Agrifood Research Finland

This study—based on systematic testing of 30 different wheat crop models against field experiments—shows that many wheat models simulate yields well, but with reduced accuracy at higher temperatures. Extrapolation of the model ensemble response indicates that global wheat production will fall by 6% for each 1 °C increase in temperature. Crop models are essential tools for assessing the threat of climate change to local and global food production1. Present models used to predict wheat grain yield are highly uncertain when simulating how crops respond to temperature2. Here we systematically tested 30 different wheat crop models of the Agricultural Model Intercomparison and Improvement Project against field experiments in which growing season mean temperatures ranged from 15 °C to 32 °C, including experiments with artificial heating. Many models simulated yields well, but were less accurate at higher temperatures. The model ensemble median was consistently more accurate in simulating the crop temperature response than any single model, regardless of the input information used. Extrapolating the model ensemble temperature response indicates that warming is already slowing yield gains at a majority of wheat-growing locations. Global wheat production is estimated to fall by 6% for each °C of further temperature increase and become more variable over space and time.

Carvacrol, (+)-carvone, thymol, and trans-cinnamaldehyde were tested for their inhibitory activity against Escherichia coli O157:H7 and Salmonella typhimurium. In addition, their toxicity to Photobacterium leiognathi was determined, utilizing a bioluminescence assay. Their effects on the cell surface were investigated by measuring the uptake of 1-N-phenylnaphthylamine (NPN), by measuring their sensitization of bacterial suspensions toward detergents and lysozyme, and by analyzing material released from cells upon treatment by these agents. Carvacrol, thymol, and trans-cinnamaldehyde inhibited E. coli and S. typhimurium at 1−3 mM, whereas (+)-carvone was less inhibitory. trans-Cinnamaldehyde was the most inhibitory component toward P. leiognathi. Carvacrol and thymol disintegrated the outer membrane and released outer membrane-associated material from the cells to the external medium; such release by (+)-carvone or trans-cinnamaldehyde was negligible. Of the tested components, carvacrol and thymol decreased the intracellular ATP pool of E. coli and also inreased extracellular ATP, indicating disruptive action on the cytoplasmic membrane. Keywords: Essential oils; carvacrol; carvone; cinnamaldehyde; thymol; antimicrobial activity; outer membrane; lipopolysaccharide

Barley (Hordeum vulgare L.) is among the world’s earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 ‘high-confidence’ genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement. An integrated high-resolution genetic, physical and shotgun sequence assembly of the barley genome, one of the earliest domesticated and most important crops, is described; it will provide a platform for genome-assisted research and future crop improvement. Two groups in this issue report the compilation and analysis of the genome sequences of major cereal crops — bread wheat and barley — providing important resources for future crop improvement. Bread wheat accounts for one-fifth of the calories consumed by humankind. It has a very large and complex hexaploid genome of 17 Gigabases. Michael Bevan and colleagues have analysed the genome using 454 pyrosequencing and compared it with diploid ancestral and progenitor genomes. The authors discovered significant loss of gene family members upon polyploidization and domestication, and expansion of gene classes that may be associated with crop productivity. Barley is one of the earliest domesticated plant crops. Although diploid, it has a very large genome of 5.1 Gigabases. Nils Stein and colleagues describe a physical map anchored to a high-resolution genetic map, on top of which they have overlaid a deep whole-genome shotgun assembly, cDNA and RNA-seq data to provide the first in-depth genome-wide survey of the barley genome.

The distribution of plant species, the species compositions of different sites, and the factors that affect them in tropical rain forests are not well understood. The main hypotheses are that species composition is either (i) uniform over large areas, (ii) random but spatially autocorrelated because of dispersal limitation, or (iii) patchy and environmentally determined. Here we test these hypotheses, using a large data set from western Amazonia. The uniformity hypothesis gains no support, but the other hypotheses do. Environmental determinism explains a larger proportion of the variation in floristic differences between sites than does dispersal limitation; together, these processes explain 70 to 75% of the variation. Consequently, it is important that management planning for conservation and resource use take into account both habitat heterogeneity and biogeographic differences.

Dietary proteins are known to carry a wide range of nutritional, functional and biological properties. Nutritionally, the proteins are a source of energy and amino acids, which are essential for growth and maintenance. Functionally, the proteins contribute to the physicochemical and sensory properties of various protein-rich foods. Furthermore, many dietary proteins possess specific biological properties which make these components potential ingredients of functional or health-promoting foods. Many of these properties are attributed to physiologically active peptides encrypted in protein molecules. Particularly rich sources of such peptides are milk and egg, but they are also found in meat of various kinds as well as many plants. These peptides are inactive within the sequence of parent protein and can be released during gastrointestinal digestion or food processing. Depending on the amino acid sequence, these peptides may exert a number of different activities in vivo, affecting, e.g., the cardiovascular, endocrine, immune and nervous systems in addition to nutrient utilization. There is increasing commercial interest in the production of bioactive peptides from various sources. Industrial-scale production of such peptides is, however, hampered by the lack of suitable technologies. Bioactive peptides can also be produced from milk proteins through fermentation of milk, by starters employed in the manufacture of fermented milks or cheese. In particular, antihypertensive peptides have been identified in fermented milk, whey and ripened cheese. A few of these peptides have been commercialised in the form of fermented milks. There is a need to develop technologies which retain or even enhance the activity of bioactive peptides in food systems. Also, it is essential to study the optimum utilization of such peptides during passage through the gastrointestinal tract.

Demand for organic foods is partially driven by consumers' perceptions that they are more nutritious. However, scientific opinion is divided on whether there are significant nutritional differences between organic and non-organic foods, and two recent reviews have concluded that there are no differences. In the present study, we carried out meta-analyses based on 343 peer-reviewed publications that indicate statistically significant and meaningful differences in composition between organic and non-organic crops/crop-based foods. Most importantly, the concentrations of a range of antioxidants such as polyphenolics were found to be substantially higher in organic crops/crop-based foods, with those of phenolic acids, flavanones, stilbenes, flavones, flavonols and anthocyanins being an estimated 19 (95 % CI 5, 33) %, 69 (95 % CI 13, 125) %, 28 (95 % CI 12, 44) %, 26 (95 % CI 3, 48) %, 50 (95 % CI 28, 72) % and 51 (95 % CI 17, 86) % higher, respectively. Many of these compounds have previously been linked to a reduced risk of chronic diseases, including CVD and neurodegenerative diseases and certain cancers, in dietary intervention and epidemiological studies. Additionally, the frequency of occurrence of pesticide residues was found to be four times higher in conventional crops, which also contained significantly higher concentrations of the toxic metal Cd. Significant differences were also detected for some other (e.g. minerals and vitamins) compounds. There is evidence that higher antioxidant concentrations and lower Cd concentrations are linked to specific agronomic practices (e.g. non-use of mineral N and P fertilisers, respectively) prescribed in organic farming systems. In conclusion, organic crops, on average, have higher concentrations of antioxidants, lower concentrations of Cd and a lower incidence of pesticide residues than the non-organic comparators across regions and production seasons.

Abstract Grassland diversity can support sustainable intensification of grassland production through increased yields, reduced inputs and limited weed invasion. We report the effects of diversity on weed suppression from 3 years of a 31‐site continental‐scale field experiment. At each site, 15 grassland communities comprising four monocultures and 11 four‐species mixtures based on a wide range of species' proportions were sown at two densities and managed by cutting. Forage species were selected according to two crossed functional traits, “method of nitrogen acquisition” and “pattern of temporal development”. Across sites, years and sown densities, annual weed biomass in mixtures and monocultures was 0.5 and 2.0 t DM ha −1 (7% and 33% of total biomass respectively). Over 95% of mixtures had weed biomass lower than the average of monocultures, and in two‐thirds of cases, lower than in the most suppressive monoculture (transgressive suppression). Suppression was significantly transgressive for 58% of site‐years. Transgressive suppression by mixtures was maintained across years, independent of site productivity. Based on models, average weed biomass in mixture over the whole experiment was 52% less (95% confidence interval: 30%–75%) than in the most suppressive monoculture. Transgressive suppression of weed biomass was significant at each year across all mixtures and for each mixture. Weed biomass was consistently low across all mixtures and years and was in some cases significantly but not largely different from that in the equiproportional mixture. The average variability (standard deviation) of annual weed biomass within a site was much lower for mixtures (0.42) than for monocultures (1.77). Synthesis and applications . Weed invasion can be diminished through a combination of forage species selected for complementarity and persistence traits in systems designed to reduce reliance on fertiliser nitrogen. In this study, effects of diversity on weed suppression were consistently strong across mixtures varying widely in species' proportions and over time. The level of weed biomass did not vary greatly across mixtures varying widely in proportions of sown species. These diversity benefits in intensively managed grasslands are relevant for the sustainable intensification of agriculture and, importantly, are achievable through practical farm‐scale actions.

• Species of arbuscular mycorrhizal fungi (AMF) differ markedly in their improvement of plant nutrition and health. However, it is not yet possible to relate the diversity of an AMF community to its functional properties due to the lack of information on the functional diversity at each taxonomic level. This study investigates the inter- and intraspecific functional diversity of four Glomus species in relation to a phylogenetic analysis of large ribosomal subunit (LSU) sequences. • Growth and P nutrition of cucumber (Cucumis sativus) associated with 24 different isolates of AMF were measured in a two-compartment system with a 33P-labelled root-free soil compartment. • Intraspecific differences were found in plant growth response and the extension of the fungal mycelium into the root-free soil patch whereas length-specific P uptake of the hyphae remained rather constant within each AMF species. Hence, the length-specific P uptake differed according to species, whereas lower phylogenetic levels were required to match functional characteristics such as fungal growth pattern and plant growth promotion. • The large intraspecific diversity observed for mycelium growth and improvement of P uptake means that AMF communities of low species diversity may still contain considerable functional heterogeneity.

The domestication of livestock represented a crucial step in human history. By using endogenous retroviruses as genetic markers, we found that sheep differentiated on the basis of their "retrotype" and morphological traits dispersed across Eurasia and Africa via separate migratory episodes. Relicts of the first migrations include the Mouflon, as well as breeds previously recognized as "primitive" on the basis of their morphology, such as the Orkney, Soay, and the Nordic short-tailed sheep now confined to the periphery of northwest Europe. A later migratory episode, involving sheep with improved production traits, shaped the great majority of present-day breeds. The ability to differentiate genetically primitive sheep from more modern breeds provides valuable insights into the history of sheep domestication.

The contents of free and total phenolic acids and alk(en)ylresorcinols were analyzed in commercial products of eight grains: oat (Avena sativa), wheat (Triticum spp.), rye (Secale cerale), barley (Hordeum vulgare), buckwheat (Fagopyrum esculentum), millet (Panicum miliaceum), rice (Oryza sativa), and corn (Zea mays). Avenanthramides were determined in three oat products. Free phenolic acids, alk(en)ylresorcinols, and avenanthramides were extracted with methanolic acetic acid, 100% methanol, and 80% methanol, respectively, and quantified by HPLC. The contents of total phenolic acids were quantified by HPLC analysis after alkaline and acid hydrolyses. The highest contents of total phenolic acids were in brans of wheat (4527 mg/kg) and rye (4190 mg/kg) and in whole-grain flours of these grains (1342 and 1366 mg/kg, respectively). In other products, the contents varied from 111 mg/kg (white wheat bread) to 765 mg/kg (whole-grain rye bread). Common phenolic acids found in the grain products were ferulic acid (most abundant), ferulic acid dehydrodimers, sinapic acid, and p-coumaric acid. The grain products were found to contain either none or only low amounts of free phenolic acids. The content of avenanthramides in oat flakes (26-27 mg/kg) was about double that found in oat bran (13 mg/kg). The highest contents of alk(en)ylresorcinols were observed in brans of rye (4108 mg/kg) and wheat (3225 mg/kg). In addition, whole-grain rye products (rye bread, rye flour, and whole-wheat flour) contained considerable levels of alk(en)ylresorcinols (524, 927, and 759 mg/kg, respectively).

Effective population size (Ne ) is a key population genetic parameter that describes the amount of genetic drift in a population. Estimating Ne has been subject to much research over the last 80 years. Methods to estimate Ne from linkage disequilibrium (LD) were developed ~40 years ago but depend on the availability of large amounts of genetic marker data that only the most recent advances in DNA technology have made available. Here we introduce SNeP, a multithreaded tool to perform the estimate of Ne using LD using the standard PLINK input file format (.ped and.map files) or by using LD values calculated using other software. Through SNeP the user can apply several corrections to take account of sample size, mutation, phasing, and recombination rate. Each variable involved in the computation such as the binning parameters or the chromosomes to include in the analysis can be modified. When applied to published datasets, SNeP produced results closely comparable with those obtained in the original studies. The use of SNeP to estimate Ne trends can improve understanding of population demography in the recent past, provided a sufficient number of SNPs and their physical position in the genome are available. Binaries for the most common operating systems are available at https://sourceforge.net/projects/snepnetrends/.

Crop models of crop growth are increasingly used to quantify the impact of global changes due to climate or crop management. Therefore, accuracy of simulation results is a major concern. Studies with ensembles of crop models can give valuable information about model accuracy and uncertainty, but such studies are difficult to organize and have only recently begun. We report on the largest ensemble study to date, of 27 wheat models tested in four contrasting locations for their accuracy in simulating multiple crop growth and yield variables. The relative error averaged over models was 24-38% for the different end-of-season variables including grain yield (GY) and grain protein concentration (GPC). There was little relation between error of a model for GY or GPC and error for in-season variables. Thus, most models did not arrive at accurate simulations of GY and GPC by accurately simulating preceding growth dynamics. Ensemble simulations, taking either the mean (e-mean) or median (e-median) of simulated values, gave better estimates than any individual model when all variables were considered. Compared to individual models, e-median ranked first in simulating measured GY and third in GPC. The error of e-mean and e-median declined with an increasing number of ensemble members, with little decrease beyond 10 models. We conclude that multimodel ensembles can be used to create new estimators with improved accuracy and consistency in simulating growth dynamics. We argue that these results are applicable to other crop species, and hypothesize that they apply more generally to ecological system models.

Abstract This paper presents the results of a questionnaire and food waste diary study on the influence of socio‐demographical, behavioural and attitudinal factors on the amount of avoidable household food waste in 380 Finnish households. The research data were collected through a 2‐week food waste diary study accompanied by a background questionnaire. The influences of socio‐demographical, behavioural and attitudinal factors on the production of food waste were studied through application of descriptive statistics. It was established that only few factors clearly correlate with the amount of avoidable food waste. The factors that influenced the amount of food wasted were the size of the household, the gender of the person mainly responsible of grocery shopping, the frequency of buying discounted food products, the respondent's own view of the potential to reduce food waste and the respondent's own view of the influence of purchasing particular food packet sizes. The main factors with which no clear correlation was detected included age of the oldest person in household; area, form and type of residence; educational level and type of work of adults in the family; and shopping, food preparation and eating habits.

Imaging using lightweight, unmanned airborne vehicles (UAVs) is one of the most rapidly developing fields in remote sensing technology. The new, tunable, Fabry-Perot interferometer-based (FPI) spectral camera, which weighs less than 700 g, makes it possible to collect spectrometric image blocks with stereoscopic overlaps using light-weight UAV platforms. This new technology is highly relevant, because it opens up new possibilities for measuring and monitoring the environment, which is becoming increasingly important for many environmental challenges. Our objectives were to investigate the processing and use of this new type of image data in precision agriculture. We developed the entire processing chain from raw images up to georeferenced reflectance images, digital surface models and biomass estimates. The processing integrates photogrammetric and quantitative remote sensing approaches. We carried out an empirical assessment using FPI spectral imagery collected at an agricultural wheat test site in the summer of 2012. Poor weather conditions during the campaign complicated the data processing, but this is one of the challenges that are faced in operational applications. The results indicated that the camera performed consistently and that the data processing was consistent, as well. During the agricultural experiments, promising results were obtained for biomass estimation when the spectral data was used and when an appropriate radiometric correction was applied to the data. Our results showed that the new FPI technology has a great potential in precision agriculture and indicated many possible future research topics.

There is increasing evidence to indicate that nutrition is an important factor involved in the onset and development of several chronic human diseases including cancer, cardiovascular disease (CVD), type II diabetes and obesity. Clinical studies implicate excessive consumption of medium-chain saturated fatty acids (SFA) and trans-fatty acids (TFA) as risk factors for CVD, and in the aetiology of other chronic conditions. Ruminant-derived foods are significant sources of medium-chain SFA and TFA in the human diet, but also provide high-quality protein, essential micronutrients and several bioactive lipids. Altering the fatty acid composition of ruminant-derived foods offers the opportunity to align the consumption of fatty acids in human populations with public health policies without the need for substantial changes in eating habits. Replacing conserved forages with fresh grass or dietary plant oil and oilseed supplements can be used to lower medium-chain and total SFA content and increase cis-9 18:1, total conjugated linoleic acid (CLA), n-3 and n-6 polyunsaturated fatty acids (PUFA) to a variable extent in ruminant milk. However, inclusion of fish oil or marine algae in the ruminant diet results in marginal enrichment of 20- or 22-carbon PUFA in milk. Studies in growing ruminants have confirmed that the same nutritional strategies improve the balance of n-6/n-3 PUFA, and increase CLA and long-chain n-3 PUFA in ruminant meat, but the potential to lower medium-chain and total SFA is limited. Attempts to alter meat and milk fatty acid composition through changes in the diet fed to ruminants are often accompanied by several-fold increases in TFA concentrations. In extreme cases, the distribution of trans 18:1 and 18:2 isomers in ruminant foods may resemble that of partially hydrogenated plant oils. Changes in milk fat or muscle lipid composition in response to diet are now known to be accompanied by tissue-specific alterations in the expression of one or more lipogenic genes. Breed influences both milk and muscle fat content, although recent studies have confirmed the occurrence of genetic variability in transcript abundance and activity of enzymes involved in lipid synthesis and identified polymorphisms for several key lipogenic genes in lactating and growing cattle. Although nutrition is the major factor influencing the fatty acid composition of ruminant-derived foods, further progress can be expected through the use of genomic or marker-assisted selection to increase the frequency of favourable genotypes and the formulation of diets to exploit this genetic potential.

The contents of soluble and total phenolic acids were analyzed in samples of 29 berries and berry products, 24 fruits and fruit peels, and 12 beverages. Variation of phenolic acids in berries was also studied. Soluble phenolic acids were extracted with methanolic acetic acid, and a tentative quantification was performed by high-performance liquid chromatography (HPLC). The total phenolic acid content was determined by HPLC after alkaline and acid hydrolyses. The content of total phenolic acids as aglycones in the above samples varied from 0 (pear cider) to 103 mg/100 g fresh weight (rowanberry). Besides rowanberry, the best phenolic acid sources among berries were chokeberry (96 mg/100 g), blueberry (85 mg/100 g), sweet rowanberry (75 mg/100 g), and saskatoon berry (59 mg/100 g). Among fruits, the highest contents (28 mg/100 g) were determined in dark plum, cherry, and one apple variety (Valkea Kuulas). Coffee (97 mg/100 g) as well as green and black teas (30-36 mg/100 g) were the best sources among beverages. Caffeic acid dominated in all of these samples except in tea brews. Variation in the phenolic acid contents of the berries was either small or moderate.

A high-performance liquid chromatographic (HPLC) method with diode-array detection (DAD) was used to identify and quantify free and total phenolic acids (m-hydroxybenzoic acid, p-hydroxybenzoic acid, protocatechuic acid, gallic acid, vanillic acid, syringic acid, o-coumaric acid, m-coumaric acid, p-coumaric acid, caffeic acid, ferulic acid, sinapic acid, chlorogenic acid, and ellagic acid) in plant foods. Free phenolic acids were extracted with a mixture of methanol and 10% acetic acid. Bound phenolic acids were liberated using first alkaline and then acid hydrolysis followed by extraction with diethyl ether/ethyl acetate (1:1). All fractions were quantified separately by HPLC. After HPLC quantification, results of alkali and acid hydrolysates were calculated to represent total phenolic acids. Ellagic acid was quantified separately after long (20 h) acid hydrolysis. The methods developed were effective for the determination of phenolic acids in plant foods. DAD response was linear for all phenolic acids within the ranges evaluated, with correlation coefficients exceeding 0.999. Coefficients of variation for 4-8 sample replicates were consistently below 10%. Recovery tests of phenolic acids were performed for every hydrolysis condition using several samples. Recoveries were generally good (mean >90%) with the exceptions of gallic acid and, in some cases, caffeic acid samples.

To date, projections of European crop yields under climate change have been based almost entirely on the outputs of crop-growth models. While this strategy can provide good estimates of the effects of climatic factors, soil conditions and management on crop yield, these models usually do not capture all of the important aspects related to crop management, or the relevant environmental factors. Moreover, crop-simulation studies often have severe limitations with respect to the number of crops covered or the spatial extent. The present study, based on agroclimatic indices, provides a general picture of agroclimatic conditions in western and central Europe (study area lays between 8.5°W–27°E and 37–63.5°N), which allows for a more general assessment of climate-change impacts. The results obtained from the analysis of data from 86 different sites were clustered according to an environmental stratification of Europe. The analysis was carried for the baseline (1971–2000) and future climate conditions (time horizons of 2030, 2050 and with a global temperature increase of 5 °C) based on outputs of three global circulation models. For many environmental zones, there were clear signs of deteriorating agroclimatic condition in terms of increased drought stress and shortening of the active growing season, which in some regions become increasingly squeezed between a cold winter and a hot summer. For most zones the projections show a marked need for adaptive measures to either increase soil water availability or drought resistance of crops. This study concludes that rainfed agriculture is likely to face more climate-related risks, although the analyzed agroclimatic indicators will probably remain at a level that should permit rainfed production. However, results suggests that there is a risk of increasing number of extremely unfavorable years in many climate zones, which might result in higher interannual yield variability and constitute a challenge for proper crop management.

We herein report on our efforts to improve the mapping resolution of a QTL with major effect on milk yield and composition that was previously mapped to bovine chromosome 20. By using a denser chromosome 20 marker map and by exploiting linkage disequilibrium using two distinct approaches, we provide strong evidence that a chromosome segment including the gene coding for the growth hormone receptor accounts for at least part of the chromosome 20 QTL effect. By sequencing individuals with known QTL genotype, we identify an F to Y substitution in the transmembrane domain of the growth hormone receptor gene that is associated with a strong effect on milk yield and composition in the general population.

Numerous in vitro and in vivo studies have suggested that dietary anthocyanins and ellagitannins or ellagic acid might have beneficial health effects. Epidemiological evidence on the disease-preventing potential of these polyphenols is lacking, due to the absence of reliable data on their contents in foods. In this study was analyzed the content of anthocyanins and ellagitannins (as ellagic acid equivalents after acid hydrolysis) in foods consumed in Finland, including berries, fruits, vegetables, and processed products, using high-performance liquid chromatographic (HPLC) methods. Anthocyanins were detected in 41 of 54 selected food items. The total anthocyanin content varied in berries from 1 to 611 mg/100 g, in fruits from 2 to 66 mg/100 g, and in vegetables from 3 to 75 mg/100 g of fresh weight as the weight of the aglycone. Ellagitannins were screened in 33 food items, but were detected only in 5 species of berries, that is, in cloudberry, raspberry, rose hip, strawberry, and sea buckthorn, the content ranging from 1 to 330 mg/100 g. The results underscore the superiority of berries, especially dark blue or red berries, as excellent sources of anthocyanins and certain berries of the Rosaceae family as the major source of ellagitannins in the Finnish diet.