrate (TNC) and N concentrations, leaf area index (LAI), and canopy carbon exchange rate (CER) were measured weekly during 28-d regrowth periods. Stem and rhizome TNC concentrations decreased with increasing N rate, ranging from 20 to 80 mg g−1 for stem and 45 to 145 mg g−1 for rhizome, and followed quadratic time trends, with minima between 7 and 14 d of regrowth, suggesting reserve utilization up to 2 wk after defoliation. Leaf, stem, rhizome, and root N concentrations increased with N rate. Leaf and stem N concentrations followed quadratic time trends, with maxima between 7 and 14 d of regrowth, and ranged from 15 to 50 mg g−1 for leaf and 10 to 40 mg g−1 for stem. Rhizome N concentrations were constant throughout regrowth. Canopy CER and LAI followed logistic time trends within each 28-d regrowth period, with upper asymptotes raised by increased N rate. Nitrogen fertilization increased TNC reserve utilization, LAI, and canopy CER, thereby increasing shoot regrowth at rates up to 90 kg N ha−1 period−1.