An In Silico DNA Sequence Comparison of the Perennial Ryegrass and Rice Genomes

Comparative mapping studies in the family Poaceae, which includes rice (a model species for this family) and perennial ryegrass (PRG) have indicated macro-colinearity of genes is generally conserved across different genomes. Genome mapping of simple sequence repeat markers derived from expressed sequence tags (EST-SSRs) for PRG (Faville et al., 2004) provides a vehicle for DNA sequence-based matching of mapped PRG genes to orthologous positions in the rice genome, which can be used to establish comparative relationships between these species’ genomes. We have initiated such an analysis using an EST-SSR-based PRG genome map. Our objective was to assess this in silico approach as a tool for candidate gene identification from rice, and for targeting markers to specified PRG genome map regions based on rice genome position

A Quantitative Trait Locus Analysis of Root Distribution in Perennial Ryegrass (\u3cem\u3eLolium Perenne\u3c/em\u3e L.)

Root system architecture impacts perennial ryegrass performance, with deeper roots potentially contributing to drought tolerance, nutrient interception, and anchoring of plants. Root mass in a perennial ryegrass sward is typically shallow, concentrated in the top 10 cm of soil (Troughton 1957). Phenotypic selection for deeper root systems in breeding programmes is limited by the inaccessibility of underground plant components. We aim to use quantitative trait locus (QTL) analysis to discover genetic factors influencing root architecture traits, including vertical root distribution, in perennial ryegrass. Ultimately, markers linked to root architecture QTL may be used in a marker-assisted selection strategy that would alleviate the limitations of conventional selection, and lead to ryegrass cultivars with improved production and environmental performance

Quantitative Trait Loci for Vegetative Traits in Perennial Ryegrass (\u3cem\u3eLolium Perenne\u3c/em\u3e L.)

Physiological (EP) research in forage grasses relates traits such as leaf elongation rate (LER), leaf elongation duration (LED), and leaf appearance interval (ALf), to forage yield (Chapman & Lemaire, 1993). This paper reveals preliminary quantitative trait locus (QTL) discovery for eight EP traits in perennial ryegrass. It also investigates the potential role of multivariate analyses such as principal component analysis (PCA) in QTL analysis of EP data

Controlled Flowering Project for Lolium Perenne at Agresearch: an Overview

Ryegrass (Lolium perenne) is an important forage crop in New Zealand. The work presented here has the goal of developing a system for complete and arbitrary control of the transition from vegetative to floral development. For this, we have pursued an integrated approach utilising genomics with both forward and reverse genetics. Like other model plants, photoperiodic and vernalization pathways are presumed to be operating in ryegrass and control the activity of the meristem identity/floral patterning genes. The candidate gene approach targeting the photoperiodic pathway is described in an accompanying abstract (Gagic et al.). Other candidate genes include the meristem identity gene LEAFY and a range of the MADS box transcription factors. Relevant expression profiles are established for these genes, i.e. vernalization time course at weekly intervals, and daily and circadian collections during the secondary induction. A detailed genetic map of ryegrass has been developed at AgResearch (see abstract by Faville et al.) which we are using to map candidate genes. We are also conducting detailed phenotypic analysis of the flowering behaviour variation within this population in an effort to isolate relevant QTLs. Ryegrass transformation has been used to ascertain functions of the candidate genes and to manipulate flowering time control directly. We are developing a universal switch to turn on the flowering that consists of a cassette of the arabidopsis genes under a control of a chemically inducible promoter

Dissecting Drought-Response Strategies of Perennial Ryegrass (\u3cem\u3eLolium perenne\u3c/em\u3e L.)

Periodic drought is a severe constraint on the profitability and sustainability of pastoral production. As a result of climate change, drought events are anticipated to increase in frequency and intensity even in regions where annual precipitation is unchanged, as well as where it is reduced. Many studies have been carried out on drought resistance of forage species (Holloway-Phillips and Brodribb 2011). However, for most experiments, it is unclear which mechanism(s) are responsible for variation in plant performance under moisture stress, whether drought response mechanisms were triggered, or whether differences in performance were simply the result of intrinsic plant vigour. The objective of the reported research was to understand the underlying physiological and genetic mechanisms responsible for production of perennial ryegrass under summer drought and recovery and regrowth after drought

A QTL analysis of host plant effects on fungal endophyte biomass and alkaloid expression in perennial ryegrass.

The association between perennial ryegrass (Loliumperenne L.) and its Epichloë fungal endophyte symbiont, Epichloëfestucae var. lolii, supports the persistence of ryegrass-based pastures principally by producing bioactive alkaloid compounds that deter invertebrate herbivory. The host plant genotype affects endophyte trait expression, and elucidation of the underlying genetic mechanisms would enhance understanding of the symbiosis and support improvement of inplanta endophyte performance through plant breeding. Rapid metabolite profiling and enzyme-linked immunosorbent assay were used to quantify endophyte alkaloids and mycelial mass (MM) in leaves harvested, in consecutive autumns, from an F1 mapping population hosting standard toxic endophyte. Co-aligned quantitative trait loci (QTL) on linkage groups (LG)2, LG4 and LG7 for MM and concentrations of alkaloids peramine and ergovaline confirmed host plant effects on both MM and alkaloid level and inferred the effect on alkaloids was modulated through the quantity of endophyte present in the leaf tissue. For ergovaline, host regulation independent of endophyte concentration was also indicated, by the presence of MM-independent ergovaline QTL on LG4 and LG7. Partitioning of host genetic influence between MM-dependent and MM-independent mechanisms was also observed for the alkaloid N-formylloline (NFL), in a second mapping population harbouring a tall fescue-sourced endophyte. Single-marker analysis on repeated MM and NFL measures identified marker-trait associations at nine genome locations, four affecting both NFL and MM but five influencing NFL concentration alone. Co-occurrence of QTL on LG3, LG4 and LG7 in both mapping populations is evidence for host regulatory loci effective across genetic backgrounds and independent of endophyte variant. Variation at these loci may be exploited using marker-assisted breeding to improve endophyte trait expression in different host population × endophyte combinations

Seed Transmission of Epichloë Endophytes in Lolium perenne Is Heavily Influenced by Host Genetics

Vertical transmission of symbiotic Epichloë endophytes from host grasses into progeny seed is the primary mechanism by which the next generation of plants is colonized. This process is often imperfect, resulting in endophyte-free seedlings which may have poor ecological fitness if the endophyte confers protective benefits to its host. In this study, we investigated the influence of host genetics and environment on the vertical transmission of Epichloë festucae var. lolii strain AR37 in the temperate forage grass Lolium perenne. The efficiency of AR37 transmission into the seed of over 500 plant genotypes from five genetically diverse breeding populations was determined. In Populations I–III, which had undergone previous selection for high seed infection by AR37, mean transmission was 88, 93, and 92%, respectively. However, in Populations IV and V, which had not undergone previous selection, mean transmission was 69 and 70%, respectively. The transmission values, together with single-nucleotide polymorphism data obtained using genotyping-by-sequencing for each host, was used to develop a genomic prediction model for AR37 seed transmission. The predictive ability of the model was estimated at r = 0.54. While host genotype contributed greatly to differences in AR37 seed transmission, undefined environmental variables also contributed significantly to seed transmission across different years and geographic locations. There was evidence for a small host genotype-by-environment effect; however this was less pronounced than genotype or environment alone. Analysis of endophyte infection levels in parent plants within Populations I and IV revealed a loss of endophyte infection over time in Population IV only. This population also had lower average tiller infection frequencies than Population I, suggesting that AR37 failed to colonize all the daughter tillers and therefore seeds. However, we also observed that infection of seed by AR37 may fail during or after initiation of floral development from plants where all tillers remained endophyte-infected over time. While the effects of environment and host genotype on fungal endophyte transmission have been evaluated previously, this is the first study that quantifies the relative impacts of host genetics and environment on endophyte vertical transmission

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Genomic Predictive Ability for Foliar Nutritive Traits in Perennial Ryegrass

Forage nutritive value impacts animal nutrition, which underpins livestock productivity, reproduction and health. Genetic improvement for nutritive traits in perennial ryegrass has been limited, as they are typically expensive and time-consuming to measure through conventional methods. Genomic selection is appropriate for such complex and expensive traits, enabling cost-effective prediction of breeding values using genome-wide markers. The aims of the present study were to assess the potential of genomic selection for a range of nutritive traits in a multi-population training set, and to quantify contributions of family, location and family-by-location variance components to trait variation and heritability for nutritive traits. The training set consisted of a total of 517 half-sibling (half-sib) families, from five advanced breeding populations, evaluated in two distinct New Zealand grazing environments. Autumn-harvested samples were analyzed for 18 nutritive traits and maternal parents of the half-sib families were genotyped using genotyping-by-sequencing. Significant (P < 0.05) family variance was detected for all nutritive traits and genomic heritability (h2g) was moderate to high (0.20 to 0.74). Family-by-location interactions were significant and particularly large for water soluble carbohydrate (WSC), crude fat, phosphorus (P) and crude protein. GBLUP, KGD-GBLUP and BayesCπ genomic prediction models displayed similar predictive ability, estimated by 10-fold cross validation, for all nutritive traits with values ranging from r = 0.16 to 0.45 using phenotypes from across two locations. High predictive ability was observed for the mineral traits sulfur (0.44), sodium (0.45) and magnesium (0.45) and the lowest values were observed for P (0.16), digestibility (0.22) and high molecular weight WSC (0.23). Predictive ability estimates for most nutritive traits were retained when marker number was reduced from one million to as few as 50,000. The moderate to high predictive abilities observed suggests implementation of genomic selection is feasible for most of the nutritive traits examined

Low pyrrolizidine alkaloid levels in perennial ryegrass is associated with the absence of a homospermidine synthase gene

Abstract Background Pyrrolizidine alkaloids (PAs) are a class of secondary metabolites that function as feeding deterrents in a range of different plant species. In perennial ryegrass (Lolium perenne L.) the only PAs that have been identified are the thesinine-rhamnoside group, which displays significant genetic variation. Homospermidine synthase (HSS) has evolved from deoxyhypusine synthase (DHS) and catalyses the first step in the PA pathway, making it a key candidate for the investigation of genes influencing observed PA trait variation. Results During PCR amplification and sequence analysis of DHS we identified two putative HSS genes in perennial ryegrass. One of the genes (LpHSS1) was absent in some perennial ryegrass plants. Thesinine-rhamnoside levels were measured using liquid chromatography coupled with mass spectrometry in a diverse association mapping population, consisting of 693 plants free of fungal endophytic symbionts. Association tests that accounted for population structure identified a significant association of absence of the LpHSS1 gene with lower levels of thesinine-rhamnoside PAs. HSS-like gene sequences were identified for other grass species of the Poaceae, including tall fescue, wheat, maize and sorghum. Conclusion HSS is situated at the crucial first step in the PA pathway making it an important candidate gene for investigation of involvement in PA phenotypic variation. In this study, PA level in perennial ryegrass was strongly associated with the presence or absence of the LpHSS1 gene. A genetic marker, developed for the presence/absence of LpHSS1, may be used for marker-assisted breeding to either lower or increase PAs in breeding populations of perennial or Italian ryegrass to investigate a potential role in the deterrence of herbivore pests. The presence of HSS-like genes in several other Poaceae species suggests that PA biosynthesis may occur in plant family members beyond perennial ryegrass and tall fescue and identifies a potential route for manipulating PA levels