Carbonate determination in soils by mid-IR spectroscopy with regional and continental scale models.

A Partial Least Squares (PLS) carbonate (CO3) prediction model was developed for soils throughout the contiguous United States using mid-infrared (MIR) spectroscopy. Excellent performance was achieved over an extensive geographic and chemical diversity of soils. A single model for all soil types performed very well with a root mean square error of prediction (RMSEP) of 12.6 g kg-1 and was further improved if Histosols were excluded (RMSEP 11.1 g kg-1). Exclusion of Histosols was particularly beneficial for accurate prediction of CO3 values when the national model was applied to an independent regional dataset. Little advantage was found in further narrowing the taxonomic breadth of the calibration dataset, but higher precision was obtained by running models for a restricted range of CO3. A model calibrated using only on the independent regional dataset, was unable to accurately predict CO3 content for the more chemically diverse national dataset. Ten absorbance peaks enabling CO3 prediction by mid-infrared (MIR) spectroscopy were identified and evaluated for individual and combined predictive power. A single-band model derived from an absorbance peak centered at 1796 cm-yielded the lowest RMSEP of 13.5 g kg-1 for carbonate prediction compared to other single-band models. This predictive power is attributed to the strength and sharpness of the peak, and an apparent minimal overlap with confounding co-occurring spectral features of other soil components. Drawing from the 10 identified bands, multiple combinations of 3 or 4 peaks were able to predict CO3 content as well as the full-spectrum national models. Soil CO3 is an excellent example of a soil parameter that can be predicted with great effectiveness and generality, and MIR models could replace direct laboratory measurement as a lower cost, high quality alternative.

Leaf-level water use efficiency determined by carbon isotope discrimination in rice seedlings: genetic variation associated with population structure and QTL mapping.

Increasing the water use efficiency (WUE) of our major crop species is an important target of agricultural research. Rice is a major water consumer in agriculture and it is also an attractive genetic model. We evaluated leaf-level WUE in young rice seedlings using carbon isotope discrimination (Delta(13)C) as an indicator of the trait. A survey of Delta(13)C was undertaken in 116 diverse germplasm accessions representing O. sativa, O. glaberrima and four wild Oryza species. O. sativa cultivars were classified into sub-populations based on SSR markers, and significant differences in Delta(13)C were observed among the five genetically defined groups. While individual accessions explained a greater proportion of the variation than did sub-population, indica rice varieties had the lowest Delta(13)C values overall, indicating superior WUE, while temperate japonica had the highest Delta(13)C. O sativa accessions had a similar or greater range of Delta(13)C values than wild Oryza species, while domesticated O. glaberrima had a narrower range. Correlation analysis identified leaf morphological and physiological traits that were significantly associated with Delta(13)C, including longer leaves, more drooping leaves, higher tillering ability, and lower leaf nitrogen content. These trait associations were investigated by quantitative trait locus (QTL) mapping using backcross inbred lines derived from a cross between Nipponbare (temperate japonica) and Kasalath (aus). Seven QTL for Delta(13)C were identified using composite interval analysis, located in five chromosomal regions. The QTL with the largest additive effect came from Kasalath and co-localized with QTL for leaf length, tiller number and nitrogen content.

Fine mapping a QTL for carbon isotope composition in tomato.

Carbon isotope composition (delta(13)C) and leaf water-use efficiency vary in concert in C3 plants, making delta(13)C useful as a proxy for plant water-use efficiency. A QTL for delta(13)C was detected in the Solanum pennellii chromosome fragment of IL5-4, an introgression line with S. lycopersicum cv. M82 background. M82 and IL 5-4 were crossed, and RFLP markers in the target region converted to PCR-based markers. Forty-one recombinants with an introgression fragment ranging in length from 1.1 to 11.4 cM were identified by marker assisted selection (MAS) among approximately 2000 F2 plants. A total of 29 markers were mapped within the introgression fragment unique to IL5-4. These markers divided the about 9 cM target region into nine intervals. A dominant QTL for delta(13)C, designated QWUE5.1 that explained 25.6% of the total phenotypic variance was mapped to an interval about 2.2 cM long. Twenty-one plants with a S. pennellii chromosome fragment shortened to a length of 2.0-9.1 cM by a second recombination event were generated by MAS of 1,125 F4 plants. Two near isogenic lines with high delta(13)C (small negative value) and carrying QWUE5.1 on the shortest introgression fragments (about 7.0 cM) were identified. The markers and genetic stocks developed are valuable for cloning the gene underlying QWUE5.1, MAS of QWUE5.1, and fine-mapping genes/QTL located in this region.

The effects of resource availability and environmental conditions on genetic rankings for carbon isotope discrimination during growth in tomato and rice.

Carbon isotope discrimination (Δ) is frequently used as an index of leaf intercellular CO2 concentration (ci) and variation in photosynthetic water use efficiency. In this study, the stability of Δ was evaluated in greenhouse-grown tomato and rice with respect to variable growth conditions including temperature, nutrient availability, soil flooding (in rice), irradiance, and root constriction in small soil volumes. Δ exhibited several characteristics indicative of contrasting set-point behaviour among genotypes of both crops. These included generally small main environmental effects and lower observed levels of genotype-by-environment interaction across the diverse treatments than observed in associated measures of relative growth rate, photosynthetic rate, biomass allocation pattern, or specific leaf area. Growth irradiance stood out among environmental parameters tested as having consistently large main affects on Δ for all genotypes screened in both crops. We suggest that this may be related to contrasting mechanisms of stomatal aperture modulation associated with the different environmental variables. For temperature and nutrient availability, feedback processes directly linked to ci and / or metabolite pools associated with ci may have played the primary role in coordinating stomatal conductance and photosynthetic capacity. In contrast, light has a direct effect on stomatal aperture in addition to feedback mediated through ci.

Hydraulic and chemical signalling in the control of stomatal conductance and transpiration.

Abscisic acid (ABA) transported in the xylem from root to shoot and perceived at the guard cell is now widely studied as an essential regulating factor in stomatal closure under drought stress. This provides the plant with a stomatal response mechanism in which water potential is perceived in the root as an indication of soil water status and available water resources. There is also ample evidence that stomata respond directly to some component of leaf water status. This provides additional information about water potential gradients developing between root and shoot as the result of water transport, allowing for a more stable regulation of shoot water status and better protection of the transport system itself. The precise location at which leaf water status is sensed, however, and the molecular events transducing this signal into a guard cell response are not yet known. Major questions therefore remain unanswered on how water stress signals perceived at root and leaf locations are integrated at the guard cell to control stomatal behaviour.

Seasonal carbon isotope discrimination in a grassland community.

Grassland communities of arid western North America are often characterized by a seasonal increase in ambient temperature and evaporative demand and a corresponding decline in soil moisture availability. As the environment changes, particular species could respond differently, which should be reflected in a number of physiological processes. Carbon isotope discrimination varies during photosynthetic activity as a function of both stomatal aperture and the biochemistry of the fixation process, and provides an integrated measure of plant response to seasonal changes in the environment. We measured the seasonal course of carbon isotope discrimination in 42 grassland species to evaluate changes in gas exchange processes in response to these varying environmental factors. The seasonal courses were then used to identify community-wide patterns associated with life form, with phenology and with differences between grasses and forbs. Significant differences were detected in the following comparisons: (1) Carbon isotope discrimination decreased throughout the growing season; (2) perennial species discriminated less than annual species; (3) grasses discriminated less than forbs; and (4) early flowering species discriminated more than the later flowering ones. These comparisons suggested that (1) species active only during the initial, less stressful months of the growing season used water less efficiently, and (2) that physiological responses increasing the ratio of carbon fixed to water lost were common in these grassland species, and were correlated with the increase in evaporative demand and the decrease in soil moisture.