Genome-wide association study for in vitro digestibility and related traits in triticale forage.

BACKGROUND: Triticale is making its way on dairy farms as an alternative forage crop. This requires the availability of high-yielding triticale varieties with good digestibility. Triticale forage breeding mainly focussed on biomass yield, but efforts to improve digestibility are increasing. We previously investigated the interrelationships among different quality traits in soft dough triticale: starch, acid detergent fibre and in vitro digestibility of organic matter (IVOMD) and of neutral detergent fibre (IVNDFD) of the total plant, IVNDFD and Klason lignin of the stems, and ear proportion and stem length. Here we determine the genetic control of these traits, using a genome-wide association (GWAS) approach. A total of 33,231 DArTseq SNP markers assessed in a collection of 118 winter triticale genotypes, including 101 varieties and 17 breeding lines, were used. RESULTS: The GWAS identified a total of 53 significant marker-trait associations (MTAs). The highest number of significantly associated SNP markers (n = 10) was identified for total plant IVNDFD. A SNP marker on chromosome 1A (4211801_19_C/T; 474,437,796 bp) was found to be significantly associated with ear proportion, and plant and stem IVNDFD, with the largest phenotypic variation for ear proportion (R²p = 0.23). Based on MTAs, candidate genes were identified which were of particular relevance for variation in in vitro digestibility (IVD) because they are putatively involved in plasma membrane transport, cytoskeleton organisation, carbohydrate metabolic processes, protein phosphorylation, and sterol and cell wall biogenesis. Interestingly, a xyloglucan-related candidate gene on chromosome 2R, SECCE2Rv1G0126340, was located in close proximity of a SNP significantly associated with stem IVNDFD. Furthermore, quantitative trait loci previously reported in wheat co-localized with significantly associated SNP markers in triticale. CONCLUSIONS: A collection of 118 winter triticale genotypes combined with DArTseq SNP markers served as a source for identifying 53 MTAs and several candidate genes for forage IVD and related traits through a GWAS approach. Taken together, the results of this study demonstrate that the genetic diversity available in this collection can be further exploited for research and breeding purposes to improve the IVD of triticale forage.

Exploiting Rye in Wheat Quality Breeding: The Case of Arabinoxylan Content.

Rye (Secale cereale subsp. cereale L.) has long been exploited as a valuable alternative genetic resource in wheat (Triticum aestivum L.) breeding. Indeed, the introgression of rye genetic material led to significant breakthroughs in the improvement of disease and pest resistance of wheat, as well as a few agronomic traits. While such traits remain a high priority in cereal breeding, nutritional aspects of grain crops are coming under the spotlight as consumers become more conscious about their dietary choices and the food industry strives to offer food options that meet their demands. To address this new challenge, wheat breeding can once again turn to rye to look for additional genetic variation. A nutritional aspect that can potentially greatly benefit from the introgression of rye genetic material is the dietary fibre content of flour. In fact, rye is richer in dietary fibre than wheat, especially in terms of arabinoxylan content. Arabinoxylan is a major dietary fibre component in wheat and rye endosperm flours, and it is associated with a variety of health benefits, including normalisation of glycaemic levels and promotion of the gut microbiota. Thus, it is a valuable addition to the human diet, and it can represent a novel target for wheat-rye introgression breeding.

Variation in potential feeding value of triticale forage among plant fraction, maturity stage, growing season and genotype.

Cereal forages, such as triticale forage, progressively gain interest as alternative crop for maize. The main study objective was to investigate the variation in potential feeding value of triticale forage among maturity stage, growing season and genotype, using total plant and stem fractions. Therefore, near infrared spectroscopy (NIRS) was evaluated as fast screening tool. The prediction ability was good (ratio of prediction to deviation, RPD ≥3.0) for total plant residual moisture, starch, sugars and for stem crude ash (CAsh) and neutral detergent fibre (aNDFom); suitable for screening (2.0 ≤ RPD <3.0) for total plant CAsh, acid detergent fibre (ADFom), in vitro digestibility of organic matter (IVOMD), in vitro digestibility of neutral detergent fibre (IVNDFD) and for stem total lignin (TL) and IVNDFD; poor (1.5 ≤ RPD <2.0) for total plant crude protein, crude fat, aNDFom, lignin (sa) and for stem Klason lignin (KL); unreliable (RPD <1.5) for stem residual moisture and acid soluble lignin (ASL). The evolution in potential feeding value of 36 genotypes harvested at the medium and late milk to the early, soft and hard dough stage was followed. The most important changes occurred between the late milk and early dough stage, with little variation in quality after the soft dough stage. During 2 growing seasons, variation in feeding value of 120 genotypes harvested at the soft dough stage was demonstrated. Interestingly, variation in stem IVNDFD is almost twice as high as for the total plant (CV 12.4% versus 6.6%). Furthermore, Spearman correlations show no link between dry matter yield and digestibility of genotypes harvested at the soft dough stage. Based on linear regression models ADFom appears as main predictor of both plant IVOMD and plant IVNDFD. Stem IVNDFD is particularly determined by KL.

Phenotypic characterization of drought responses in red clover (Trifolium pratense L.).

Introduction: Red clover (Trifolium pratense) is a protein-rich, short-lived perennial forage crop that can achieve high yields, but suffers increasingly from drought in different cultivation areas. Breeding for increased adaptation to drought is becoming essential, but at this stage it is unclear which traits breeders should target to phenotype responses to drought that allow them to identify the most promising red clover genotypes. In this study, we assessed how prolonged periods of drought affected plant growth in field conditions, and which traits could be used to distinguish better adapted plant material. Methods: A diverse panel of 395 red clover accessions was evaluated during two growing seasons. We simulated 6-to-8-week drought periods during two consecutive summers, using mobile rain-out shelters, while an irrigated control field was established in an adjacent parcel. Plant growth was monitored throughout both growing seasons using multiple flights with a drone equipped with RGB and thermal sensors. At various observation moments throughout both growing seasons, we measured canopy cover (CC) and canopy height (CH). The crop water stress index (CWSI) was determined at two moments, during or shortly after the drought event. Results: Manual and UAV-derived measurements for CH were well correlated, indicating that UAV-derived measurements can be reliably used in red clover. In both years, CC, CH and CWSI were affected by drought, with measurable growth reductions by the end of the drought periods, and during the recovery phase. We found that the end of the drought treatment and the recovery phase of approximately 20 days after drought were suitable periods to phenotype drought responses and to distinguish among genotypes. Discussion: Multifactorial analysis of accession responses revealed interactions of the maturity type with drought responses, which suggests the presence of two independent strategies in red clover: 'drought tolerance' and 'drought recovery'. We further found that a large proportion of the accessions able to perform well under well-watered conditions were also the ones that were less affected by drought. The results of this investigation are interpreted in view of the development of breeding for adaptation to drought in red clover.

Genetic control of tolerance to drought stress in soybean.

BACKGROUND: Drought stress limits the production of soybean [Glycine max (L.) Merr.], which is the most grown high-value legume crop worldwide. Breeding for drought tolerance is a difficult endeavor and understanding the genetic basis of drought tolerance in soybean is therefore crucial for harnessing the genomic regions involved in the tolerance mechanisms. A genome-wide association study (GWAS) analysis was applied in a soybean germplasm collection (the EUCLEG collection) of 359 accessions relevant for breeding in Europe, to identify genomic regions and candidate genes involved in the response to short duration and long duration drought stress (SDS and LDS respectively) in soybean. RESULTS: The phenotypic response to drought was stronger in the long duration drought (LDS) than in the short duration drought (SDS) experiment. Over the four traits considered (canopy wilting, leaf senescence, maximum absolute growth rate and maximum plant height) the variation was in the range of 8.4-25.2% in the SDS, and 14.7-29.7% in the LDS experiments. The GWAS analysis identified a total of 17 and 22 significant marker-trait associations for four traits in the SDS and LDS experiments, respectively. In the genomic regions delimited by these markers we identified a total of 12 and 16 genes with putative functions that are of particular relevance for drought stress responses including stomatal movement, root formation, photosynthesis, ABA signaling, cellular protection and cellular repair mechanisms. Some of these genomic regions co-localized with previously known QTLs for drought tolerance traits including water use efficiency, chlorophyll content and photosynthesis. CONCLUSION: Our results indicate that the mechanism of slow wilting in the SDS might be associated with the characteristics of the root system, whereas in the LDS, slow wilting could be due to low stomatal conductance and transpiration rates enabling a high WUE. Drought-induced leaf senescence was found to be associated to ABA and ROS responses. The QTLs related to WUE contributed to growth rate and canopy height maintenance under drought stress. Co-localization of several previously known QTLs for multiple agronomic traits with the SNPs identified in this study, highlights the importance of the identified genomic regions for the improvement of agronomic performance in addition to drought tolerance in the EUCLEG collection.

Response of a Diverse European Soybean Collection to "Short Duration" and "Long Duration" Drought Stress.

Drought causes significant damage to a high value crop of soybean. Europe has an increasing demand for soybean and its own production is insufficient. Selection and breeding of cultivars adapted to European growth conditions is therefore urgently needed. These new cultivars must have a shorter growing cycle (specifically for adaptation to North-West Europe), high yield potential under European growing conditions, and sufficient drought resistance. We have evaluated the performance of a diverse collection of 359 soybean accessions under drought stress using rain-out shelters for 2 years. The contrasting weather conditions between years and correspondingly the varying plant responses demonstrated that the consequences of drought for an individual accession can vary strongly depending on the characteristics (e.g., duration and intensity) of the drought period. Short duration drought stress, for a period of four to 7 weeks, caused an average reduction of 11% in maximum canopy height (CH), a reduction of 17% in seed number per plant (SN) and a reduction of 16% in seed weight per plant (SW). Long duration drought stress caused an average reduction of 29% in CH, a reduction of 38% in SN and a reduction of 43% in SW. Drought accelerated plant development and caused an earlier cessation of flowering and pod formation. This seemed to help some accessions to better protect the seed yield, under short duration drought stress. Drought resistance for yield-related traits was associated with the maintenance of growth under long duration drought stress. The collection displayed a broad range of variation for canopy wilting and leaf senescence but a very narrow range of variation for crop water stress index (CWSI; derived from canopy temperature data). To the best of our knowledge this is the first study reporting a detailed investigation of the response to drought within a diverse soybean collection relevant for breeding in Europe.

Physicochemical Characterization of Thirteen Quinoa (Chenopodium quinoa Willd.) Varieties Grown in North-West Europe-Part II.

Quinoa cultivation has gained increasing interest in Europe but more research on the characteristics of European varieties is required to help determine their end use applications. A comparative study was performed on 13 quinoa varieties cultivated under North-West European field conditions during three consecutive growing seasons (2017-2019). The seeds were milled to wholemeal flour (WMF) to evaluate the physicochemical properties. The WMFs of 2019 were characterized by the highest water absorption capacity (1.46-2.06 g/g), while the water absorption index (WAI) between 55 °C (2.04-3.80 g/g) and 85 °C (4.04-7.82 g/g) increased over the years. The WMFs of 2018 had the highest WAI at 95 °C (6.48-9.48 g/g). The pasting profiles were characterized by a high viscosity peak (1696-2560 mPa.s) and strong breakdown (-78-643 mPa.s) in 2017. The peak viscosity decreased in 2018 and 2019 (823-2492 mPa.s), while breakdown (-364-555 mPa.s) and setback (19-1037 mPa.s) increased. Jessie, Summer Red, Rouge Marie, Vikinga, and Zwarte WMFs were characterized by low WAIs and high shear resistance. Bastille WMF developed high viscosities and, along with Faro WMF, showed a high breakdown. The wide variation in physicochemical properties suggests that the potential food applications of WMFs depend on the variety and growing conditions.

Yield and Nutritional Characterization of Thirteen Quinoa (Chenopodium quinoa Willd.) Varieties Grown in North-West Europe-Part I.

The cultivation of quinoa has gained increasing interest in Europe. Different European varieties exist, but more research is required to understand the individual variety characteristics for end-use applications. The objective of this study is to evaluate the agronomic performance of 13 quinoa varieties under North-West European field conditions during three growing seasons (2017-2019). Furthermore, seeds were qualitatively characterized based on characteristics and composition. Yield differed among varieties and growing seasons (0.47-3.42 ton/ha), with lower yields obtained for late-maturing varieties. The saponin content varied from sweet to very bitter. The seeds contained high protein levels (12.1-18.8 g/100 g dry matter), whereas varieties had a similar essential amino acid profile. The main fatty acids were linoleic (53.0-59.8%), α-linolenic (4.7-8.2%), and oleic acid (15.5-22.7%), indicating a high degree of unsaturation. The clustering of varieties/years revealed subtle differences between growing seasons but also reflected the significant interaction effects of variety and year. Most varieties perform well under North-West European conditions, and their nutritional content is well within the values previously described for other cultivation areas. However, optimal yield and quality traits were not combined in one variety, illustrating the importance of breeding for adapted quinoa varieties.

A Genome-Wide Genetic Diversity Scan Reveals Multiple Signatures of Selection in a European Soybean Collection Compared to Chinese Collections of Wild and Cultivated Soybean Accessions.

Targeted and untargeted selections including domestication and breeding efforts can reduce genetic diversity in breeding germplasm and create selective sweeps in crop genomes. The genomic regions at which selective sweeps are detected can reveal important information about signatures of selection. We have analyzed the genetic diversity within a soybean germplasm collection relevant for breeding in Europe (the EUCLEG collection), and have identified selective sweeps through a genome-wide scan comparing that collection to Chinese soybean collections. This work involved genotyping of 480 EUCLEG soybean accessions, including 210 improved varieties, 216 breeding lines and 54 landraces using the 355K SoySNP microarray. SNP calling of 477 EUCLEG accessions together with 328 Chinese soybean accessions identified 224,993 high-quality SNP markers. Population structure analysis revealed a clear differentiation between the EUCLEG collection and the Chinese materials. Further, the EUCLEG collection was sub-structured into five subgroups that were differentiated by geographical origin. No clear association between subgroups and maturity group was detected. The genetic diversity was lower in the EUCLEG collection compared to the Chinese collections. Selective sweep analysis revealed 23 selective sweep regions distributed over 12 chromosomes. Co-localization of these selective sweep regions with previously reported QTLs and genes revealed that various signatures of selection in the EUCLEG collection may be related to domestication and improvement traits including seed protein and oil content, phenology, nitrogen fixation, yield components, diseases resistance and quality. No signatures of selection related to stem determinacy were detected. In addition, absence of signatures of selection for a substantial number of QTLs related to yield, protein content, oil content and phenological traits suggests the presence of substantial genetic diversity in the EUCLEG collection. Taken together, the results obtained demonstrate that the available genetic diversity in the EUCLEG collection can be further exploited for research and breeding purposes. However, incorporation of exotic material can be considered to broaden its genetic base.

Seasonal Differences in Structural and Genetic Control of Digestibility in Perennial Ryegrass.

Perennial ryegrass is an important forage crop in dairy farming, either for grazing or haying purposes. To further optimise the forage use, this study focused on understanding forage digestibility in the two most important cuts of perennial ryegrass, the spring cut at heading and the autumn cut. In a highly diverse collection of 592 Lolium perenne genotypes, the organic matter digestibility (OMD) and underlying traits such as cell wall digestibility (NDFD) and cell wall components (cellulose, hemicellulose, and lignin) were investigated for 2 years. A high genotype × season interaction was found for OMD and NDFD, indicating differences in genetic control of these forage quality traits in spring versus autumn. OMD could be explained by both the quantity of cell wall content (NDF) and the quality of the cell wall content (NDFD). The variability in NDFD in spring was mainly explained by differences in hemicellulose. A 1% increase of the hemicellulose content in the cell wall (HC.NDF) resulted in an increase of 0.81% of NDFD. In autumn, it was mainly explained by the lignin content in the cell wall (ADL.NDF). A 0.1% decrease of ADL.NDF resulted in an increase of 0.41% of NDFD. The seasonal traits were highly heritable and showed a higher variation in autumn versus spring, indicating the potential to select for forage quality in the autumn cut. In a candidate gene association mapping approach, in which 503 genes involved in cell wall biogenesis, plant architecture, and phytohormone biosynthesis and signalling, identified significant quantitative trait loci (QTLs) which could explain from 29 to 52% of the phenotypic variance in the forage quality traits OMD and NDFD, with small effects of each marker taken individually (ranging from 1 to 7%). No identical QTLs were identified between seasons, but within a season, some QTLs were in common between digestibility traits and cell wall composition traits confirming the importance of hemicellulose concentration for spring digestibility and lignin concentration in NDF for autumn digestibility.

Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass.

Germplasm from perennial ryegrass (Lolium perenne L.) natural populations is useful for breeding because of its adaptation to a wide range of climates. Climate-adaptive genes can be detected from associations between genotype, phenotype and climate but an integrated framework for the analysis of these three sources of information is lacking. We used two approaches to identify adaptive loci in perennial ryegrass and their effect on phenotypic traits. First, we combined Genome-Environment Association (GEA) and GWAS analyses. Then, we implemented a new test based on a Canonical Correlation Analysis (CANCOR) to detect adaptive loci. Furthermore, we improved the previous perennial ryegrass gene set by de novo gene prediction and functional annotation of 39,967 genes. GEA-GWAS revealed eight outlier loci associated with both environmental variables and phenotypic traits. CANCOR retrieved 633 outlier loci associated with two climatic gradients, characterized by cold-dry winter versus mild-wet winter and long rainy season versus long summer, and pointed out traits putatively conferring adaptation at the extremes of these gradients. Our CANCOR test also revealed the presence of both polygenic and oligogenic climatic adaptations. Our gene annotation revealed that 374 of the CANCOR outlier loci were positioned within or close to a gene. Co-association networks of outlier loci revealed a potential utility of CANCOR for investigating the interaction of genes involved in polygenic adaptations. The CANCOR test provides an integrated framework to analyse adaptive genomic diversity and phenotypic responses to environmental selection pressures that could be used to facilitate the adaptation of plant species to climate change.

Rewired phenolic metabolism and improved saccharification efficiency of a Zea mays cinnamyl alcohol dehydrogenase 2 (zmcad2) mutant.

Lignocellulosic biomass is an abundant byproduct from cereal crops that can potentially be valorized as a feedstock to produce biomaterials. Zea mays CINNAMYL ALCOHOL DEHYDROGENASE 2 (ZmCAD2) is involved in lignification, and is a promising target to improve the cellulose-to-glucose conversion of maize stover. Here, we analyzed a field-grown zmcad2 Mutator transposon insertional mutant. Zmcad2 mutant plants had an 18% lower Klason lignin content, whereas their cellulose content was similar to that of control lines. The lignin in zmcad2 mutants contained increased levels of hydroxycinnamaldehydes, i.e. the substrates of ZmCAD2, ferulic acid and tricin. Ferulates decorating hemicelluloses were not altered. Phenolic profiling further revealed that hydroxycinnamaldehydes are partly converted into (dihydro)ferulic acid and sinapic acid and their derivatives in zmcad2 mutants. Syringyl lactic acid hexoside, a metabolic sink in CAD-deficient dicot trees, appeared not to be a sink in zmcad2 maize. The enzymatic cellulose-to-glucose conversion efficiency was determined after 10 different thermochemical pre-treatments. Zmcad2 yielded significantly higher conversions compared with controls for almost every pre-treatment. However, the relative increase in glucose yields after alkaline pre-treatment was not higher than the relative increase when no pre-treatment was applied, suggesting that the positive effect of the incorporation of hydroxycinnamaldehydes was leveled off by the negative effect of reduced p-coumarate levels in the cell wall. Taken together, our results reveal how phenolic metabolism is affected in CAD-deficient maize, and further support mutating CAD genes in cereal crops as a promising strategy to improve lignocellulosic biomass for sugar-platform biorefineries.

High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (Lolium perenne L.).

The natural genetic diversity of agricultural species is an essential genetic resource for breeding programs aiming to improve their ecosystem and production services. A large natural ecotype diversity is usually available for most grassland species. This could be used to recombine natural climatic adaptations and agronomic value to create improved populations of grassland species adapted to future regional climates. However describing natural genetic resources can be long and costly. Molecular markers may provide useful information to help this task. This opportunity was investigated for Lolium perenne L., using a set of 385 accessions from the natural diversity of this species collected right across Europe and provided by genebanks of several countries. For each of these populations, genotyping provided the allele frequencies of 189,781 SNP markers. GWAS were implemented for over 30 agronomic and/or putatively adaptive traits recorded in three climatically contrasted locations (France, Belgium, Germany). Significant associations were detected for hundreds of markers despite a strong confounding effect of the genetic background; most of them pertained to phenology traits. It is likely that genetic variability in these traits has had an important contribution to environmental adaptation and ecotype differentiation. Genomic prediction models calibrated using natural diversity were found to be highly effective to describe natural populations for almost all traits as well as commercial synthetic populations for some important traits such as disease resistance, spring growth or phenological traits. These results will certainly be valuable information to help the use of natural genetic resources of other species.

Artificial Chromosome Doubling in Allotetraploid Calendula officinalis.

Calendula officinalis L. is known as an ornamental plant as well as a source of biochemical compounds used in cosmetics and industry. C. officinalis has a complex karyotype. Published chromosome numbers differ between 2n = 4x = 28 or 32. We have estimated genome sizes in nine commercial cultivars and evaluated the ploidy level by karyotyping and fluorescent in situ hybridization (FISH) using 5S and 45S rDNA loci. The detection of chromosome sets of two rather than four homologues would suggest that C. officinalis has an allotetraploid background. In addition, four signals for 45S but only two for 5S were found by using FISH. Artificial chromosome doubling is a common technique in plant breeding, as polyploidization results in several consequences for plant growth and development. Especially the suggested allotetraploid background in C. officinalis is interesting when examining the effect of chromosome doubling on the plant phenotype. Here we describe chromosome doubling of three allotetraploid cultivars of C. officinalis, 'Nova,' 'WUR 1553-7' and 'Orange Beauty'. Three antimitotic agents - colchicine, oryzalin and trifluralin - were used in different concentrations to find the combination of the best agent and the best dosage to obtain octaploids. For all three cultivars a few octaploids were obtained. A concentration of 200 and 400 ppm of colchicine was most efficient for chromosome doubling in 'Nova' and 'Orange Beauty,' respectively. For 'WUR 1553-7' the treatment with 20 ppm oryzalin was also effective. Cell numbers and first observations of the phenotype in the chromosome doubled plants show thicker leaves and bigger cells, as commonly observed after ploidy doubling. Due to the low number of chromosome doubled plants obtained more elaborate phenotyping will be performed on following generations cultivated under field conditions.

Population genomic structure of the gelatinous zooplankton species Mnemiopsis leidyi in its nonindigenous range in the North Sea.

Nonindigenous species pose a major threat for coastal and estuarine ecosystems. Risk management requires genetic information to establish appropriate management units and infer introduction and dispersal routes. We investigated one of the most successful marine invaders, the ctenophore Mnemiopsis leidyi, and used genotyping-by-sequencing (GBS) to explore the spatial population structure in its nonindigenous range in the North Sea. We analyzed 140 specimens collected in different environments, including coastal and estuarine areas, and ports along the coast. Single nucleotide polymorphisms (SNPs) were called in approximately 40 k GBS loci. Population structure based on the neutral SNP panel was significant (F ST .02; p < .01), and a distinct genetic cluster was identified in a port along the Belgian coast (Ostend port; pairwise F ST .02-.04; p < .01). Remarkably, no population structure was detected between geographically distant regions in the North Sea (the Southern part of the North Sea vs. the Kattegat/Skagerrak region), which indicates substantial gene flow at this geographical scale and recent population expansion of nonindigenous M. leidyi. Additionally, seven specimens collected at one location in the indigenous range (Chesapeake Bay, USA) were highly differentiated from the North Sea populations (pairwise F ST .36-.39; p < .01). This study demonstrates the utility of GBS to investigate fine-scale population structure of gelatinous zooplankton species and shows high population connectivity among nonindigenous populations of this recently introduced species in the North Sea. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at: The DNA sequences generated for this study are deposited in the NCBI sequence read archive under SRA accession numbers SRR6950721-SRR6950884, and will be made publically available upon publication of this manuscript.

Environmental sustainability of conventional and organic farming: Accounting for ecosystem services in life cycle assessment.

Today, there is an ongoing debate about the environmental sustainability of the products of organic farming. To compare the performance of conventional and organic farming systems regarding environmental impact and productivity, the comprehensive environmental assessment tool 'life cycle assessment' can be used. The lower crop yields attained by organic systems compared to conventional farming systems might, however, outweigh the benefits of the use of more environmental-friendly practices when evaluating the environmental impact per product unit. Although these practices are beneficial for the environment, which is reflected in the delivery of a range of ecosystem services (ES), the focus is traditionally put only on the (harvested) product. Because the agricultural product involves actually a bundle of ES, the impact should be allocated among the whole output of an agricultural system. In this study, we propose an allocation procedure based on the capacity of agricultural systems to deliver ES to divide the environmental impact over all agricultural outputs (i.e. provisioning and other ES). Allocation factors are developed for conventional and organic arable farming systems. Applying these allocation factors, we demonstrate that for about half of the studied food products (including maize, potato), organic farming has clear environmental benefits in terms of resource consumption in comparison to conventional cultivation methods. This allocation approach allows a more complete comparison of the environmental sustainability of organically and conventionally produced food.

Single Nucleotide Polymorphisms and Biochemical Markers As Complementary Tools To Characterize Hops ( Humulus lupulus L.) in Brewing Practice.

In brewing practice, the use of the appropriate hop variety is essential to produce consistent and high-quality beers. Yet, hop batches of the same variety cultivated in different geographical regions can display significant biochemical differences, resulting in specific taste- and aroma-related characteristics in beer. In this study, we illustrate the complementarity of genetic and biochemical fingerprinting methods to fully characterize hop batches. Using genotyping-by-sequencing (GBS), a set of 1 830 polymorphic single nucleotide polymorphism (SNP) markers generated 48 unique genetic fingerprints for a collection of 56 commercial hop varieties. Three groups of varieties, consisting of somaclonal variants, could not be further differentiated using this set of markers. Biochemical marker information offered added value to characterize hop samples from a given variety grown at different geographical locations. We demonstrate the power of combining genetic and biochemical fingerprints for quality control of hop batches in the brewing industry.

Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne).

Revealing DNA sequence variation within the Lolium perenne genepool is important for genetic analysis and development of breeding applications. We reviewed current literature on plant development to select candidate genes in pathways that control agronomic traits, and identified 503 orthologues in L. perenne. Using targeted resequencing, we constructed a comprehensive catalogue of genomic variation for a L. perenne germplasm collection of 736 genotypes derived from current cultivars, breeding material and wild accessions. To overcome challenges of variant calling in heterogeneous outbreeding species, we used two complementary strategies to explore sequence diversity. First, four variant calling pipelines were integrated with the VariantMetaCaller to reach maximal sensitivity. Additional multiplex amplicon sequencing was used to empirically estimate an appropriate precision threshold. Second, a de novo assembly strategy was used to reconstruct divergent alleles for each gene. The advantage of this approach was illustrated by discovery of 28 novel alleles of LpSDUF247, a polymorphic gene co-segregating with the S-locus of the grass self-incompatibility system. Our approach is applicable to other genetically diverse outbreeding species. The resulting collection of functionally annotated variants can be mined for variants causing phenotypic variation, either through genetic association studies, or by selecting carriers of rare defective alleles for physiological analyses.

Temporal changes in genetic diversity and forage yield of perennial ryegrass in monoculture and in combination with red clover in swards.

Agricultural grasslands are often cultivated as mixtures of grasses and legumes, and an extensive body of literature is available regarding interspecific interactions, and how these relate to yield and agronomic performance. However, knowledge of the impact of intraspecific diversity on grassland functioning is scarce. We investigated these effects during a 4-year field trial established with perennial ryegrass (Lolium perenne) and red clover (Trifolium pratense). We simulated different levels of intraspecific functional diversity by sowing single cultivars or by combining cultivars with contrasting growth habits, in monospecific or bispecific settings (i.e. perennial ryegrass whether or not in combination with red clover). Replicate field plots were established for seven seed compositions. We determined yield parameters and monitored differences in genetic diversity in the ryegrass component among seed compositions, and temporal changes in the genetic composition and genetic diversity at the within plot level. The composition of cultivars of both species affected the yield and species abundance. In general, the presence of clover had a positive effect on the yield. The cultivar composition of the ryegrass component had a significant effect on the yield, both in monoculture, and in combination with clover. For the genetic analyses, we validated empirically that genotyping-by-sequencing of pooled samples (pool-GBS) is a suitable method for accurate measurement of population allele frequencies, and obtained a dataset of 22,324 SNPs with complete data. We present a method to investigate the temporal dynamics of cultivars in seed mixtures grown under field conditions, and show how cultivar abundances vary during subsequent years. We screened the SNP panel for outlier loci, putatively under selection during the cultivation period, but none were detected.

Introduction of a natural resource balance indicator to assess soil organic carbon management: Agricultural Biomass Productivity Benefit.

The rising demand for feed and food has put an increasing pressure on agriculture, with agricultural intensification as a direct response. Notwithstanding the higher crop productivity, intensive agriculture management entails many adverse environmental impacts. Worldwide, soil organic carbon (SOC) decline is hereby considered as a main danger which affects soil fertility and productivity. The life cycle perspective helps to get a holistic overview when evaluating the environmental sustainability of agricultural systems, though the impact of farm management on soil quality aspects is often not integrated. In this paper, we introduce an indicator called Agricultural Biomass Productivity Benefit of SOC management (ABB_SOC), which, relying on natural resource consumption, enables to estimate the net effect of the efforts made to attain a better soil quality. Hereby the focus is put on SOC. First, we introduce a framework to describe the SOC trend due to farm management decisions. The extent to which remediation measures are required are used as a measure for the induced SOC losses. Next, ABB_SOC values are calculated as the balance between the natural resource consumption of the inputs (including remediation efforts) and the desired output of arable crop production systems. The models RothC and EU-Rotate_N are used to simulate the SOC evolution due to farm management and the response of the biomass productivity, respectively. The developed indicator is applied on several rotation systems in Flanders, comparing different remediation strategies. The indicator could be used as a base for a method to account for soil quality in life cycle analysis.