Soil organic carbon (C) plays a critical role in supporting the productive capacity of soils and their ability to provide a wide range of ecologically important functions including the storage of atmospherically derived carbon dioxide (CO2). The present paper collates available information on Scottish soil C stocks and C losses and reviews the potential pressures on terrestrial C, which may threaten future C stocks. Past, present and possible future land use, land management practices and land use changes (LUCs) including forestry, agriculture, nitrogen (N) additions, elevated CO2 and climate change for Scotland are discussed and evaluated in relation to the anthropogenic pressures on soil C.

The review deduces that current available data show little suggestion of significant changes in C stocks of Scottish soils, although this may be due to a lack of long-term trend data. However, it can be concluded that there are many pressures, such as climate change, intensity of land use practices, scale of LUC, soil erosion and pollution, which may pose significant threats to the future of Scottish soil C if these factors are not taken into consideration in future land management decisions. In particular, this is due to the land area covered by vulnerable peats and highly organic soils in Scotland compared with other areas in the UK. It is therefore imperative that soil C stocks for different land use, management practices and LUCs are monitored in more detail to provide further insight into the potential changes in sequestered C and subsequent greenhouse gas emissions, as advised by the United Nations Framework Convention on Climate Change (UNFCCC).

The identification of factors determining the adaptation and nitrogen (N) utilization of spelt wheat is important for the successful introduction of the crop to a new environment. The present study was carried out to investigate the relative importance of grain-filling rate and duration of grain growth and to analyse the nitrogen utilization efficiency (NUtE) and biomass production efficiency of spelt under Mediterranean conditions. The performance of spelt was evaluated in relation to a well-adapted bread wheat cultivar. Three spelt cultivars (Ressac, Poème and Cosmos) and one bread wheat cultivar (Centauro) were grown for two growing seasons on a silty clay soil under two N levels (0 and 100 kg N/ha). Grain-filling parameters were estimated using the cubic polynomial model. This model provided good fit to the grain-filling data of spelt cultivars, with high coefficients of determination (R2) that ranged from 0·868 to 0·999. Cultivar differences were found for all grain-filling parameters studied, and these differences accounted for most of the variation observed within each particular grain-filling component in both years. Grain filling of spelt plants took place under adverse environmental conditions, mainly high temperatures, which led to a shortening of the grain-filling period. This fact was not fully compensated by the increase in the grain-filling rate, and eventually resulted in a reduction of the final spelt grain weight. Selection for early-flowering cultivars could be a successful strategy to moderate the influence of the environment on grain filling and improve the adaptation of spelt under Mediterranean conditions. The mean grain-filling rate was positively correlated with dry matter translocation, suggesting the crucial role of reserve assimilates in the vegetative tissues for the grain growth of spelt. The efficiency of N utilization to produce biomass was greater during the grain-filling period than the vegetative period. Averaged across N application rates, NUtE in spelt ranged from 20·1 to 29·5 g grain/g plant N. Cultivar differences in NUtE were observed in both years. Grain yield per unit grain N (grain DM/grain total N at maturity) contributed more to the total variation in NUtE among spelt cultivars compared with N harvest index (NHI). Spelt showed lower NUtE values, probably due to its higher grain N concentration and lower NHI compared with wheat. Low straw N concentration at maturity may be an indicator of improved NUtE in spelt, as evidenced by the negative relationship detected between the two variables. These results provide a better understanding of factors related with the adaptation and N utilization of spelt under Mediterranean conditions.

Alfalfa is a model plant defined as less sensitive than others to iron (Fe) deficiency. In the present work, some mechanisms induced in low Fe availability conditions were studied, including the effect of inoculation of alfalfa seeds with Pseudomonas putida. The effect of different Fe contents in the nutrient solution on the growth parameters was evaluated at 3 and 10 days, observing that low Fe conditions promoted biomass accumulation. Activation in the mechanisms of Fe acquisition, through acidification of the media and an increase in the ferric chelate reductase (FCR) activity, was observed in the absence of Fe at 10 days. The presence of P. putida KT2442 in the rhizosphere eliminated FCR activation through the excretion of siderophores. The effect of the siderophores on the modulation of FCR activity was demonstrated using a ppsD mutant strain, unable to segregate them, observing an activation of the activity similar to that observed in the absence of the bacteria. This, together with the demonstrated mechanisms to increase Fe availability, contributed to the conclusion that alfalfa can be used for recovery programmes of soils with low Fe availability.

Incorporation of rice straw into soil has traditionally been an important method of recycling nutrients and improving soil productivity. Currently, although the effects of straw incorporation on disease severity have been documented, the dynamics of the pathogen in soil after straw incorporation are poorly understood. In the present study, rice straw with various proportions of diseased straw was incorporated at three separate locations (SuPu town, SuSong County and FengYang County) in Anhui province, China. The pathogen dynamics in paddy soil and disease severity of sheath blight during two continuous years from April 2010 to April 2012 were investigated. For all three locations, the amount of pathogen inoculum that persisted in the soil increased with increases in the proportion of diseased straw incorporated. Incorporation of 0·3 and 0·5 diseased straw into soil increased the amount of pathogen inoculum in the soil significantly, whereas incorporation of 0·1 diseased straw into soil had no significant effect on the pathogen inoculum compared with the control (no straw incorporated) or disease severity. Incorporation of healthy rice straw (no disease) resulted in a significant decrease in disease severity, whereas proportions of 0·3 and 0·5 diseased straw resulted in a significant increase of disease severity compared with the control. These results suggested that incorporation of diseased straw enhanced pathogen numbers in soil during the whole decomposition period and increased disease severity. To avoid soil-borne disease accumulation, severely diseased straw should be removed from the field or pre-treated before incorporation.

Cultivated lentil (Lens culinaris L.) landraces offer a challenge to exploiting their genetic variability and deriving new pure-line varieties. For insect-transmitted viruses, low densities favour increased virus spread. The objective of the present work was to evaluate a selection procedure applied within a landrace under ultra-low plant density and low-input conditions toward the isolation of high-performing genotypes that escape virus infection. Field trials were conducted through four growing seasons (2006–2011) in the Democritus University of Thrace research farm in Orestiada, Greece. Selection of individual plants for high grain yield was applied for three generations, while virus presence was tested by enzyme-linked immunosorbent assay in the seeds used or the plants selected in each selection cycle. Early high plant-to-plant phenotypic variability, reflected by high coefficient of variation (CV) values, was partly attributed to virus infection. However, sister lines were consistently higher yielding and of lower CV than the mother population (MP). Second generation lines yielded up to 136 and 23% more than the source landrace at the ultra-low density and dense stand, respectively. Pea seed-borne mosaic virus was detected in the seeds of the MP, whereas bean yellow mosaic virus and bean leafroll virus were mainly involved in the subsequent selection rounds. In general, the highest-yielding plants were free of the viruses detected during experimentation. It was concluded that selection at ultra-low density of the highest-yielding plants from the sister lines with the lowest CV constitute an effective way to improve the health status of the seeds produced and result in high yielding and potentially virus-tolerant pure-line varieties.

Two winter wheat (Triticum aestivum L.) cultivars, Jimai20 and Shannong12, differing in phosphorus (P) utilization efficiency, were selected to study the effect of P application rate on changes in glutenin macropolymer (GMP) size distribution and the content of high-molecular-weight glutenin subunits (HMW-GS) in wheat grain. Four P levels (0, 40, 100 and 160 kg/ha) were applied under N1 (112·5 kg/ha) and N2 (225 kg/ha) conditions in the field, in 2008/09 and 2009/10. The results showed that increased P levels favoured HMW-GS synthesis under N1 conditions, but had a less pronounced effect under N2. When compared with the control, the volume proportions of <10 μm GMP particles in grains of both cultivars were significantly decreased, and those of >100 μm were increased in response to P application. The volume proportions of 10–100 μm GMP particles in the cultivars Jimai20 and Shannong12 were respectively lower and higher in response to P application than with no P fertilizer. At maturity, for both cultivars, total HMW-GS content was negatively correlated with GMP particle volume of <10 μm, but positively correlated with that of >100 μm. These observations suggest that both P and N affect protein synthesis in wheat grains and there exists a relationship between HMW-GS content and the synthesis of large GMP particles (>100 μm). The N×P interaction was the most important factor to regulate the HMW-GS and GMP contents.

Winter oilseed rape (Brassica napus) is an important crop for human consumption and biofuel production and its production is increasing worldwide. It is generally assumed that cross-pollination by insects increases oilseed rape yield but testing of this has been restricted to a few rapeseed varieties and produced varying results. The present study determines whether cross-pollination benefits a number of oilseed rape varieties by comparing yield in the presence and absence of insects. Four rapeseed varieties (Sherlock, Traviata, Treffer and Visby) were used with ten individuals each in four pollination treatments: (1) supplementary hand-pollination, (2) open pollination with insects able to access the flowers, (3) wind pollination and (4) autonomous self-pollination. Across all four varieties, open and supplementary hand-pollination treatments resulted in higher fruit set, numbers of seeds per pod and seed yield compared with wind and self-pollination. The cross-pollination benefits, however, differed among rapeseed varieties: Treffer and Visby had a higher dependence on open (insects) and supplementary cross-pollination than Sherlock and Traviata. Across all four varieties, seed weight compensated for reduced fruit set and was highest when plants were self-pollinated. The present results highlight the importance of considering varietal differences in crop pollination research. Information on the pollination requirements of crop varieties is required by farmers to optimize management decisions in a world of increasing agropollination deficits.

Helianthus tuberosus L. is regarded as one of the most important bioenergy crops because of its tolerance to arid conditions and its high biomass production. Future breeding programmes will rely on the available germplasm, thus necessitating a critical assessment of genetic diversity and differentiation in the species. The germplasm diversity and regional differentiation of H. tuberosus L. was assessed for 60 accessions collected from East Asia and Europe by means of amplified fragment length polymorphisms (AFLPs), phenotypic traits and chemical analysis. The analysis did not reveal separate clusters for accessions from East Asia and Europe, with 5% for genetic and 0·27% for phenotypic variability, although some regional accessions were closely related to each other with respect to morphological, chemical and genetic variation. Both phenotypic and genetic relationships showed a moderate correlation with colour of tubers, which can be used as an important criterion for germplasm management of the crop. Three major genetic groups were identified from the accessions. Within the groups derived from the genetic data, both morphological and chemical traits were very variable. The most important features of Groups I, II and III were: Group I, strong sexual reproduction, higher above-ground biomass and nutrient content; Group II, longer vegetative growth; Group III, higher tuber yield and total sugar content. High diversity was found in both European and East Asian accessions as well as within each genetic group, suggesting that there is a strong base for future breeding from these plants.

Changes of sucrose metabolism in the subtending leaf to cotton (Gossypium hirsutum L.) boll at different fruiting branch nodes (FBN) were investigated. Two cotton cultivars, Kemian 1 and Sumian 15, were grown in the field at three planting dates in 2009 and 2011. Cotton planted on different dates but experiencing similar climatic factors flowered on the same date and had similar boll opening dates, but had different FBN. In the present study, boll weight and carbohydrate content were significantly affected by both flowering date (FD) and FBN. However, only cystolic fructose-1,6-bisphosphatase (cy-FBPase) and sucrose-phosphate synthase (SPS) activities of the sucrose-metabolizing enzymes were influenced significantly by FBN, and the influence of FBN was lower with delayed FD. In general, effects of FBN on boll weight and sucrose metabolism in the subtending leaf were higher at the optimal FD (13 August) than those at later FD (9 September 2009 and 2 September 2011), and total fruiting branches were used to characterize cotton physiological age in the current study. Sucrose transport capacity (Tn) and SPS in the subtending leaf had significantly positive correlations with boll weight at 17–24 days post anthesis (DPA), a crucial period when boll weight was significantly affected. In addition, higher SPS activity was favourable for sucrose export and boll weight during boll development.

Feed makes up c. 0·7 of total variable costs on Irish beef farms. A period of reduced growth (caused by nutritional restriction) followed by a period of accelerated growth (compensatory growth) can be used to take advantage of lower cost feedstuffs (grazed grass) during the grazing season. The Grange Dairy Beef Systems Model (GDBSM) was modified to capture more accurately the implications of compensatory growth and, thus, the energy demand of beef cattle was partitioned into energy required for maintenance and energy required for growth. For the current study, three production systems were evaluated where the male progeny of dairy cows were finished as steers at 24 (S24), 28 (S28) and 30 (S30) months of age. Three different live weight gains (RESLWG; 0·4, 0·6 and 0·8 kg/day), reflecting different levels of nutritional restriction, were simulated during the first winter feeding period (November–February) for S24 and during the second winter feeding period for S28 and S30. This allowed the effect of different live weight gains during a nutritional restriction period on farm profitability to be determined. Results indicated that for S24 the most profitable RESLWG was 0·6 kg/day. However, for S28 and S30 the most profitable systems were RESLWG of 0·4 kg/day. Financial performance of all systems was very sensitive to variation in beef carcass and calf prices but less sensitive to concentrate and fertilizer price variation. Furthermore, sensitivity analysis showed that the level of maintenance energy reduction and the duration of this reduction had a modest impact on results. The GDBSM is demonstrated as a quantitative framework for simulating compensatory growth and determining its effects on the profitability of dairy calf-to-beef production systems.

The classification of land usage in mountain grassland bovine areas is important for the management of forage production and grazing in grass-based livestock systems. The present paper proposes a novel, hierarchical neural network-based approach towards the classification of land usage in these areas. A survey of 72 farms was conducted in the Massif Central (France). Information was gathered on geographical characteristics and cutting and/or grazing practices on three general groups of fields: cut only, cut and grazed and grazed only fields. To classify land usage, the data were clustered and visualized in a hierarchical fashion. This was done by using a novel method for the analysis and classification of data based on growing hierarchical self-organizing maps (GHSOM). Self-organizing maps (SOM) have been shown to be successful for the analysis of highly dimensional input data in data mining applications as well as for data visualization. Moreover, the hierarchical architecture of the GHSOM is more flexible than a single SOM in the adaptation process to input data, capturing inherent hierarchical relationships among them. Experimental results show the utility of this approach.

The objective of the current study was to assess the use of nonlinear mixed model methodology to fit the growth curves (weight v. time) of two dairy goat genotypes (Alpine, +A and Saanen, +S). The nonlinear functions evaluated included Brody, Von Bertalanffy, Richards, Logistic and Gompertz. The growth curve adjustment was performed using two steps. First, random effects u1, u2 and u3 were linked to the asymptotic body weight (β1), constant of integration (β2) and rate constant of growth (β3) parameters, respectively. In addition to a traditional fixed-effects model, four combinations of models were evaluated using random variables: all parameters associated with random effects (u1, u2 and u3), only β1 and β2 (u1 and u2), only β1 and β3 (u1 and u3) and only β1 (u1). Second, the fit of the best adjusted model was refined by using the power variance and modelling the error structure. Residual variance ($\sigma _e^2 $) and the Akaike information criterion were used to evaluate the models. After the best fitting model was chosen, the genotype curve parameters were compared. The residual variance was reduced in all scenarios for which random effects were considered. The Richards (u1 and u3) function had the best fit to the data. This model was reparameterized using two isotropic error structures for unequally spaced data, and the structure known in the literature as SP(MATERN) proved to be a better fit. The growth curve parameters differed between the two genotypes, with the exception of the constant that determines the proportion of the final size at which the inflection point occurs (β4). The nonlinear mixed model methodology is an efficient tool for evaluating growth curve features, and it is advisable to assign biologically significant parameters with random effects. Moreover, evaluating error structure modelling is recommended to account for possible correlated errors that may be present even when using random effects. Different Richard growth curve parameters should be used for the predominantly Alpine and Saanen genotypes because there are differences in their growth patterns.

There is increasing concern about balancing agronomic and environmental gains from nitrogen (N) usage on dairy farms. Data from a 3-year (2009–2011) survey were used to assess farm-gate N balances and N use efficiency (NUE) on 21 intensive grass-based dairy farms operating under the good agricultural practice (GAP) regulations in Ireland. Mean stocking rate (SR) was 2·06 livestock units (LU)/ha, mean N surplus was 175 kg/ha, or 0·28 kg N/kg milk solids (MS), and mean NUE was 0·23. Nitrogen inputs were dominated by inorganic fertilizer (186 kg N/ha) and concentrates (26·6 kg N/ha), whereas outputs were dominated by milk (40·2 kg N/ha) and livestock (12·8 kg N/ha). Comparison with similar studies carried out before the introduction of the GAP regulations in 2006 would suggest that N surplus, both per ha and per kg MS, have significantly decreased (by 40 and 32%, respectively) and NUE increased (by 27%), mostly due to decreased inorganic fertilizer N input and improvements in N management, with a notable shift towards spring application of organic manures, indicating improved awareness of the fertilizer value of organic manures and good compliance with the GAP regulations regarding fertilizer application timing. These results would suggest a positive impact of the GAP regulations on dairy farm N surplus and NUE, indicating an improvement in both environmental and economic sustainability of dairy production through improved resource-use efficiencies. Such improvements will be necessary to achieve national targets of improved water quality and increased efficiency/sustainability of the dairy industry. The weak impact of SR on N surplus found in the present study would suggest that, with good management, increased SR and milk output per ha may be achievable, while decreasing N surplus per ha. Mean N surplus was lower than the overall mean surplus (224 kg N/ha) from six studies of northern and continental European dairy farms, while mean NUE was similar, largely due to the low input/output system that is more typical in Ireland, with seasonal milk production (compact spring calving), low use of concentrates, imported feed and forages, high use of grazed grass and lower milk yields per ha.

In view of environmental concerns with regard to phosphorus (P) pollution and the expected global P scarcity, there is increasing interest in improving P utilization in dairy cattle. In high-producing dairy cows, P requirements for milk production comprise a significant fraction of total dietary P requirements. Although variation in P content of milk can affect the efficiency of P utilization for milk production (i.e. the fraction of ingested P that is incorporated in milk), this variation is poorly understood. It was hypothesized that the P content of milk is related to both milk protein and milk lactose content, but not necessarily to milk fat content. Three existing experiments comprising individual animal data on milk yield and fat, protein, lactose and P content of milk (in total 278 observations from 121 cows) were analysed to evaluate this hypothesis using a mixed model analysis. The models including the effects of both protein and lactose content of milk yielded better prediction of milk P content in terms of root-mean-square prediction error (RMSPE) and concordance correlation coefficient (CCC) statistics than models with only protein included as prediction variable; however, estimates of effect sizes varied between studies. The inclusion of milk fat content in equations already including protein and lactose did not further improve prediction of milk P content. Equations developed to describe the relationship between milk protein and lactose contents (g/kg) and milk P content (g/kg) were: (Expt 1) P in milk=−0·44(±0·179)+0·0253(±0·00300)×milk protein+0·0133(±0·00382)×milk lactose (RMSPE: 5·2%; CCC: 0·71); (Expt 2) P in milk=−0·26 (±0·347)+0·0174(±0·00328)×milk protein+0·0143 (±0·00611)×milk lactose (RMSPE: 6·3%; CCC: 0·40); and (Expt 3) P in milk=−0·36(±0·255)+0·0131(±0·00230)×milk protein+0·0193(±0·00490)×milk lactose (RMSPE: 6·5%; CCC: 0·55). Analysis of the three experiments combined, treating study as a random effect, resulted in the following equation to describe the same relationship as in the individual study equations: P in milk=−0·64(±0·168)+0·0223(±0·00236)×milk protein+0·0191(±0·00316)×milk lactose (RMSPE: 6·2%; CCC: 0·61). Although significant relationships between milk protein, milk lactose and milk P were found, a considerable portion of the observed variation remained unexplained, implying that factors other than milk composition may affect the P content of milk. The equations developed may be used to replace current fixed milk P contents assumed in P requirement systems for cattle.