Ruth Sanderson

The link between Multiplicative Scatter Correction (MSC) and Standard Normal Variate (SNV) transformations of NIR spectra

We demonstrate that set-dependent multiplicative scatter correction and set-independent standard normal variate transformations of NIR spectra are linearly related as theoretically expected. It is shown that the mean and standard deviation of the set-mean-spectrum together with the correlation coefficient between each individual spectrum and set-mean-spectrum are required to link these two transformations. It is through these three quantities, that set-dependency is incorporated into spectra derived by application of multiplicative scatter correction. MSC and SNV are two alternative approaches to reduce particle size effects and they are interconvertible.

An association mapping approach to identify flowering time genes in natural populations of Lolium perenne (L.)

We describe an association mapping approach using natural populations of perennial ryegrass (Lolium perenne L.) to identify molecular markers associated with heading date, an important trait affecting seasonal production, tillering, digestibility and grassland management regimes. Twenty-three natural populations originating from throughout Europe, with heading date phenotypes ranging from very early to very late, as well as three synthetic populations (varieties) were used for molecular marker genotyping using AFLP. In total, 589 polymorphic markers were identified. Hierarchical clustering, principal coordinate and other statistical analyses identified four outlying populations forming a clearly distinct sub-group. Removal of those four populations from the subsequent analysis reduced population sub-structure twofold. However, this made relatively little difference to the result of the association analysis. Linear regression identified three markers whose frequency of occurrence correlated with the heading date phenotype. Moreover, these markers were shown to be closely linked to each other within a major QTL on Chromosome 7, explaining 70% of the total variation in heading date. Pairwise linkage disequilibrium among them was also significant. These results suggest that association mapping approaches may be feasible in L. perenne, and that the use of natural populations could provide a useful source of genetic variation in traits of importance in crop improvement.

Association of Candidate Genes With Flowering Time and Water-Soluble Carbohydrate Content in Lolium perenne (L.)

We describe a candidate gene approach for associating SNPs with variation in flowering time and water-soluble carbohydrate (WSC) content and other quality traits in the temperate forage grass species Lolium perenne. Three analysis methods were used, which took the significant population structure into account. First, a linear mixed model was used enabling a structured association analysis to be incorporated with the nine populations identified in the structure analysis as random variables. Second, a within-population analysis of variance was performed. Third, a tree-scanning method was used, in which haplotype trees were associated with phenotypes on the basis of inferred haplotypes. Analysis of variance within populations identified several associations between WSC, nitrogen (N), and dry matter digestibility with allelic variants within an alkaline invertase candidate gene LpcAI. These associations were only detected in material harvested in one of the two years. By contrast, consistent associations between the L. perenne homolog (LpHD1) of the rice photoperiod control gene HD1 and flowering time were identified. One SNP, in the immediate upstream region of the LpHD1 coding sequence (C-4443-A), was significant in the linear mixed model. Within-population analysis of variance and tree-scanning analysis confirmed and extended this result to the 2118 polymorphisms in some of the populations. The merits of the tree-scanning method are compared to the single SNP analysis. The potential usefulness of the 4443 SNP in marker-assisted selection is currently being evaluated in test crosses of genotypes from this work with turf-grass varieties.

Nitric oxide contributes both to papilla-based resistance and the hypersensitive response in barley attacked by Blumeria graminis f. sp.hordei

SUMMARY Nonspecific penetration resistance due to papilla formation and race-specific hypersensitive response (HR) can both contribute to Blumeria graminis resistance in barley. Some effective papillae form even in the susceptible cv. Pallas and the isoline P01 carries the additional Mla1 allele conditioning HR. The NO-specific stain DAF-2DA (4,5-diaminofluorescein-2-diacetate) revealed a transient NO generation burst commencing 10 h after inoculation (h.a.i.) in close association with sites of papilla formation in both barley lines. In P01 a burst of NO production throughout some attacked cells was initiated around 10-12 h.a.i. and this preceded whole-cell autofluorescence indicative of HR. The specificity of DAF-2DA staining was demonstrated by the suppression of staining following application of the NO scavenger C-PTIO (1H-imidazol-1-yloxy-2-(4-carboxyphenyl)-4,5-dihydro-4,4,5,5-tetramethyl-3-oxide). In addition, C-PTIO application increased penetration frequencies in both barley lines, indicating a role for NO in papilla-based resistance. Furthermore, C-PTIO application slightly delayed HR in P01 whereas, conversely, application of an NO donor, sodium nitroprusside, slightly accelerated HR in P01 and increased cell death frequency in Pallas. Thus, NO generation is one of the earliest responses of barley epidermal cell defence against B. graminis attack and may be important in both the initiation and the development of effective papillae and cell death due to HR.

Allelic Variation in the Perennial Ryegrass FLOWERING LOCUS T Gene Is Associated with Changes in Flowering Time across a Range of Populations

The Arabidopsis (Arabidopsis thaliana) FLOWERING LOCUS T (FT) gene and its orthologs in other plant species (e.g. rice [Oryza sativa] OsFTL2/Hd3a) have an established role in the photoperiodic induction of flowering response. The genomic and phenotypic variations associated with the perennial ryegrass (Lolium perenne) ortholog of FT, designated LpFT3, was assessed in a diverse collection of nine European germplasm populations, which together constituted an association panel of 864 plants. Sequencing and genotyping of a series of amplicons derived from the nine populations, containing the complete exon and intron sequences as well as 5′ and 3′ noncoding sequences of LpFT3, identified a total of seven haplotypes. Genotyping assays designed to detect the genomic variation showed that three haplotypes were present in approximately equal proportions and represented 84% of the total, with a fourth representing a further 11%. Of the three major haplotypes, two were predicted to code for identical protein products and the third contained two amino acid substitutions. Association analysis using either a mixed model with a relationship matrix to correct for population structure and relatedness or structured association with further correction using genomic control indicated significant associations between LpFT3 and variation in flowering time. These associations were corroborated in a validation population segregating for the same major alleles. The most “diagnostic” region of genomic variation was situated 5′ of the coding sequence. Analysis of this region identified that the interhaplotype variation was closely associated with sequence motifs that were apparently conserved in the 5′ region of orthologs of LpFT3 from other plant species. These may represent cis-regulatory elements involved in influencing the expression of this gene.

Genotyping by RAD sequencing enables mapping of fatty acid composition traits in perennial ryegrass (Lolium perenne (L.))

Perennial ryegrass (Lolium perenne L.) is the most important forage crop in temperate livestock agriculture. Its nutritional quality has significant impact on the quality of meat and milk for human consumption. Evidence suggests that higher energy content in forage can assist in reducing greenhouse gas emissions from ruminants. Increasing the fatty acid content (especially α-linolenic acid, an omega-3 fatty acid) may thus contribute to better forage, but little is known about the genetic basis of variation for this trait. To this end, quantitative trait loci (QTLs) were identified associated with major fatty acid content in perennial ryegrass using a population derived from a cross between the heterozygous and outbreeding high-sugar grass variety AberMagic and an older variety, Aurora. A genetic map with 434 restriction-associated DNA (RAD) and SSR markers was generated. Significant QTLs for the content of palmitic (C16:0) on linkage groups (LGs) 2 and 7; stearic (C18:0) on LGs 3, 4 and 7; linoleic (C18:2n-6) on LGs 2 and 5; and α-linolenic acids (C18:3n-3) on LG 1 were identified. Two candidate genes (a lipase and a beta-ketoacyl CoA synthase), both associated with C16:0, and separately with C18:2n-6 and C18:0 contents, were identified. The physical positions of these genes in rice and their genetic positions in perennial ryegrass were consistent with established syntenic relationships between these two species. Validation of these associations is required, but the utility of RAD markers for rapid generation of genetic maps and QTL analysis has been demonstrated for fatty acid composition in a global forage crop.

Use of near infrared reflectance spectroscopy to predict and compare the composition of carcass samples from young steers

The aim of the current study was to investigate the effects of level of feeding and level offish-meal supplementation on the carcass composition of young steers and in doing so, to assess the potential for employing near infrared reflectance spectroscopy (NIRS) in such studies. In addition to wet chemical techniques, NIRS was used to examine carcass samples from animals offered silage-based diets at one of four levels of feeding ranging from near maintenance to ad libitum and with one of four levels offish meal (0, 50,100 or 150 g/kg silage dry matter). Wet chemical data indicated an increase in fat concentration (P < 0·001) and decrease in crude protein concentration (P < 0·05) in the fresh carcass in response to increasing level of feeding but no statistically significant effect of level of fish meal. Ash concentration was not affected significantly by either level of feeding or level of fish-meal supplementation. Ground, freeze-dried samples were scanned in the wavelength range 1100 to 2498 nm. Calibration equations for ash, fat and crude protein concentration (g/kg carcass) were derived using a modified partial least-squares regression technique. Equations were found to be superior for fat compared with those for crude protein and ash. Standard errors of calibration (g/kg carcass) and multiple correlation coefficients of 6·96 and 0·42, 6·61 and 0·95 and 4·36 and 0·61 were obtained for ash, fat and crude protein respectively with corresponding standard errors of cross validation of 7·71, 7·82 and 4·96 g/kg carcass respectively. Qualitative analysis of spectral information using multivariate techniques and difference spectra clearly showed differences in carcass composition resulting from the different levels of feeding and less so the different levels offish-meal supplementation. It is shown, that NIRS can be used both quantitatively and qualitatively to study the effects of nutrition on carcass composition.

Effects of Chicory/Perennial Ryegrass Swards Compared with Perennial Ryegrass Swards on the Performance and Carcass Quality of Grazing Beef Steers

An experiment investigated whether the inclusion of chicory (Cichorium intybus) in swards grazed by beef steers altered their performance, carcass characteristics or parasitism when compared to steers grazing perennial ryegrass (Lolium perenne). Triplicate 2-ha plots were established with a chicory/ryegrass mix or ryegrass control. Forty-eight Belgian Blue-cross steers were used in the first grazing season and a core group (n = 36) were retained for finishing in the second grazing season. The experiment comprised of a standardisation and measurement period. During standardisation, steers grazed a ryegrass/white clover pasture as one group. Animals were allocated to treatment on the basis of liveweight, body condition and faecal egg counts (FEC) determined 7 days prior to the measurement period. The measurement period ran from 25 May until 28 September 2010 and 12 April until 11 October 2011in the first and second grazing year. Steers were weighed every 14 days at pasture or 28 days during housing. In the first grazing year, faecal samples were collected for FEC and parasite cultures. At the end of the first grazing year, individual blood samples were taken to determine O. ostertagi antibody and plasma pepsinogen levels. During winter, animals were housed as one group and fed silage. In the second grazing year, steers were slaughtered when deemed to reach fat class 3. Data on steer performance showed no differences in daily live-weight gain which averaged 1.04 kg/day. The conformation, fat grade and killing out proportion of beef steers grazing chicory/ryegrass or ryegrass were not found to differ. No differences in FEC, O. ostertagi antibody or plasma pepsinogen levels of beef steers grazing either chicory/ryegrass or ryegrass were observed. Overall, there were no detrimental effects of including chicory in swards grazed by beef cattle on their performance, carcass characteristics or helminth parasitism, when compared with steers grazing ryegrass.

Extending Miscanthus Cultivation with Novel Germplasm at Six Contrasting Sites

Miscanthus is a genus of perennial rhizomatous grasses with C4 photosynthesis which is indigenous in a wide geographic range of Asian climates. The sterile clone, Miscanthus × giganteus (M. × giganteus), is a naturally occurring interspecific hybrid that has been used commercially in Europe for biomass production for over a decade. Although, M. × giganteus has many outstanding performance characteristics including high yields and low nutrient offtakes, commercial expansion is limited by cloning rates, slow establishment to a mature yield, frost, and drought resistance. In this paper, we evaluate the performance of 13 novel germplasm types alongside M. × giganteus and horticultural “Goliath” in trials in six sites (in Germany, Russia, The Netherlands, Turkey, UK, and Ukraine). Mean annual yields across all the sites and genotypes increased from 2.3 ± 0.2 t dry matter ha−1 following the first year of growth, to 7.3 ± 0.3, 9.5 ± 0.3, and 10.5 ± 0.2 t dry matter ha−1 following the second, third, and fourth years, respectively. The highest average annual yields across locations and four growth seasons were observed for M. × giganteus (9.9 ± 0.7 t dry matter ha−1) and interspecies hybrid OPM-6 (9.4 ± 0.6 t dry matter ha−1). The best of the new hybrid genotypes yielded similarly to M. × giganteus at most of the locations. Significant effects of the year of growth, location, species, genotype, and interplay between these factors have been observed demonstrating strong genotype × environment interactions. The highest yields were recorded in Ukraine. Time needed for the crop establishment varied depending on climate: in colder climates such as Russia the crop has not achieved its peak yield by the fourth year, whereas in the hot climate of Turkey and under irrigation the yields were already high in the first growing season. We have identified several alternatives to M. × giganteus which have provided stable yields across wide climatic ranges, mostly interspecies hybrids, and also Miscanthus genotypes providing high biomass yields at specific geographic locations. Seed-propagated interspecific and intraspecific hybrids, with high stable yields and cheaper reliable scalable establishment remain a key strategic objective for breeders.

The impact of using alternative forages on the nutrient value within slurry and its implications for forage productivity in agricultural systems.

Alternative forages can be used to provide valuable home-grown feed for ruminant livestock. Utilising these different forages could affect the manure value and the implications of incorporating these forages into farming systems, needs to be better understood. An experiment tested the hypothesis that applying slurries from ruminants, fed ensiled red clover (Trifolium pratense), lucerne (Medicago sativa) or kale (Brassica oleracea) would improve the yield of hybrid ryegrass (Lolium hybridicum), compared with applying slurries from ruminants fed ensiled hybrid ryegrass, or applying inorganic N alone. Slurries from sheep offered one of four silages were applied to ryegrass plots (at 35 t ha−1) with 100 kg N ha−1 inorganic fertiliser; dry matter (DM) yield was compared to plots only receiving ammonium nitrate at rates of 0, 100 and 250 kg N ha−1 year−1. The DM yield of plots treated with 250 kg N, lucerne or red clover slurry was significantly higher than other treatments (P<0.001). The estimated relative fertiliser N equivalence (FNE) (fertiliser-N needed to produce same yield as slurry N), was greatest for lucerne (114 kg) >red clover (81 kg) >kale (44 kg) >ryegrass (26 kg ha−1 yr−1). These FNE values represent relative efficiencies of 22% (ryegrass), 52% (kale), 47% (red clover) and 60% for lucerne slurry, with the ryegrass slurry efficiency being lowest (P = 0.005). Soil magnesium levels in plots treated with legume slurry were higher than other treatments (P<0.001). Overall, slurries from ruminants fed alternative ensiled forages increased soil nutrient status, forage productivity and better N efficiency than slurries from ruminants fed ryegrass silage. The efficiency of fertiliser use is one of the major factors influencing the sustainability of farming systems, these findings highlight the cascade in benefits from feeding ruminants alternative forages, and the need to ensure their value is effectively captured to reduce environmental risks.