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This research was funded by UK Research and Innovation (BBSRC Grant # BB/L011840/1; Ecology and Epidemiology of Infectious Diseases), by the Scottish Government's Rural and Environment Science and Analytical Services (RESAS) Division, and by the James Hutton Institute. The aims of this study were: i) to investigate mature plant resistance (MPR) against four strains of Potato virus Y (PVYO, PVYN, PVYNTN and PVYN−Wi) in potato cultivars that differ in maturity (e.g. early or maincrop) at different developmental stages, and ii) to determine whether phloem translocation of photoassimilates at different stages including the source-sink transition influences MPR. The data showed that MPR was functional by the flowering stage in all cultivars, and that the host-pathogen interaction is highly complex, with all three variables (potato cultivar, virus strain and developmental stage of infection) having a significant effect on the outcome. However, virus strain was the most important factor, and MPR was less effective in protecting tubers from recombinant virus strains (PVYNTN and PVYN−Wi). Development of MPR was unrelated to foliar phloem connectivity, which was observed at all developmental stages, but a switch from symplastic to apoplastic phloem unloading early in tuber development may be involved in the prevention of tuber infections with PVYO. Recombinant virus strains were more infectious than parental strains and PVYNTN has a more effective silencing suppressor than PVYO, another factor that may contribute to the efficiency of MPR. The resistance conferred by MPR against PVYO or PVYN may be associated with or enhanced by the presence of the corresponding strain-specific HR resistance gene in the cultivar. Publisher PDF

Physiological and physical traits are excellent indicators of many crop characteristics, but precise phenotyping of these traits is time consuming and, therefore, limits progress in crop breeding and the speed of crop monitoring. Hyperspectral imaging offers an opportunity to overcome these barriers as a technique for high throughput field measurements. Using a recently developed hyperspectral imaging platform devised for plantations of the perennial crop raspberry, this study aimed to further develop the tool and test its capacity as an innovative approach for high throughput field phenotyping, data collection and analysis. Hyperspectral imaging and visual crop assessments were carried out over two growing seasons in a field-grown raspberry mapping population, and data were subject to Quantitative Trait Loci (QTL) analysis. The findings show that reflectance intensity at multiple wavelengths can be linked to known genetic markers in raspberry, and many of these 'spectral traits' are expressed consistently through the growing season and between years, for example spectral ratio 719 nm / 691 nm shows up consistently as a QTL on LG4. Spectral traits were identified that co-located with previously mapped physical traits, such as 719 nm / 691 nm and cane density. The study indicates that hyperspectral imaging can be used as an innovative approach for high throughput field phenotyping of raspberry and could be transferred readily to other perennial crops. Our approach provides a pipeline for automated field data collection and analysis that can be used for rapid QTL detection of spectral traits.

MotivationThe investigation of quantitative trait loci (QTL) is an essential component in our understanding of how organisms vary phenotypically. However, many important crop species are polyploid (carrying more than two copies of each chromosome), requiring specialised tools for such analyses. Moreover, deciphering meiotic processes at higher ploidy levels is not straightforward, but is necessary to understand the reproductive dynamics of these species, or uncover potential barriers to their genetic improvement.ResultsHere we present polyqtlR, a novel software tool to facilitate such analyses in (auto)polyploid crops. It performs QTL interval mapping in F1 populations of outcrossing polyploids of any ploidy level using identity-by-descent (IBD) probabilities. The allelic composition of discovered QTL can be explored, enabling favourable alleles to be identified and tracked in the population. Visualisation tools within the package facilitate this process, and options to include genetic co-factors and experimental factors are included. Detailed information on polyploid meiosis including prediction of multivalent pairing structures, detection of preferential chromosomal pairing and location of double reduction events can be performed.Availability and implementationpolyqtlR is freely available from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polyqtlR.Contactpeter.bourke@wur.nl or chris.maliepaard@wur.nlSupplementary informationSupplementary data are available

Purpose Rhizodeposition shapes soil microbial communities that perform important processes such as soil C mineralization, but we have limited understanding of the plant genetic regions influencing soil microbes. Here, barley chromosome regions affecting soil microbial biomass-C (MBC), dissolved organic-C (DOC) and root biomass were characterised. Methods A quantitative trait loci analysis approach was applied to identify barley chromosome regions affecting soil MBC, soil DOC and root biomass. This was done using barley Recombinant Chromosome Substitution Lines (RCSLs) developed with a wild accession (Caesarea 26-24) as a donor parent and an elite cultivar (Harrington) as recipient parent. Results Significant differences in root-derived MBC and DOC and root biomass among these RCSLs were observed. Analysis of variance using single nucleotide polymorphisms genotype classes revealed 16 chromosome regions influencing root-derived MBC and DOC. Of these chromosome regions, five on chromosomes 2H, 3H and 7H were highly significant and two on chromosome 3H influenced both root-derived MBC and DOC. Potential candidate genes influencing root-derived MBC and DOC concentrations in soil were identified. Conclusion The present findings provide new insights into the barley genetic influence on soil microbial communities. Further work to verify these barley chromosome regions and candidate genes could promote marker assisted selection and breeding of barley varieties that are able to more effectively shape soil microbes and soil processes via rhizodeposition, supporting sustainable crop production systems.

The golden and white potato cyst nematodes (Globodera rostochiensis and G. pallida, respectively) are devastating quarantine pests of potatoes. The most widely distributed pathotype of the golden nematode, Ro1, is well controlled by the H1 resistance gene. A pathotype that overcomes H1, Ro2, has been detected on several farms in New York State. To map Ro2 resistance gene(s), two autotetraploid parental clones – NY121 (Ro2 resistant) and NY115 (susceptible) – along with 182 F1 offspring were genotyped with 8303 SNP markers, and the resistance of each clone to Ro2 was assessed with a greenhouse pot assay. Analysis with TetraploidSNPMap identified two Ro2 resistance QTL on chromosome 5: one QTL was located at 26 cM and explained 24.4% of the variation for resistance, while the second at 59 cM co-localized with a marker (57R) known to be tightly linked to H1 and explained 23.8% of the residual variation. Subsequent inoculation with G. pallida revealed that the chromosome 5 locus at 26 cM also conferred some resistance against pathotype Pa2/3, explaining 9.2% of the variation. A second QTL that increased susceptibility to Pa2/3 was located at 15 cM on chromosome 10 and explained 6.9% of the variation. The resistance gene(s) at 26 cM on chromosome 5 may correspond to previously described Grp1; a marker diagnostic for this region would be useful for applied potato breeding.

Cultivar mixtures of winter barley and spring barley, together with their component monocultures, were grown in field trials to assess the effect of cultivar combinations on both straw and grain yield. The overall grain yields for all trials were significantly higher for the cultivar mixtures than for the corresponding component monocultures. Also, significant decreases in rhynchosporium disease severity for cultivar mixtures were recorded for most non-fungicide treatments. The size of these responses was often significantly correlated with the component number of the mixtures. The amount of straw produced in mixtures was sometimes changed significantly, but not always in a positive direction and it was only correlated with increasing mixture component number in two environments. No correlation of straw yield potential of cultivars with performance in mixtures was found. Cultivar × cultivar mixture × environment interactions appeared to affect the relative yield of grain and straw differentially and therefore it was not possible to predict the effect of mixtures on the harvest index.

Background The changing climate is altering timing of key fruit ripening processes and increasing the occurrence of fruit defects. This work aimed to expand our knowledge of the genetic control of the ripening process in raspberry by examining a biennial x primocane F1 population to determine if the progeny exhibited both primocane and biennial flowering modes, which if any was dominant, and to identify QTL and genome locations associated with fruit development to understand how developmental control in this population differs from a biennial x biennial F1 population previously studied. Results The progeny from this biennial x primocane population exhibited primocane fruiting completing their lifecycle in a single season and also fruiting on second-year wood not removed in season one. QTL associated with rate of fruit development were identified on both primocane and fruiting canes with both parents impacting. Conclusions Novel QTL associated with the developmental process of primocane fruiting were identified. These in the main, differed from developmental QTL for similar developmental stages on fruiting canes (second year canes) with only one significant overlap on linkage group 6. In general, the process of development on fruiting canes overall differed from that in a biennial x biennial population, with the differences being greatest on linkage groups 3 and 6 suggesting control of development differs in the different fruiting types. Further understanding will be achieved by examining genome regions linked to QTL to allow breeding to meet climate requirements for yield stability.

Modern cereal cultivars are highly adapted to, and normally bred and trialled under, high input, high soil disturbance conditions. On-farm conditions are often suboptimal for high yield and frequently use minimal soil tillage, sometimes no-tillage, and therefore, cultivars may be differentially adapted to such conditions. We report a series of trials across 10 years comparing multiple cultivars within years and smaller numbers across years to identify stable cultivars showing preferential adaptation to different levels of soil tillage. Cultivars responded differentially to inversion and non-inversion tillage but were not affected by the level of cultivation within each of these tillage types. Yield declined over time but much more so in the non-inversion tillage treatment. Rhynchosporium symptoms were also increasingly suppressed in the non-inversion tillage type. Several cultivars were identified that showed strong adaptation to tillage type, and some of these were consistent across several trial years. These cultivars can be used to identify traits and genotypes associated with tillage adaptation to target breeding for on-farm conditions.

Flower shape and colour are key plant traits which are often strongly correlated with pollinator choice and reproductive isolation. To understand the genetic changes underlying variation in these traits, we performed the first QTL analyses of these traits in Streptocarpus (Gesneriaceae) using a segregating backcross (BC) population of (S. rexii × S. grandis) × S. grandis. Composite traits of floral dimensions were dissected into smallest definable subtraits to examine the efficiency of QTL mapping and correlation between composite and subtrait-specific QTLs. Strong dominance effects were observed in the F1 for many S. rexii traits but for few S. grandis traits. In the BC plants new phenotypes appeared that may be the result of transgressive segregation. Many phenotypic correlations were found between floral dimension traits, which was probably due to the co-localisation of QTLs on the linkage groups. Two regions were associated with large numbers of size and shape traits (17 linked on LG1 and eight linked on LG12), to which the first principal component was also mapped. QTLs of composite traits were mostly overlapping with subtraits, although a few QTLs were newly discovered in subtrait mapping. Strong QTLs were detected for time to flowering and for floral pigmentation traits, ventral lobe pigmentation and the yellow spot. The absence of linkage of floral dimension traits and flower pigmentation suggests that genetic regulation of floral form in Streptocarpus allows versatility, perhaps allowing fast response to changing selective pressures from pollinators.

Background The changing climate is altering timing of key fruit ripening processes and increasing the occurrence of fruit defects. To improve our understanding of the genetic control of raspberry fruit development an enhanced genetic linkage map was developed and used to examine ripening phenotypic data. Results In this study we developed an enhanced genetic linkage map for the raspberry cvs. Glen Moy x Latham reference mapping population using genotyping by sequencing (GbS). Alignment to a newly sequenced draft reference genome of red raspberry, cultivar (cv.) Glen Moy, identified 8019 single nucleotide polymorphisms (SNPs). After stringent filtering to take account of read coverage over all the progeny individuals, association with a single chromosome, heterozygosity and marker regression mapping, 2348 high confidence SNPs were retained and integrated with an existing raspberry genetic map. The linkage map contained many more SNPs segregating in Latham than in Glen Moy. This caused difficulties in quantitative trait loci (QTL) mapping with standard software and a novel analysis based on a hidden Markov model was used to improve the mapping. QTL mapping using the newly generated dense genetic map not only corroborated previously identified genetic locations but also provided additional genetic elements controlling fruit ripening in raspberry. Conclusion The high-density GbS map located the QTL peaks more precisely than in earlier studies, aligned the QTLs with Glen Moy genome scaffolds, narrowed the range of potential candidate genes to these regions that can be utilised in other populations or in gene expression studies to confirm their role and increased the repertoire of markers available to understand the genetic control of fruit ripening traits. Electronic supplementary material The online version of this article (10.1186/s12863-018-0666-z) contains supplementary material, which is available to authorized users.

Streptocarpus shows a great diversity of shoot and flower morphology, but lacks resources for genetic studies. RAD sequencing with NGS technologies provides large amounts of genotyping data quickly and cost effectively and is very useful for genetic map construction. In this study, three approaches for constructing RAD loci were combined to build the first genetic map for Streptocarpus (Gesneriaceae). A backcross population between Streptocarpus grandis and S. rexii was used as the mapping population. The parents are both diploid (2n = 32) and largely autogamous. Streptocarpus grandis is unifoliate, retaining the enlarged macrocotyledon as sole foliar organ which is monocarpic, and S. rexii is rosulate and perennial. 233 backcross plants were genotyped, and the data from 200 or 150 individuals used to generate the maps. The RAD reads were assembled using a de novo approach, aligned on the reference draft genome sequences of S. rexii using BWA or Stampy, and finally all markers were analyzed combined. In the latter, 599 mappable markers were generated which were assigned to 16 linkage groups, with an average inter-marker distance of 2.6 cM. This work provides a valuable genetic resource for further studies in the large and morphologically diverse genus Streptocarpus.

This research was funded by the Royal Society University Research Fellowship, BBSRC BB/J000868/1, BB/L026058/1, BB/J011460/1, NERC NE/L00237/1, EPSRC EP/M020355/1 and ERC Consolidator grant DIMR 646809. The contributions to this project by the James Hutton Institute and Biomathematics and Statistics Scotland were funded by the Scottish Government. The GC–MS analysis was carried out by Sheffield Hallam University.

Potato tuber necrotic ringspot disease (PTNRD) is a tuber deformity associated with infection by the tuber necrotic strain ofPotato virus Y(PVYNTN). PTNRD negatively impacts tuber quality and marketability and poses a serious threat to seed and commercial potato production worldwide. PVYNTNsymptoms differ in the cultivars Waneta and Pike: Waneta expresses severe PTNRD and foliar mosaic with vein and leaf necrosis, whereas Pike does not express PTNRD and mosaic is the only foliar symptom. To map loci that influence tuber and foliar symptoms, 236 F1progeny of a cross between Waneta and Pike were inoculated with PVYNTNisolate NY090029 and genotyped using 12,808 Potato SNPs. Foliar symptom type and severity were monitored for 10 weeks, while tubers were evaluated for PTNRD expression at harvest and again after 60 days in storage. Pairwise correlation analyses indicate a strong association between PTNRD and vein necrosis (τ = 0.4195). QTL analyses revealed major-effect QTLs on chromosomes 4 and 5 for mosaic, 4 for PTNRD, and 5 for foliar-necrosis symptoms. Locating QTLs associated with PVY-related symptoms provides a foundation for breeders to develop markers that can be used to screen out potato clones with undesirable phenotypes, e.g., those likely to develop PTNRD or to be symptomless carriers of PVY.

Commercially, blackcurrants (Ribes nigrum L.) are grown mainly for processing, especially for juice production. They are valued for their high levels of polyphenols, especially anthocyanins, which contribute to their characteristic deep colour, but also as a good source of vitamin C. Recently, evidence has accrued that polyphenols, such as anthocyanins, may have specific human health benefits. The aims of this study were to investigate the genetic control of polyphenols and other key juice processing traits in blackcurrants. The levels, over 2 years, of vitamin C, citrate, malate, succinate, total organic acids, total anthocyanins and total phenolics together with 46 mainly polyphenol metabolites were measured in a blackcurrant biparental mapping population. Quantitative trait loci (QTLs) for these traits were mapped onto a high-density SNP linkage map. At least one QTL was detected for each trait, with good consistency between the 2 years. Clusters of QTLs were found on each of the eight linkage groups (LG). For example, QTLs for the major anthocyanidin glucosides, delphinidin-3-O-glucoside and cyanidin-3-O-glucoside, co-localised with a QTL for total anthocyanin content on LG3 whereas the major anthocyanidin rutinosides, delphinidin-3-O-rutinoside and cyanidin-3-O-rutinoside, had QTLs on LG1 and LG2. Many of the QTLs explained a high proportion of the trait variation, with the most significant region, on LG3 at ~ 35 cM, explaining more than 60% of the variation in the coumaroylated metabolites, Cyanidin-coumaroyl-glucose, Delphinidin-coumaroyl-glucose, Kaempferol-coumaroyl-glucose and Myricetin-coumaroyl-glucose. The identification of robust QTLs for key polyphenol classes and individual polyphenols in blackcurrant provides great potential for marker-assisted breeding for improved levels of key components.

New genotyping technologies, offering the possibility of high genetic resolution at low cost, have helped fuel a surge in interest in the genetic analysis of polyploid species. Nevertheless, autopolyploid species present extra challenges not encountered in diploids and allopolyploids, such as polysomic inheritance or double reduction. Here we investigate the power and precision of quantitative trait locus (QTL) analysis in outcrossing autopolyploids, comparing the results of a model that assumes random bivalent chromosomal pairing during meiosis to one that also allows for multivalents and double reduction. Through a series of simulation studies we found that marginal gains in QTL detection power are achieved using the double reduction model when multivalent pairing occurs. However, when exploring the effect of variable genotypic information across parental homologs, we found that both QTL detection power and precision require high and uniform genotypic information contents. This effect far outweighed considerations regarding bivalent or multivalent pairing (and double reduction) during meiosis. We propose that autopolyploid QTL studies be accompanied by both marker coverage information and per-homolog genotypic information coefficients (GIC). Application of these methods to an autotetraploid potato (Solanum tuberosum L.) mapping population confirmed our ability to locate and dissect QTL in highly heterozygous outcrossing autotetraploid populations.

Background Exploring the natural occurring genetic variation of the wild barley genepool has become a major target of barley crop breeding programmes aiming to increase crop productivity and sustainability in global climate change scenarios. However this diversity remains unexploited and effective approaches are required to investigate the benefits that unadapted genomes could bring to crop improved resilience. In the present study, a set of Recombinant Chromosome Substitution Lines (RCSLs) derived from an elite barley cultivar ‘Harrington’ as the recurrent parent, and a wild barley accession from the Fertile Crescent ‘Caesarea 26–24’, as the donor parent (Matus et al. Genome 46:1010–23, 2003) have been utilised in field and controlled conditions to examine the contribution of wild barley genome as a source of novel allelic variation for the cultivated barley genepool. Methods Twenty-eight RCSLs which were selected to represent the entire genome of the wild barley accession, were genotyped using the 9 K iSelect SNP markers (Comadran et al. Nat Genet 44:1388–92, 2012) and phenotyped for a range of morphological, developmental and agronomic traits in 2 years using a rain-out shelter with four replicates and three water treatments. Data were analysed for marker traits associations using a mixed model approach. Results We identified lines that differ significantly from the elite parent for both qualitative and quantitative traits across growing seasons and water regimes. The detailed genotypic characterisation of the lines for over 1800 polymorphic SNP markers and the design of a mixed model analysis identified chromosomal regions associated with yield related traits where the wild barley allele had a positive response increasing grain weight and size. In addition, variation for qualitative characters, such as the presence of cuticle waxes on the developing spikes, was associated with the wild barley introgressions. Despite the coarse location of the QTLs, interesting candidate genes for the major marker-trait associations were identified using the recently released barley genome assembly. Conclusion This study has highlighted the role of exotic germplasm to contribute novel allelic variation by using an optimised experimental approach focused on an exotic genetic library. The results obtained constitute a step forward to the development of more tolerant and resilient varieties. Electronic supplementary material The online version of this article (10.1186/s12870-018-1527-7) contains supplementary material, which is available to authorized users.

The paper proposes and validates a robust method for rapid construction of high-density linkage maps suitable for autotetraploid species. Modern genotyping techniques are producing increasingly high numbers of genetic markers that can be scored in experimental populations of plants and animals. Ordering these markers to form a reliable linkage map is computationally challenging. There is a wide literature on this topic, but most has focussed on populations derived from diploid, homozygous parents. The challenge of ordering markers in an autotetraploid population has received little attention, and there is currently no method that runs sufficiently rapidly to investigate the effects of omitting problematic markers on map order in larger datasets. Here, we have explored the use of multidimensional scaling (MDS) to order markers from a cross between autotetraploid parents, using simulated data with 74–152 markers on a linkage group and also experimental data from a potato population. We compared different functions of the recombination fraction and LOD score to form the MDS stress function and found that an LOD2 weighting generally performed well, including when missing values and genotyping errors are present. We conclude that an initial analysis using unconstrained MDS gives a rapid method to detect and remove problematic markers, and that a subsequent analysis using either constrained MDS or principal curve analysis gives reliable marker orders. The latter approach is also particularly rapid, taking less than 10 s on a set of 258 markers compared to 6 days for the JoinMap software. This MDS approach could also be applied to experimental populations of diploid species.

Cultivars and some cultivar mixtures of spring barley were grown under inversion and non-inversion tillage conditions for three or four years and assessed for disease and yield in order to obtain genotypes that can be used to determine the mechanisms of cultivation adaptation. In general, the higher-yielding cultivars under inversion tillage conditions gave lower yields under non-inversion tillage, whereas low-yielding older cultivars showed relatively smaller reductions in yield under non-inversion tillage. A few cultivars showed preferential yield performance for either inversion or non-inversion tillage and this was irrespective of their overall yield performance. There was no pedigree or breeding programme link between these cultivars and no above-ground gross morphological trait observed was associated with tillage adaptation. Root hairs may contribute to inversion tillage adaptation as a root hair absence mutant was associated with non-inversion adaptation and it is likely that other root-associated traits are responsible also for tillage adaptation. There was no overall cultivar or tillage interaction with rhynchosporium symptoms but a differential tillage interaction may occur in individual years. We have identified clearly contrasting cultivars and tested their across-season robustness with respect to tillage treatment for further detailed mechanistic studies and identification of tillage adaptation traits.

An earlier software application of ours, TetraploidMap for Windows, enabled linkage analysis and quantitative trait locus interval mapping to be carried out in an experimental cross of an autotetraploid species, using both dominant markers such as amplified fragment length polymorphisms and codominant markers such as simple sequence repeats. The size was limited to 800 markers, and quantitative trait locus mapping was conducted for each parent separately due to the difficulties in obtaining a reliable consensus map for the 2 parents. Modern genotyping technologies now give rise to datasets of thousands of single nucleotide polymorphisms, and these can be scored in autotetraploid species as single nucleotide polymorphism dosages, distinguishing among the heterozygotes AAAB, AABB, and ABBB, rather than simply using the presence or absence of an allele. The dosage data is more informative about recombination and leads to higher density linkage maps. The current program, TetraploidSNPMap, makes full use of the dosage data, and has new facilities for displaying the clustering of single nucleotide polymorphisms, rapid ordering of large numbers of single nucleotide polymorphisms using a multidimensional scaling analysis, and phase calling. It also has new routines for quantitative trait locus mapping based on a hidden Markov model, which use the dosage data to model the effects of alleles from both parents simultaneously. A Windows-based interface facilitates data entry and exploration. It is distributed with a detailed user guide. TetraploidSNPMap is freely available from our GitHub repository.

peer-reviewed Background Recent advances in the mapping of biochemical traits have been reported in Lolium perenne. Although the mapped traits, including individual sugars and fatty acids, contribute greatly towards ruminant productivity, organic acids and amino acids have been largely understudied despite their influence on the ruminal microbiome. Results In this study, we used a targeted gas-chromatography mass spectrometry (GC-MS) approach to profile the levels of 25 polar metabolites from different classes (sugars, amino acids, phenolic acids, organic acids and other nitrogen-containing compounds) present in a L. perenne F2 population consisting of 325 individuals. A quantitative trait (QTL) mapping approach was applied and successfully identified QTLs regulating seven of those polar metabolites (L-serine, L-leucine, glucose, fructose, myo-inositol, citric acid and 2, 3-hydroxypropanoic acid).Two QTL mapping approaches were carried out using SNP markers on about half of the population only and an imputation approach using SNP and DArT markers on the entire population. The imputation approach confirmed the four QTLs found in the SNP-only analysis and identified a further seven QTLs. Conclusions These results highlight the potential of utilising molecular assisted breeding in perennial ryegrass to modulate a range of biochemical quality traits with downstream effects in livestock productivity and ruminal digestion. This study was financed through a Research Stimulus Fund Grant by the Irish Department of Agriculture, Fisheries and Marine (RSF 06–346). AF, CH and DS acknowledge support from The Scottish Government’s Rural and Environment Science and Analytical Services Division.

In recent years advances in quantitative trait loci (QTL) mapping of complex metabolomics traits have been made in plants. This study is a two-phase experiment in which we have profiled transesterified non-polar metabolites in a Lolium perenne population consisting of parents, F1 and 325 F2 genotypes. These were grown in a replicated field trial, then analysed in batches by a targeted approach using gas-chromatography mass spectrometry (GC–MS), which identified 17 metabolites. The metabolite data was analysed using a mixed model that included random effects of field replicate, laboratory batch and technical replication to derive genotype means for QTL mapping. Using a linkage map of 326 markers, mainly Diversity Array Technology markers, QTLs were detected for seven of the metabolites. The most heritable metabolite was octacosanol, where a single QTL on linkage group four explained 42 % of the trait variance.

Key message Dense linkage maps derived by analysing SNP dosage in autotetraploids provide detailed information about the location of, and genetic model at, quantitative trait loci. Abstract Recent developments in sequencing and genotyping technologies enable researchers to generate high-density single nucleotide polymorphism (SNP) genotype data for mapping studies. For polyploid species, the SNP genotypes are informative about allele dosage, and Hackett et al. (PLoS ONE 8:e63939, 2013) presented theory about how dosage information can be used in linkage map construction and quantitative trait locus (QTL) mapping for an F1 population in an autotetraploid species. Here, QTL mapping using dosage information is explored for simulated phenotypic traits of moderate heritability and possibly non-additive effects. Different mapping strategies are compared, looking at additive and more complicated models, and model fitting as a single step or by iteratively re-weighted modelling. We recommend fitting an additive model without iterative re-weighting, and then exploring non-additive models for the genotype means estimated at the most likely position. We apply this strategy to re-analyse traits of high heritability from a potato population of 190 F1 individuals: flower colour, maturity, height and resistance to late blight (Phytophthora infestans (Mont.) de Bary) and potato cyst nematode (Globodera pallida), using a map of 3839 SNPs. The approximate confidence intervals for QTL locations have been improved by the detailed linkage map, and more information about the genetic model at each QTL has been revealed. For several of the reported QTLs, candidate SNPs can be identified, and used to propose candidate trait genes. We conclude that the high marker density is informative about the genetic model at loci of large effects, but that larger populations are needed to detect smaller QTLs. Electronic supplementary material The online version of this article (doi:10.1007/s00122-014-2347-2) contains supplementary material, which is available to authorized users.

Part of the reason for the under-exploitation of physical resistance traits in plant breeding is that the genetic basis and heritability of these traits is poorly characterised, and any associations of particular traits with pest and disease resistances have yet to be determined. In raspberry, some associations between architectural traits and disease resistances have been demonstrated, for example cane hairs and resistance to cane diseases. The aim of this work is to examine a range of traits, including leaf trichomes, leaf density, cane density, bush density, lateral length and lateral numbers, to determine the heritability and therefore breeding potential of these traits. The effect of these traits against aphids and spider mites, two important pests in raspberry, was examined. Chromosomal regions with candidate genes regulating these traits were identified as the first step to understanding the genetic control.

A genotyping by sequencing (GbS) approach is reported in blackcurrant (Ribes nigrum L.) using a de novo read assembly method developed because of the current absence of a reference genome sequence for this species. A new approach to single nucleotide polymorphism (SNP) genotype calling is described, where individual genotypes for a large number of SNPs were characterised from the GbS counts using a novel method based on a functional regression of major and minor allele read counts. The high-quality GbS SNPs were combined with SNPs and simple sequence repeats generated from other technologies to develop a linkage map with increased marker density and improved genome coverage, containing up to 204 SNPs on each linkage group. SNPs of lower quality were then located on the map using quantitative trait locus (QTL) interval mapping of the proportion of the major allele. Two QTL each for 100-berry weight and Brix scores, measured over three years, were identified using the map. The use of this approach to identify and map a significant number of novel SNPs in a woody species with hitherto limited genomic resources may have generic application to other under-resourced and minor species in the development of cost-effective and efficient high-density genetic maps.

Potato (Solanum tuberosum L.) cv. Sante was grown over 2 years under both conventional and organic fertiliser and crop protection regimes. The tuber metabolome was analysed using mass-spectrometry (MS) based approaches, principally liquid chromatography (LC)–MS and gas chromatography (GC)–MS. Data were analysed using Principal Components Analysis (PCA) and Analysis of Variance (ANOVA) to assess any differences between production practices. GC–MS analysis of non-polar metabolites did not detect any statistically significant differences, but GC–MS analysis of polar compounds identified 83 metabolites showing significant differences in the metabolome between the fertiliser treatments. Of the 62 metabolites that were less abundant in tuber samples from organic compared with conventionally fertilised crops, consistent year on year differences were dominated by free amino acids. The effect on free amino acids is associated with the lower nitrogen (N) content of the organically grown potatoes in this instance (50 % lower than for conventional production). LC–MS provided indications that levels of certain glycoalkaloids may be lower under the organic fertiliser regime in one growing season. Differences associated with the crop protection measures used were much less consistent, and relatively small, compared with the fertiliser effects found.

QTL mapping identifies a range of underlying and unrelated genes with apparent roles in raspberry fruit ripening and softening that show characteristic developing fruit expression profiles. Fruit softening is an important agronomical trait that involves a complex interaction of plant cell processes. We have used both qualitative and quantitative scoring of fruit firmness, length, mass, and resistance to applied force to identify QTL in a raspberry mapping population. QTLs were located primarily on linkage group (LG) 3 with other significant loci on LG 1 and LG 5 and showed mostly additive effects between the two parents. The expression of key genes that underlie these QTLs with roles in cell-wall solubility, water uptake, polyamine synthesis, transcription, and cell respiration was tested across five stages of fruit development, from immature green to red ripe fruit, using real-time RT-qPCR. Gene expression patterns showed variable expression patterns across fruit development with a highly significant positive and negative correlation between genes, supporting precise regulation of expression of different cell processes throughout raspberry fruit development. Variable timing in expression was also found in some genes at different fruit development stages between soft and firm cultivars. Multiple processes have a role to play in fruit softening and this will require development of multiple marker combinations to genes that characterise raspberry fruit softening.

The construction of the first genetic map in autotetraploid blueberry has been made possible by the development of new SNP markers developed using genotyping by sequencing in a mapping population created from a cross between two key highbush blueberry cultivars, Draper × Jewel (Vaccinium corymbosum). The novel SNP markers were supplemented with existing SSR markers to enable the alignment of parental maps. In total, 1794 single nucleotide polymorphic (SNP) markers and 233 simple sequence repeat (SSR) markers exhibited segregation patterns consistent with a random chromosomal segregation model for meiosis in an autotetraploid. Of these, 700 SNPs and 85 SSRs were utilized for construction of the ‘Draper’ genetic map, and 450 SNPs and 86 SSRs for the ‘Jewel’ map. The ‘Draper’ map comprises 12 linkage groups (LG), associated with the haploid chromosome number for blueberry, and totals 1621 cM while the ‘Jewel’ map comprises 20 linkage groups totalling 1610 cM. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents.

Cane splitting, a normal feature of raspberry growth, can lead to plant infestation by cane midge followed by fungal infection, with losses in yield of up to 50 % if left untreated. The extent of splitting in the Latham × Glen Moy reference mapping population was assessed over six years and in three environments and quantitative trait loci (QTL) were identified across linkage groups (LG) 2, 3, 5 and 6. Cane splitting QTL on LG 3 and 5 co-locate with QTL for plant vigour. The cane splitting QTL on LG 6 is associated with the QTL for resistance to root rot caused by Phytophthora rubi. Broad-sense heritability for cane splitting ranged from 25.6 % in 2007 to 49.1 % in 2008 in this population. Season and environment were also found to influence cane splitting in this population. Several genes involved in general plant growth and in defence responses lie within these QTL. This is a first step towards identifying the genetic basis of cane splitting in raspberry and the development of genetic markers for use in raspberry breeding programmes.

Nitrogen is a macronutrient present in a wide range of cellular compounds including proteins, nucleic acids, amino acids and lipids. The levels of nitrogen often regulate many aspects of plant metabolism, growth and development. Extensive research has been conducted into the effects of N nutrition in model plants, however relatively little is known about the metabolic response of perennial ryegrass (Lolium perenne) grown under different N-supply conditions. This study aimed to identify key metabolic responses activated rapidly after challenging plants with different levels of N-supply. The metabolic response of the leaves of seven different L. perenne genotypes to three N treatments (low, medium and high levels of N) was characterized using a GC–MS approach. After 24 h it was observed that the levels of amino acids correlated with the levels of N-supply. Furthermore the results indicated that plants experiencing N-limitation accumulated very-long chain fatty acids and precursors of secondary aromatic metabolites while sugar levels were not significantly affected indicating a remobilization of carbon. Plants grown under high levels of N were found to have enhanced levels of inositol and threonic acid which could reflect an alteration of the redox potential under stress. Further analysis of Pearson’s correlation coefficient provided evidence that the chlorophyll metabolism may also be regulated in plants grown at high N concentrations.

Fruit consumption in the UK, particularly of berry fruits, is expanding rapidly and consumer demand for blueberries (Vaccinium spp.) is at record levels with UK growers unable to meet current demand. Consumers are aware that eating fruit can be pleasurable and with appropriate packaging, convenient, but blueberry remains unfamiliar to a wide cross section of UK consumers. There is great potential for UK growers to supply high quality fresh blueberries across a wide season so that consumption of this healthy fruit can be integrated into the British diet. A genetic framework for future crop improvement is required to develop a thriving and sustainable industry. The genetic component of this project builds on the statistical developments derived from the software program, TetraploidMap, to identify fruit quality, health, and agronomic-related quantitative trait loci in tetraploid blueberry for marker assisted breeding.

This study examined the total phenol content (TPC) and total anthocyanin content (TAC) in ripe fruit of progeny of a mapping population generated from a cross between the European red raspberry cv. Glen Moy ( Rubus ideaus var. idaeus) and the North American red raspberry cv. Latham ( Rubus ideaus var. strigosus) over five seasons in two different growing environments. Measurements of antioxidant capacity (FRAP and TEAC) were also carried out. TPC was highly correlated with TEAC and FRAP across the entire data set. The subset of anthocyanin content was genotype-dependent but also correlated with TPC, although the proportion of anthocyanin compounds varied between progeny. Quantitative trait locus (QTL) analysis was carried out, and key markers were tested for consistency of effects over sites and years. Four regions, on linkage groups 2, 3, 5, and 6, were identified. These agree with QTLs from a previous study over a single season and indicate that QTL effects were robust over seasons.

The analysis of association mapping populations is frequently complicated by substructure within the population. If this is unaccounted for, it generally results in many false positive marker-trait associations. In this study, we simulate a large barley population, modelling inbreeding and selection, and compare five models for analysing marker-trait associations. One of these includes no population substructure, one includes information about geographical origin and type of barley to represent structure within the population and three use different approaches that have been proposed for estimating marker-based kinship. Kinship methods reduced the number of false positives substantially compared to the other models but none of these approaches had a clear advantage over the others. One solution is to fit more than one model and to consider as candidate associations those markers that are significant by all models. None of the approaches were very successful at detecting true associations at the lowest level of heritability considered (25%), suggesting it is important to consider power in association mapping studies to avoid missing some true associations and overestimating others.

The first genetic linkage map of blackcurrant, published by Brennan et al. (Euphytica 161:19-34, 2008), identified regions where quantitative trait loci (QTLs) for some important traits were located. The analysis was complicated by the fact that the mapping population was found to contain two subgroups, with segregation ratios consistent with these being crossed and selfed offspring. The QTL analysis was based on the trait mean over 3 years and focused on the crossed offspring. Here we proposed a mixed model multi-environment approach for this population. The 3 years are considered as three separate environments, the data from both the selfed and crossed offspring are combined and different residual terms are explored to model the correlation between the years. This permits tests for interactions between the QTLs, the year and the type of offspring (selfed or crossed). This is applied to re-analyse two important traits, anthocyanin concentration and budbreak. Several additional QTLs were identified, some affecting the trait in both the selfed and crossed offspring, others in just one.

Consumption of raspberries promotes human health through intake of pharmaceutically active antioxidants, including cyanidin and pelargonidin anthocyanins; products of flavonoid metabolism and also pigments conferring colour to fruit. Raspberry anthocyanin contents could be enhanced for nutritional health and quality benefits utilising DNA polymorphisms in modern marker assisted breeding. The objective was to elucidate factors determining anthocyanin production in these fruits. HPLC quantified eight anthocyanin cyanidin and pelargonidin glycosides: -3-sophoroside, -3-glucoside, -3-rutinoside and -3-glucosylrutinoside across two seasons and two environments in progeny from a cross between two Rubus subspecies, Rubus idaeus (cv. Glen Moy)xRubus strigosus (cv. Latham). Significant seasonal variation was detected across pigments less for different growing environments within seasons. Eight antioxidants mapped to the same chromosome region on linkage group (LG) 1, across both years and from fruits grown in field and under protected cultivation. Seven antioxidants also mapped to a region on LG 4 across years and for both growing sites. A chalcone synthase (PKS 1) gene sequence mapped to LG 7 but did not underlie the anthocyanin quantitative traits loci (QTL) identified. Other candidate genes including basic-helix-loop-helix (bHLH), NAM/CUC2-like protein and bZIP transcription factor underlying the mapped anthocyanins were identified.

BACKGROUND: Mixtures of cereal cultivars grown together generally enhance yield and reduce disease but end-users will not accept them for quality uses. Some combinations with very different quality may be problematic, others complementary. The common origin of Maris Otter for quality in winter barley may enable the benefits of complex mixtures to be exploited without quality compromises. RESULTS: Seven winter barley cultivar monocultures and all their equal proportion mixtures were trialled and data analysed by ANOVA, REML and principal component analyses to determine the contribution of particular varieties or combinations to crop performance. Agronomic yield was positively correlated with component number. Pipkin contributed negatively to thousand grain weight (TGW), but positively to several quality traits; Gleam negatively to the same quality traits but strongly positively to yield; and Melanie combined strong yield and TGW characteristics with neutral quality traits. Interactions in mixtures with Maris Otter, from which most of the cultivars are likely to derive some of their quality traits, were less apparent for quality than for yield. CONCLUSIONS: Complex mixtures gave yield benefits generally without compromising quality, and analysis methods were developed to identify the beneficial or negative effects of component cultivars on malting quality traits, thereby providing data for optimising mixtures design. Copyright © 2008 Society of Chemical Industry

A glasshouse experiment was set up to compare processes and organisms in two soils planted with genetically modified (GM) herbicide tolerant (HT) maize treated with appropriate herbicides. This was part of a wider project (ECOGEN) looking at the consequences of GM cropping systems on soil biology using a tiered approach at laboratory, glasshouse and field scales. Soil for the experiment was taken from field sites where the same maize cultivars were grown to allow comparison between results under glasshouse and field conditions. The maize cultivars T25 (GM HT glufosinate-ammonium tolerant), Orient (non HT near isogenic control for T25) and Monumental (a conventional, non HT variety) were grown in contrasting sandy loam and clay loam soils, half were sprayed with the appropriate herbicide as used in the field and soil samples were taken at the five-leaf and flowering plant growth stage. The main effects on all measured parameters were those of soil type and plant growth stage, with four categories of subsequent interaction: (1) there were no effects of herbicide on plant growth or soil microarthropods: (2) the maize cultivar (but not the GM HT trait) had effects on the decomposition of cotton strips and the nematode community; (3) herbicide application in general altered the community level physiological profile of the microbial community and reduced both soil basal respiration and the abundance of protozoa; and (4) the specific application of glufosinate-ammonium to T25 maize altered soil microbial community structure measured by ester linked fatty acids. The results from this glasshouse experiment support the findings from the field that there are effects of herbicide application on the soil microbial and meso-faunal community but that, compared to other standard agricultural practices, the differences are relatively small.

Identifying barley genomic regions influencing the response of yield and its components to water deficits will aid in our understanding of the genetics of drought tolerance and the development of more drought tolerant cultivars. We assembled a population of 192 genotypes that represented landraces, old, and contemporary cultivars sampling key regions around the Mediterranean basin and the rest of Europe. The population was genotyped with a stratified set of 50 genomic and EST derived molecular markers, 49 of which were Simple Sequence Repeats (SSRs), which revealed an underlying population sub-structure that corresponded closely to the geographic regions in which the genotypes were grown. A more dense whole genome scan was generated by using Diversity Array Technology (DArT®) to generate 1130 biallelic markers for the population. The population was grown at two contrasting sites in each of seven Mediterranean countries for harvest 2004 and 2005 and grain yield data collected. Mean yield levels ranged from 0.3 to 6.2 t/ha, with highly significant genetic variation in low-yielding environments. Associations of yield with barley genomic regions were then detected by combining the DArT marker data with the yield data in mixed model analyses for the individual trials, followed by multiple regression of yield on markers to identify a multi-locus subset of significant markers/QTLs. QTLs exhibiting a pre-defined consistency across environments were detected in bins 4, 6, 6 and 7 on barley chromosomes 3H, 4H, 5H and 7H respectively.

The first genetic linkage map of blackcurrant (Ribes nigrum L.) was constructed using AFLP, SSR (genomic and EST-derived) and SNP markers, in a mapping population derived from two diverse breeding clones of blackcurrant from the SCRI breeding programme. Cluster analysis of the population revealed that the individuals within the population formed two distinct sub-populations, with segregation ratios consistent with one sub-population having the two intended parents, and the other being selfed segregants. The latter sub-population improves the map by providing a more informative estimate of recombination frequency than the crossed sub-population for some marker configurations, and also revealed the presence of two unlinked loci affecting viability. Several important phenological, agronomic and fruit quality traits were evaluated in the mapping population, and QTLs affecting these are located on the linkage map. This provides a framework for the development of marker-assisted breeding strategies for blackcurrant, to improve breeding efficiency and time to cultivar.

Background Single Nucleotide Polymorphisms (SNPs) are widely used molecular markers, and their use has increased massively since the inception of Next Generation Sequencing (NGS) technologies, which allow detection of large numbers of SNPs at low cost. However, both NGS data and their analysis are error-prone, which can lead to the generation of false positive (FP) SNPs. We explored the relationship between FP SNPs and seven factors involved in mapping-based variant calling — quality of the reference sequence, read length, choice of mapper and variant caller, mapping stringency and filtering of SNPs by read mapping quality and read depth. This resulted in 576 possible factor level combinations. We used error- and variant-free simulated reads to ensure that every SNP found was indeed a false positive. Results The variation in the number of FP SNPs generated ranged from 0 to 36,621 for the 120 million base pairs (Mbp) genome. All of the experimental factors tested had statistically significant effects on the number of FP SNPs generated and there was a considerable amount of interaction between the different factors. Using a fragmented reference sequence led to a dramatic increase in the number of FP SNPs generated, as did relaxed read mapping and a lack of SNP filtering. The choice of reference assembler, mapper and variant caller also significantly affected the outcome. The effect of read length was more complex and suggests a possible interaction between mapping specificity and the potential for contributing more false positives as read length increases. Conclusions The choice of tools and parameters involved in variant calling can have a dramatic effect on the number of FP SNPs produced, with particularly poor combinations of software and/or parameter settings yielding tens of thousands in this experiment. Between-factor interactions make simple recommendations difficult for a SNP discovery pipeline but the quality of the reference sequence is clearly of paramount importance. Our findings are also a stark reminder that it can be unwise to use the relaxed mismatch settings provided as defaults by some read mappers when reads are being mapped to a relatively unfinished reference sequence from e.g. a non-model organism in its early stages of genomic exploration. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0801-z) contains supplementary material, which is available to authorized users.

The objective of this study was to construct a single nucleotide polymorphism (SNP)-based genetic map at the cultivated tetraploid level to locate quantitative trait loci (QTL) contributing to economically important traits in potato (Solanum tuberosum L.). The 156 F1 progeny and parents of a cross (MSL603) between “Jacqueline Lee” and “MSG227-2” were genotyped using the Infinium 8303 Potato Array. Furthermore, the progeny and parents were evaluated for foliar late blight reaction to isolates of the US-8 genotype of Phytophthora infestans (Mont.) de Bary and vine maturity. Linkage analyses and QTL mapping were performed using a novel approach that incorporates allele dosage information. The resulting genetic maps contained 1972 SNP markers with an average density of 1.36 marker per cM. QTL mapping identified the major source of late blight resistance in “Jacqueline Lee.” The best SNP marker mapped ∼0.54 Mb from a resistance hotspot on the long arm of chromosome 9. For vine maturity, the major-effect QTL was located on chromosome 5 with allelic effects from both parents. A candidate SNP marker for this trait mapped ∼0.25 Mb from the StCDF1 gene, which is a candidate gene for the maturity trait. The identification of markers for P. infestans resistance will enable the introgression of multiple sources of resistance through marker-assisted selection. Moreover, the discovery of a QTL for late blight resistance not linked to the QTL for vine maturity provides the opportunity to use marker-assisted selection for resistance independent of the selection for vine maturity classifications.

Metabolite profiling (liquid chromatography–mass spectrometry (LC–MS) and gas chromatography (GC–MS)) was used to assess the impact of light on the composition of transgenic potato (Solanum tuberosum L. cv. Desiree) with reduced glycoalkaloid content via the down-regulation of the SGT1 gene. Transgenic tubers exhibited an almost complete knock-out of α-solanine production and light had little impact on its accumulation. Levels of α-chaconine increased significantly in the peel of both the control and transgenic lines when exposed to light, particularly in the transgenic line. Major differences in metabolite profiles existed between outer and inner tuber tissues, and between light and dark-treated tubers. Many of the light-induced changes are explicable in terms of pathways known to be affected by stress responses. The impact of transgenesis on profiles was much less than that of tissue type or light and most differences were explicable in terms of the modification to the glycoalkaloid pathway.

Metabolite profiling has been used to assess the potential for unintended composition changes in potato (Solanum tuberosum L. cv. Desiree) tubers, which have been genetically modified (GM) to reduce glycoalkaloid content, via the independent down-regulation of three genes SGT1, SGT2 and SGT3 known to be involved in glycoalkaloid biosynthesis. Differences between the three groups of antisense lines and control lines were assessed using liquid chromatography-mass spectrometry (LC-MS) and gas chromatography (GC)-MS, and data analysed using principal component analysis and analysis of variance. Compared with the wild-type (WT) control, LC-MS revealed not only the expected changes in specific glycoalkaloid levels in the GM lines, but also significant changes in several other metabolites, some of which were explicable in terms of known pathways. Analysis of polar and non-polar metabolites by GC-MS revealed other significant (unintended) differences between SGT lines and the WT, but also between the WT control and other control lines used.