Molecular breeding of barley for quality traits and resilience to climate change.

Barley grains are a rich source of compounds, such as resistant starch, beta-glucans and anthocyanins, that can be explored in order to develop various products to support human health, while lignocellulose in straw can be optimised for feed in husbandry, bioconversion into bioethanol or as a starting material for new compounds. Existing natural variations of these compounds can be used to breed improved cultivars or integrated with a large number of mutant lines. The technical demands can be in opposition depending on barley's end use as feed or food or as a source of biofuel. For example beta-glucans are beneficial in human diets but can lead to issues in brewing and poultry feed. Barley breeders have taken action to integrate new technologies, such as induced mutations, transgenics, marker-assisted selection, genomic selection, site-directed mutagenesis and lastly machine learning, in order to improve quality traits. Although only a limited number of cultivars with new quality traits have so far reached the market, research has provided valuable knowledge and inspiration for future design and a combination of methodologies to achieve the desired traits. The changes in climate is expected to affect the quality of the harvested grain and it is already a challenge to mitigate the unpredictable seasonal and annual variations in temperature and precipitation under elevated [CO2] by breeding. This paper presents the mutants and encoded proteins, with a particular focus on anthocyanins and lignocellulose, that have been identified and characterised in detail and can provide inspiration for continued breeding to achieve desired grain and straw qualities.

Trait Expression and Environmental Responses of Pea (Pisum sativum L.) Genetic Resources Targeting Cultivation in the Arctic.

In the Arctic part of the Nordic region, cultivated crops need to specifically adapt to adverse and extreme climate conditions, such as low temperatures, long days, and a short growing season. Under the projected climate change scenarios, higher temperatures and an earlier spring thaw will gradually allow the cultivation of plants that could not be previously cultivated there. For millennia, Pea (Pisum sativum L.) has been a major cultivated protein plant in Nordic countries but is currently limited to the southern parts of the region. However, response and adaptation to the Arctic day length/light spectrum and temperatures are essential for the productivity of the pea germplasm and need to be better understood. This study investigated these factors and identified suitable pea genetic resources for future cultivation and breeding in the Arctic region. Fifty gene bank accessions of peas with a Nordic landrace or cultivar origin were evaluated in 2-year field trials at four Nordic locations in Denmark, Finland, Sweden, and Norway (55° to 69° N). The contrasting environmental conditions of the trial sites revealed differences in expression of phenological, morphological, crop productivity, and quality traits in the accessions. The data showed that light conditions related to a very long photoperiod partly compensated for the lack of accumulated temperature in the far north. A critical factor for cultivation in the Arctic is the use of cultivars with rapid flowering and maturation times combined with early sowing. At the most extreme site (69°N), no accession reached full maturation. Nonetheless several accessions, predominantly landraces of a northern origin, reached a green harvest state. All the cultivars reached full maturation at the sub-Arctic latitude in northern Sweden (63°N) when plants were established early in the season. Seed yield correlated positively with seed number and aboveground biomass, but negatively with flowering time. A high yield potential and protein concentration of dry seed were found in many garden types of pea, confirming their breeding potential for yield. Overall, the results indicated that pea genetic resources are available for breeding or immediate cultivation, thus aiding in the northward expansion of pea cultivation. Predicted climate changes would support this expansion.

Characterisation of the class III peroxidase gene family in carrot taproots and its role in anthocyanin and lignin accumulation.

Plant class III peroxidases (CIII Prxs) are involved in numerous essential plant life processes, such as plant development and differentiation, lignification and seed germination, and defence against pathogens. However, there is limited information about the structure-function relationships of Prxs in carrots. This study identified 75 carrot peroxidases (DcPrxs) and classified them into seven subgroups based on phylogenetic analysis. Gene structure analysis revealed that these DcPrxs had between one and eight introns, while conserved motif analysis showed a typical motif composition and arrangement for CIII Prx. In addition, eighteen tandem duplication events, but only eight segmental duplications, were identified among these DcPrxs, indicating that tandem duplication was the main contributor to the expansion of this gene family. Histochemical analyses showed that lignin was mainly localised in the cell walls of xylem, and Prx activity was determined in the epidermal region of taproots. The xylem always showed higher lignin concentration and lower Prx activity compared to the phloem in the taproots of both carrot cultivars. Combining these observations with RNA sequencing, some Prx genes were identified as candidate genes related to lignification and pigmentation. Three peroxidases (DcPrx30, DcPrx32, DcPrx62) were upregulated in the phloem of both genotypes. Carrot taproots are an attractive resource for natural food colourants and this study elucidated genome-wide insights of Prx for the first time, developing hypotheses concerning their involvement with lignin and anthocyanin in purple carrots. The findings provide an essential foundation for further studies of Prx genes in carrot, especially on pigmentation and lignification mechanisms.

Genome Wide Identification and Comparative Analysis of the Serpin Gene Family in Brachypodium and Barley.

Serpins (serine protease inhibitors) constitute one of the largest and most widely distributed superfamilies of protease inhibitors and have been identified in nearly all organisms. To gain significant insights, a comprehensive in silico analysis of the serpin gene family was carried out in the model plant for temperate grasses Brachypodium distachyon and barley Hordeum vulgare using bioinformatic tools at the genome level for the first time. We identified a total of 27 BdSRPs and 25 HvSRP genes in Brachypodium and barley, respectively, showing an unexpectedly high gene number in these model plants. Gene structure, conserved motifs and phylogenetic comparisons of serpin genes supported the role of duplication events in the expansion and evolution of serpin gene family. Further, purifying selection pressure was found to be a main driving force in the evolution of serpin genes. Genome synteny analysis indicated that BdSRP genes were present in syntenic regions of barley, rice, sorghum and maize, suggesting that they evolved before the divergence of these species from common ancestor. The distinct expression pattern in specific tissues further suggested a specialization of functions during development and in plant defense. These results suggest that the LR serpins (serpins with Leu-Arg residues at P2-P1') identified here can be utilized as candidates for exploitation in disease resistance, pest control and preventing stress-induced cell death. Additionally, serpins were identified that could lead to further research aimed at validating and functionally characterizing the role of potential serpin genes from other plants.

Transcriptome Analysis Reveals Candidate Genes Related to Anthocyanin Biosynthesis in Different Carrot Genotypes and Tissues.

Black carrots are characterized by a significant amount of anthocyanins, which are not only a good source of natural food colorant, but can also provide many health benefits to humans. In the present work, taproots of different carrot genotypes were used to identify the candidate genes related to anthocyanin synthesis, with particular a focus on R2R3MYB, bHLH transcription factors, and glutathione S-transferase gene (GST). The RNA-sequencing analysis (RNA-Seq) showed that DcMYB6 and DcMYB7 had a genotypic dependent expression and they are likely involved in the regulation of anthocyanin biosynthesis. They were specifically upregulated in solid black taproots, including both black phloem and xylem. DcbHLH3 (LOC108204485) was upregulated in all black samples compared with the orange ones. We also found that GST1 (LOC108205254) might be an important anthocyanin transporter, and its upregulated expression resulted in the increasing of vacuolar anthocyanin accumulation in black samples. Moreover, high performance liquid chromatographic (HPLC) analysis and liquid chromatography coupled to mass spectrometry (LC-MS) were used to identify the individual anthocyanin in the purple tissues of two carrot cultivars. The results showed that five main anthocyanin compounds and the most abundant anthocyanin were the same in different tissues, while the second-highest anthocyanin between three tissues was different, even in the same cultivar. In conclusion, this study combined anthocyanin profiles and comparative transcriptomic analysis to identify candidate genes involved in anthocyanin biosynthesis in carrots, thus providing a better foundation for improving anthocyanin accumulation in carrots as a source of colorants.

Defining lncRNAs Correlated with CHO Cell Growth and IgG Productivity by RNA-Seq.

How the long non-coding RNA (lncRNA) genome in recombinant protein producing Chinese hamster ovary (CHO) cell lines relates to phenotype is not well described. We therefore defined the CHO cell lncRNA transcriptome from cells grown in controlled miniature bioreactors under fed-batch conditions using RNA-Seq to identify lncRNAs and how the expression of these changes throughout growth and between IgG producers. We identify lncRNAs including Adapt15, linked to ER stress, GAS5, linked to mTOR signaling/growth arrest, and PVT1, linked to Myc expression, which are differentially regulated during fed-batch culture and whose expression correlates to productivity and growth. Changes in (non)-coding RNA expression between the seed train and the equivalent day of fed-batch culture are also reported and compared with existing datasets. Collectively, we present a comprehensive lncRNA CHO cell profiling and identify targets for engineering growth and productivity characteristics of CHO cells.

Breeding for dual-purpose wheat varieties using marker-trait associations for biomass yield and quality traits.

KEY MESSAGE: This study demonstrates that an active breeding nursery with rotation can be used to identify marker-trait associations for biomass yield and quality parameters that are important for biorefinery purposes. Wheat straw is a valuable feedstock for bioethanol production, but due to the recalcitrant nature of lignocellulose, its efficient use in biorefineries is limited by its low digestibility and difficult conversion of structural carbohydrates into free sugars. A genome-wide association study (GWAS) was conducted to search for significant SNP markers that could be used in a breeding programme to improve the value of wheat straw in a biorefinery setting. As part of a 3-year breeding programme (2013-2016), 190 winter wheat lines were phenotyped for traits that affect the yield and quality of the harvested biomass. These traits included straw yield, plant height, lodging at three growth stages and Septoria tritici blotch (STB) susceptibility. Release of glucose, xylose and arabinose was determined after hydrothermal pretreatment and enzymatic hydrolysis of the straw. The lines were genotyped using 15 K SNP markers and 5552 SNP markers could be used after filtering. Heritability for all traits ranged from 0.02 to 0.74. GWASs were conducted using CMLM, SUPER and FarmCPU algorithms, to analyse which algorithm could detect the highest number of marker-trait associations (MTAs). Comparable tendencies were obtained from CMLM and FarmCPU, but FarmCPU produced the most significant results. MTAs were obtained for lodging, harvest index, plant height, STB, glucose, xylose and arabinose at a significance level of p < 9.01 × 10-6. MTAs in chromosome 6A were observed for glucose, xylose and arabinose, and could be of importance for increasing sugar release for bioethanol production.

Barley isochorismate synthase mutant is phylloquinone-deficient, but has normal basal salicylic acid level.

Salicylic acid (SA) is an important signaling hormone in plant immunity. It can be synthesized by either the phenylpropanoid pathway or the isochorismate pathway, but mutant studies of this have been scarce in other species than Arabidopsis. Here we identified a mutation that introduced a stop-codon early in the barley gene for isochorismate synthase (ICS). We found that homozygous ics plants wilted if not sprayed with 1,4-dihydroxy-2-naphthoic acid, a precursor of phylloquinone, also synthesized via the isochorismate pathway. Interestingly, ics had unchanged SA, suggesting that the basal level of SA is synthesized via the phenylpropanoid pathway. Previous studies have failed seeing increased SA levels in barley after attack by the powdery mildew fungus, Blumeria graminis f.sp. hordei (Bgh), and indeed, we saw no changes in the interaction of ics with this fungus. Overall, we hope this mutant will be useful for other studies of SA in barley.

Expression analysis of proteinase inhibitor-II under OsRGLP2 promoter in response to wounding and signaling molecules in transgenic Nicotiana benthamiana.

Proteinase inhibitor-II (PI-II) genes are important defense related genes that play critical regulatory roles in plant growth and development. In the present study, the expression of tomato PI-II gene was investigated under the control of a wound-inducible OsRGLP2 (Oryza sativa root germin like protein 2) promoter in transgenic tobacco plants after wounding, ABA and MeJA applications. Transcript level of target gene in transgenic plants was confirmed by quantitative real time PCR (qPCR). In response to ABA treatment at different concentrations, PI-II gene was strongly induced under OsRGLP2 promoter at higher concentration (100 µM), while considerable level of target gene expression was observed with MeJA application at 50 µM concentration. Upon wounding, relatively high PI-II gene expression was observed after 36-h treatment. Correspondingly, high GUS activity was detected at 36 h with histochemical assay and microscopic analysis in the vascular regions of leaves, stem and roots in wounded transgenic plants. This inducibility of PI-II gene by wounding, ABA and MeJA indirectly indicates its role in plant defense mechanism against biotic and abiotic stresses. Moreover, it was also suggested that ABA and MeJA dependent signaling pathways are involved in stimulation of PI-II gene. To the best of our knowledge, this is the first report describing the induction of PI-II gene under the regulation of OsRGLP2 promoter under stress conditions. The results of present research are useful for potential role of PI-II gene to improve stress tolerance in transgenic crops. Thus, efficacy of this gene can potentially be exploited to test the responses of different plants to various environmental stresses.

TILLING in Brachypodium distachyon.

TILLING is a low-cost screening method that allows for identification of mutations in a gene-of-interest within a range of few base pairs. TILLING can be applied to mutant populations or to plant collections of cultivars, landraces or crop wild relatives (Eco-TILLING). The method is based on the Cel1 enzyme cleavage of mismatches in PCR products amplified with labeled primers. The cleavage can be detected due to the labeled primers by different methods including capillary electrophoresis. Here, we introduce the development of the mutant population BRACHYLIFE and present a Brachypodium TILLING protocol based on fluorescing primers for PCR, enzymatic cleavage, and detection with Applied Biosystems 3130xl Genetic Analyzer.

Genome-wide association mapping in winter barley for grain yield and culm cell wall polymer content using the high-throughput CoMPP technique.

A collection of 112 winter barley varieties (Hordeum vulgare L.) was grown in the field for two years (2008/09 and 2009/10) in northern Italy and grain and straw yields recorded. In the first year of the trial, a severe attack of barley yellow mosaic virus (BaYMV) strongly influenced final performances with an average reduction of ~ 50% for grain and straw harvested in comparison to the second year. The genetic determination (GD) for grain yield was 0.49 and 0.70, for the two years respectively, and for straw yield GD was low in 2009 (0.09) and higher in 2010 (0.29). Cell wall polymers in culms were quantified by means of the monoclonal antibodies LM6, LM11, JIM13 and BS-400-3 and the carbohydrate-binding module CBM3a using the high-throughput CoMPP technique. Of these, LM6, which detects arabinan components, showed a relatively high GD in both years and a significantly negative correlation with grain yield (GYLD). Overall, heritability (H2) was calculated for GYLD, LM6 and JIM and resulted to be 0.42, 0.32 and 0.20, respectively. A total of 4,976 SNPs from the 9K iSelect array were used in the study for the analysis of population structure, linkage disequilibrium (LD) and genome-wide association study (GWAS). Marker-trait associations (MTA) were analyzed for grain yield and cell wall determination by LM6 and JIM13 as these were the traits showing significant correlations between the years. A single QTL for GYLD containing three MTAs was found on chromosome 3H located close to the Hv-eIF4E gene, which is known to regulate resistance to BaYMV. Subsequently the QTL was shown to be tightly linked to rym4, a locus for resistance to the virus. GWAs on arabinans quantified by LM6 resulted in the identification of major QTLs closely located on 3H and hypotheses regarding putative candidate genes were formulated through the study of gene expression levels based on bioinformatics tools.

Mapping of common bunt resistance gene Bt9 in wheat.

KEY MESSAGE: The Bt9 resistance locus was mapped and shown to be distinct from the Bt10 locus. New markers linked to Bt9 have been identified and may be used to breed for resistance towards the seed-borne disease. Increasing organic wheat production in Denmark, and in other wheat-producing areas, in conjunction with legal requirements for organic seed production, may potentially lead to a rise in common bunt occurrence. As systemic pesticides are not used in organic farming, organic wheat production systems may benefit from genetic resistances. However, little is known about the underlying genetic mechanisms and locations of the resistance factors for common bunt resistance in wheat. A double haploid (DH) population segregating for common bunt resistance was used to identify the chromosomal location of common bunt resistance gene Bt9. DH lines were phenotyped in three environments and genotyped with DArTseq and SSR markers. The total length of the resulting linkage map was 2882 cM distributed across all 21 wheat chromosomes. Bt9 was mapped to the distal end of chromosome 6DL. Since wheat common bunt resistance gene Bt10 is also located on chromosome 6D, the possibility of their co-location was investigated. A comparison of marker sequences linked to Bt9 and Bt10 on physical maps of chromosome 6D confirmed that Bt9 and Bt10 are two distinct resistance factors located at the distal (6DL) and proximal (6DS) end, respectively, of chromosome 6D. Five new SSR markers Xgpw4005-1, Xgpw7433, Xwmc773, Xgpw7303 and Xgpw362 and many SNP and PAV markers flanking the Bt9 resistance locus were identified and they may be used in the future for marker-assisted selection.

Fast, cross cultivar determination of total carotenoids in intact carrot tissue by Raman spectroscopy and Partial Least Squares calibration.

In order to speed up the breeding of orange carrots for high carotenoid content it is imperative to develop a fast and non-destructive technique. 332 roots from 86 carrot varieties grown in 2014 at the experimental farm in Høje Taastrup (DK) form the basis of this study. All roots were measured by Raman spectroscopy. The carotenoid content of the very same roots was estimated through a wet chemistry method coupled with UV-VIS at 447nm and 540nm. For the Raman spectroscopy, measurements were made on a cross section disk approximately 10cm from the root top at three different positions in the phloem. Since the top of the carrot is intact, it may still be used for growing. The final calibration model shows an uncertainty (RMSECV) of 20.5ppm, and a R(2)=0.86. It has thus proven to be well suited for prediction of carotenoids in orange carrots, and especially for ranking them according to the content.

Association Mapping in Scandinavian Winter Wheat for Yield, Plant Height, and Traits Important for Second-Generation Bioethanol Production.

A collection of 100 wheat varieties representing more than 100 years of wheat-breeding history in Scandinavia was established in order to identify marker-trait associations for plant height (PH), grain yield (GY), and biomass potential for bioethanol production. The field-grown material showed variations in PH from 54 to 122 cm and in GY from 2 to 6.61 t ha(-1). The release of monomeric sugars was determined by high-throughput enzymatic treatment of ligno-cellulosic material and varied between 0.169 and 0.312 g/g dm for glucose (GLU) and 0.146 and 0.283 g/g dm for xylose (XYL). As expected, PH and GY showed to be highly influenced by genetic factors with repeatability (R) equal to 0.75 and 0.53, respectively, while this was reduced for GLU and XYL (R = 0.09 for both). The study of trait correlations showed how old, low-yielding, tall varieties released higher amounts of monomeric sugars after straw enzymatic hydrolysis, showing reduced recalcitrance to bioconversion compared to modern varieties. Ninety-three lines from the collection were genotyped with the DArTseq(®) genotypic platform and 5525 markers were used for genome-wide association mapping. Six quantitative trait loci (QTLs) for GY, PH, and GLU released from straw were mapped. One QTL for PH was previously reported, while the remaining QTLs constituted new genomic regions linked to trait variation. This paper is one of the first studies in wheat to identify QTLs that are important for bioethanol production based on a genome-wide association approach.

Stability and genetic control of morphological, biomass and biofuel traits under temperate maritime and continental conditions in sweet sorghum (Sorghum bicolour).

KEY MESSAGE: Eight morphological, biomass and biofuel traits were found with high broad-sense heritability and 18 significant QTLs discovered including one locus controlling the stem juice trait for sorghum grown in Denmark and China. Sweet sorghum with tall plant, fast maturation and high stem Brix content can be bred as a biofuel crop for Northern Europe. Sweet sorghum (Sorghum bicolour), a native tropical C4 crop, has attracted interest as a bioenergy crop in northern countries due to its juice-rich stem and high biomass production. Little is known about the traits important for its adaptation to high altitude climatic conditions and their genetic controls. Recombinant inbred lines derived from a cross between a sweet and a grain kaoliang sorghum were used in five field trials in Denmark and in China to identify the stability and genetic controls of morphological, biomass and biofuel traits during three consecutive summers with short duration, cool temperatures and long days. Eight out of 15 traits were found with high broad-sense heritability. Strong positive correlations between plant height and biomass traits were observed, while Brix and juice content were under different genetic controls. Using newly developed PAV (presence and absence variant) markers, 53 QTLs were detected, of which 18 were common for both countries, including a locus controlling stem juice (LOD score = 20.5, r (2) = 37.5 %). In Denmark, the heading stage correlated significantly with biomass and morphology traits, and two significant maturity QTLs detected on chromosomes SBI01 and SBI02 co-localised with QTLs previously associated with early-stage chilling tolerance, suggesting that accelerating maturation might be a means of coping with low-temperature stress. Our results suggest that selection for tall and fast maturating sorghum plants combined with high Brix content represents a high potential for breeding bioenergy crop for Northern Europe.

Update on the genomics and basic biology of Brachypodium: International Brachypodium Initiative (IBI).

The scientific presentations at the First International Brachypodium Conference (abstracts available at http://www.brachy2013.unimore.it) are evidence of the widespread adoption of Brachypodium distachyon as a model system. Furthermore, the wide range of topics presented (genome evolution, roots, abiotic and biotic stress, comparative genomics, natural diversity, and cell walls) demonstrates that the Brachypodium research community has achieved a critical mass of tools and has transitioned from resource development to addressing biological questions, particularly those unique to grasses.

Quantification of amylose, amylopectin, and ß-glucan in search for genes controlling the three major quality traits in barley by genome-wide association studies.

Genome-wide association studies (GWAS) for amylose, amylopectin and ß-glucan concentration in a collection of 254 European spring barley varieties allowed to identify 20, 17, and 21 single nucleotide polymorphic (SNP) markers, respectively, associated with these important grain quality traits. Negative correlations between the content of amylose and ß-glucan (R = -0.62, P < 0.01) and amylopectin and ß-glucan (R = -0.487, P < 0.01) were found in this large collection of spring barley varieties. Besides HvCslF6, amo1 and AGPL2, sex6, and waxy were identified among the major genes responsible for ß-glucan, amylose and amylopectin content, respectively. Several minor genes like HvGSL4, HvGSL3, and HvCesA6, PWD were also detected by GWAS for the first time. Furthermore, the gene encoding ß-fructofuranosidase, located on the short arm of chromosome 7H at 1.49 cM, and SRF6, encoding "leucine-rich repeat receptor kinase protein" on chromosome 2 H, are proposed to be new candidate genes for amylopectin formation in barley endosperm. Several of the associated SNPs on chromosome 1, 5, 6, and 7H mapped to overlapping regions containing QTLs and genes controlling the three grain constituents. In particular chromosomes 5 and 7H carry many QTLs controlling barley grain quality. Amylose, amylopectin and ß-glucan were interacted among each other through a metabolic network connected by UDP showing pleiotropic effects. Taken together, these results showed that cereal quality traits related each other and regulated through an interaction network, the identified major genes and genetic regions for amylose, amylopectin and ß-glucan is a helpful for further research on carbohydrates and barley breeding.

Overexpression of the AtSHI gene in poinsettia, Euphorbia pulcherrima, results in compact plants.

Euphorbia pulcherrima, poinsettia, is a non-food and non-feed vegetatively propagated ornamental plant. Appropriate plant height is one of the most important traits in poinsettia production and is commonly achieved by application of chemical growth retardants. To produce compact poinsettia plants with desirable height and reduce the utilization of growth retardants, the Arabidopsis SHORT INTERNODE (AtSHI) gene controlled by the cauliflower mosaic virus 35S promoter was introduced into poinsettia by Agrobacterium-mediated transformation. Three independent transgenic lines were produced and stable integration of transgene was verified by PCR and Southern blot analysis. Reduced plant height (21-52%) and internode lengths (31-49%) were obtained in the transgenic lines compared to control plants. This correlates positively with the AtSHI transcript levels, with the highest levels in the most dwarfed transgenic line (TL1). The indole-3-acetic acid (IAA) content appeared lower (11-31% reduction) in the transgenic lines compared to the wild type (WT) controls, with the lowest level (31% reduction) in TL1. Total internode numbers, bract numbers and bract area were significantly reduced in all transgenic lines in comparison with the WT controls. Only TL1 showed significantly lower plant diameter, total leaf area and total dry weight, whereas none of the AtSHI expressing lines showed altered timing of flower initiation, cyathia abscission or bract necrosis. This study demonstrated that introduction of the AtSHI gene into poinsettia by genetic engineering can be an effective approach in controlling plant height without negatively affecting flowering time. This can help to reduce or avoid the use of toxic growth retardants of environmental and human health concern. This is the first report that AtSHI gene was overexpressed in poinsettia and transgenic poinsettia plants with compact growth were produced.

Consumption of organic diets does not affect intake and absorption of zinc and copper in men - evidence from two cross-over trials.

Agricultural methods may affect the nutritional composition of plants and cause complex changes in the food matrix. Whether this affects the dietary absorption of minerals that are important for maintaining health thorough life remains unclear. We compared the effects of organic and conventional diets on intake and absorption of zinc and copper in men. Two double-blinded, cross-over, intervention trials (3 dietary periods of 12 days with 2-week-long wash-out) were performed in 2008 (n = 17) and 2009 (n = 16) in young men. The diets were based on 9 crops grown in rigidly controlled organic and conventional systems in 2 replications over 2 years. The primary outcomes were intake and absorption of zinc and copper. The absorption was determined by faecal excretion of stable enriched isotopes extrinsically added to the entire menu. Within each year, the intake and absorption of zinc (overall mean ± SD; 12.35 ± 0.47 mg per 10 MJ and 44.6% ± 12.1, respectively) and copper (overall mean ± SD; 2.12 ± 0.28 mg per 10 MJ and 41.2% ± 13.2, respectively) were not different between the organic and conventional diets. The growing season had no effect on zinc intake and absorption, but the copper intake was higher (P = 0.01) and absorption lower (P < 0.005) in 2008 compared with 2009 (overall mean absorption ± SD; 35.3% ± 13.5 in 2008 and 54.0% ± 10.7 in 2009). In conclusion, organic agriculture does not affect the intake and absorption of copper and zinc in men. Consequently, it does not seem to promote the health beneficial role of these minerals in vivo.