Genetic variation, population structure, and linkage disequilibrium in European elite germplasm of perennial ryegrass

Perennial ryegrass (Lolium perenne L.) is a highly valued temperate climate grass species grown as forage crop and for amenity uses. Due to its outbreeding nature and recent domestication, a high degree of genetic diversity is expected among cultivars. The aim of this study was to assess the extent of linkage disequilibrium (LD) within European elite germplasm and to evaluate the appropriate methodology for genetic association mapping in perennial ryegrass. A high level of genetic diversity was observed in a set of 380 perennial ryegrass elite genotypes when genotyped with 40 SSRs and 2 STS markers. A Bayesian structure analysis identified two subpopulations, which were confirmed by principal coordinate analysis (PCoA). One subpopulation consisted mainly of genotypes originating from the UK, while germplasm mostly from Continental Europe was grouped into the second subpopulation. LD (r²) decay was rapid and occurred within 0.4 cM across European varieties, when population structure was taken into consideration. However, an extended LD of up to 6.6 cM was detected within the variety Aberdart. High genetic diversity and rapid LD decay provide means for high resolution association mapping in elite materials of perennial ryegrass. However, different strategies need to be applied depending on the material used. Genome-wide association study (GWAS) with several hundred markers can be applied within synthetic varieties to identify large (up to 10 cM) genomic regions affecting trait variation. A combination of available and novel DNA markers is needed to achieve resolution required for GWAS in elite breeding materials. An even higher marker density of several million SNPs might be needed for GWAS in diverse ecotype collections, potentially resulting in quantitative trait polymorphism (QTP) identification.     

Assessment of genetic diversity in cultivars of white clover (Trifolium repens L.) detected by SSR polymorphisms.

White clover (Trifolium repens L.) is an important temperate pasture legume that plays a key role as a companion to grass species, such as perennial ryegrass (Lolium perenne L.). Due to the outbreeding nature of white clover, cultivars are highly heterogeneous. Genetic diversity was assessed using 16 elite cultivars from Europe, North and South America, Australia, and New Zealand. Fifteen simple sequence repeat markers that detect single, codominant polymorphic genetic loci were selected for the study. The genetic relationships among individuals were compared using phenetic clustering, and those among cultivars were compared using nonmetric multidimensional scaling. Intrapopula tion variability exceeded interpopulation variability, with substantial overlap among populations and weak interpopula tion differentiation. No obvious or significant differentiation was observed on the basis of morphology or geographic origin of the cultivars. The number of parental genotypes used to derive each cultivar was not a major determinant of genome-wide genetic diversity. The outcomes of this assessment of genetic variation in elite white clover germplasm pools have important implications for the feasibility of molecular marker-based cultivar discrimination, and will be used to assist the design of linkage disequilibrium mapping strategies for marker-trait association.     

Tolerance to ryegrass mosaic virus and its inheritance

Plant yield within and between four cultivars of perennial ryegrass infected with ryegrass mosaic virus (RMV) was closely related to symptom severity. Distribution of symptom severity was continuous in four perennial ryegrass and four Italian ryegrass cultivars infected with a severe RMV isolate, and also in another perennial ryegrass cultivar infected with a severe isolate of the virus, a mild one and one of intermediate severity. Symptom expression was polygenically inherited in both Italian (cv. RvP) and perennial (cv. S.24) ryegrass. Both additive and non-additive genetic variation was present in RvP, but the variation in S.24 was additive only. No significant maternal inheritance was present in either species.     

A DNA marker assay based on high-resolution melting curve analysis for distinguishing species of the Festuca–Lolium complex

The grass breeding industry is interested in a fast and cheap method of identifying contamination in seeds of Italian and perennial ryegrass (Lolium perenne L. and L. multiflorum Lam., respectively). This study shows that high-resolution melting curve analysis in combination with an unlabelled probe assay is an effective method of detecting single nucleotide polymorphisms (SNPs) in diverse Italian and perennial ryegrass backgrounds. This method proved efficient in differentiating ryegrass species and reducing the effect of additional DNA sequence polymorphisms close to the target SNP on the melting curve profiles. For the identification of contamination in Italian and perennial ryegrass seed production, high-resolution melting curve analysis shows great potential, as it is a single closed-tube PCR reaction with an easy workflow, providing results in <2 h after DNA extraction.     

Resistance to rust fungi in Lolium perenne depends on within-species variation and performance of the host species in grasslands of different plant diversity

The hypothesis that plant species diversity and genetic variation of the host species decrease the severity of plant diseases is supported by studies of agricultural systems, but experimental evidence from more complex systems is scarce. In an experiment with grassland communities of varying species richness (1, 2, 4, 8, 16, and 60 species) and functional group richness (1, 2, 3, and 4 functional groups), we used different cultivars of Lolium perenne (perennial ryegrass) to study effects of biodiversity and cultivar identity on the occurrence and severity of foliar fungal diseases caused by Puccinia coronata (crown rust) and P. graminis (stem rust). Cultivar monocultures of perennial ryegrass revealed strong differences in pathogen susceptibility among these cultivars. Disease intensity caused by both rust fungi decreased significantly with growing species richness of species mixtures. The response to the diversity gradient was related to the decreased density and size of the host individuals with increasing species richness. The occurrence of other grass species known to be possible hosts of the pathogens in the experimental mixtures did not promote disease intensity in L. perenne, indicating that there was a high host specificity of pathogen strains. Differences in pathogen susceptibility among perennial ryegrass cultivars persisted independent of diversity treatment, host density and host individual size, but resulted in a cultivar-specific pattern of changes in pathogen infestation across the species-richness gradient. Our study provided evidence that within-species variation in pathogen susceptibility and competitive interactions of the host species with the environment, as caused by species diversity treatments, are key determinants of the occurrence and severity of fungal diseases. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Water Use Characteristics of Dactylis glomerata L., Lolium perenne L. and L. multiflorum Lam. Plants

Cocksfoot (Dactylis glomerata L.). perennial ryegrass (Loliumperenne L.) and Italian ryegrass (L. multiflorum Lam.) plantswere grown on deep (75–95 cm) columns of soil in glasshousesand growth rooms with and without irrigation. The species inwhich growth declined least rapidly after water had been withheldwere those which transpired most slowly. During early establishmentin the glasshouse cocksfoot transpired least because of slowroot growth. In the growth room, when root systems were deeperand denser, perennial ryegrass transpired least because of lowleaf water conductance. Results are discussed in relation to(a) drought resistance in the three species; (b) breeding forincreased drought resistance through modifying root distributionand leaf water conductance; and (c) the use of isolated soilcolumns in water relations studies. Dactylis glomerata L., Lolium perenne L., Lolium multiflorum Lam., cocksfoot, perennial ryegrass, Italian ryegrass, transpiration, roots, leaf water conductance     

Development of EST-derived CAPS and AFLP markers linked to a gene for resistance to ryegrass blast (Pyricularia sp.) in Italian ryegrass (Lolium multiflorum Lam.)

Ryegrass blast, also called gray leaf spot, is caused by the fungus Pyricularia sp. It is one of the most serious diseases of Italian ryegrass (Lolium multiflorum Lam.) in Japan. We analyzed segregation of resistance in an F₁ population from a cross between a resistant and a susceptible cultivar. The disease severity distribution in the F₁ population suggested that resistance was controlled by a major gene (LmPi1). Analysis of amplified fragment length polymorphisms with bulked segregant analysis identified several markers tightly linked to LmPi1. To identify other markers linked to LmPi1, we used expressed sequence tag-cleaved amplified polymorphic sequence (EST-CAPS) markers mapped in a reference population of Italian ryegrass. Of the 30 EST-CAPS markers screened, one marker, p56, flanking the LmPi1 locus was found. The restriction pattern of p56 amplification showed a unique fragment corresponding to the resistant allele at the LmPi1 locus. A linkage map constructed from the reference population showed that the LmPi1 locus was located in linkage group 5 of Italian ryegrass. Genotype results obtained from resistant and susceptible cultivars indicate that the p56 marker is useful for introduction of the LmPi1 gene into susceptible germplasm in order to develop ryegrass cultivars with enhanced resistance to ryegrass blast.     

A Comparison of AFLP and RAPD Markers for Genetic Diversity and Cultivar Identification in Cotton

AFLP and RAPDmarkers were employed in sixteen diploid cotton (Gossypium sp) cultivars for genetic diversity estimation and cultivar identification. Polymorphism information content (PIC) and percent polymorphism were found to be more for AFLP markers as compared to RAPD markers. Average Jaccard’s genetic similarity index was found to be almost similar using either AFLP or RAPD markers. All the cultivars could be distinguished from one another using AFLP markers and also by the combined RAPD profiles. Cultivar identification indicators like resolving power, marker index and probability of chance identity of two cultivars suggested the usefulness of AFLP markers over the RAPD markers. AFLP and RAPD analyses revealed limited genetic diversity in the studied cultivars. Cluster analysis of both RAPD and AFLP data produced two clusters, one containing cultivars of G. herbaceum and another containing cultivars of G. arboreum species. Highly positive correlation between cophenetic matrices using RAPD and AFLP markers was observed. AFLP markers were found to be more efficient for genetic diversity estimation, polymorphism detection and cultivar identification.     

Prospects for Hybrid Breeding in Bioenergy Grasses

Biofuels obtained from biomass have the potential to replace a substantial fraction of petroleum-based hydrocarbons that contribute to carbon emissions and are limited in supply. With the ultimate goal to maximize biomass yield for biofuel production, this review aims to evaluate prospects of different hybrid breeding schemes to optimally exploit heterosis for biomass yield in perennial ryegrass (Lolium perenne L.) and switchgrass (Panicum virgatum), two perennial model grass species for bioenergy production. Starting with a careful evaluation of current population and synthetic breeding methods, we address crucial topics to implement hybrid breeding, such as the availability and development of heterotic groups, as well as biological mechanisms for hybridization control such as self-incompatibility (SI) and male sterility (MS). Finally, we present potential hybrid breeding schemes based on SI and MS for the two bioenergy grass species, and discuss how molecular tools and synteny can be used to transfer relevant information for genes controlling these biological mechanisms across grass species.     

Construction of a high-density linkage map of Italian ryegrass (Lolium multiflorum Lam) using restriction fragment length polymorphism, amplified fragment length polymorphism, and telomeric repeat associated sequence markers.

To construct a high-density molecular linkage map of Italian ryegrass (Lolium multiflorum Lam), we used a two-way pseudo-testcross F1 population consisting of 82 individuals to analyze three types of markers: restriction fragment length polymorphism markers, which we detected by using genomic probes from Italian ryegrass as well as heterologous anchor probes from other species belonging to the Poaceae family, amplified fragment length polymorphism markers, which we detected by using PstI/MseI primer combinations, and telomeric repeat associated sequence markers. Of the restriction fragment length polymorphism probes that we generated from a PstI genomic library, 74% (239 of 323) of randomly selected probes detected hybridization patterns consistent with single-copy or low-copy genetic locus status in the screening. The 385 (mostly restriction fragment length polymorphism) markers that we selected from the 1226 original markers were grouped into seven linkage groups. The maps cover 1244.4 cM, with an average of 3.7 cM between markers. This information will prove useful for gene targeting, quantitative trait loci mapping, and marker-assisted selection in Italian ryegrass.     

An enhanced molecular marker based genetic map of perennial ryegrass (Lolium perenne) reveals comparative relationships with other Poaceae genomes.

A molecular-marker linkage map has been constructed for perennial ryegrass (Lolium perenne L.) using a one-way pseudo-testcross population based on the mating of a multiple heterozygous individual with a doubled haploid genotype. RFLP, AFLP, isoenzyme, and EST data from four collaborating laboratories within the International Lolium Genome Initiative were combined to produce an integrated genetic map containing 240 loci covering 811 cM on seven linkage groups. The map contained 124 codominant markers, of which 109 were heterologous anchor RFLP probes from wheat, barley, oat, and rice, allowing comparative relationships between perennial ryegrass and other Poaceae species to be inferred. The genetic maps of perennial ryegrass and the Triticeae cereals are highly conserved in terms of synteny and colinearity. This observation was supported by the general agreement of the syntenic relationships between perennial ryegrass, oat, and rice and those between the Triticeae and these species. A lower level of synteny and colinearity was observed between perennial ryegrass and oat compared with the Triticeae, despite the closer taxonomic affinity between these species. It is proposed that the linkage groups of perennial ryegrass be numbered in accordance with these syntenic relationships, to correspond to the homoeologous groups of the Triticeae cereals.     

Novel perennial ryegrass-Neotyphodium endophyte associations: relationships between seed weight,seedling vigour and endophyte presence

Two forage cultivars of perennial ryegrass (Lolium perenne) colonised by the mutualistic fungal endophyte Neotyphodium lolii, strain AR37, were used to investigate relationships between seed weight, seed vigour and endophyte presence. Seed was separated into six fractions according to weight, with each fraction divided into two further groups with the first being subject to accelerated ageing. Seed germination rates and proportions of viable and total endophyte frequencies were assessed for each fraction. Heavier fractions of seed produced a higher number of endophyte infected seedlings sooner than the lighter fractions for both cultivars. The highest proportion of viable endophyte was found in the fastest germinating perennial ryegrass seed for all weight fractions, from both cultivars, indicating a strong relationship between endophyte presence and seed germination rate. For one of the cultivars, after accelerated ageing, as seed weight increased the proportion of viable endophyte increased and the discrepancy between the proportion of endophyte in fresh and accelerated aged seed was reduced. This implies that for this cultivar heavier ryegrass seed provides a more favourable habitat to the dormant endophyte than lighter seed during storage and/or allowed for a greater biomass of endophyte hyphae to proliferate in the seed tissues prior to seed dormancy, thus allowing the fungus to develop more propagules and greater nutritional reserves.     

Hybrids between tetraploid Italian and perennial ryegrass

Summary Hybridization frequency was investigated between tetraploid perennial and Italian ryegrass (Lolium perenne X multiflorum) without emasculation by using genetic markers. The Italian phenotypes, fluorescentroots and awned florets, were dominant. About 82% of the plants in perennial X Italian and nearly 93 % of the plants in the reciprocal crosses were hybrids. The hybrids had a high multivalent frequency and involved homoeologous chromosome pairing. Aneuploids with 2n = 26, 27 and 29 chromosomes were present. The hybrids were highly fertile. The cytogenetic behaviour of these allopolyploids suggested that the genomes of the parental species have undergone little repatterning and have free genetic exchanges. The species maintained their self-incompatibility and cross-compatibility at the tetraploid level.     

Development of simple sequence repeat (SSR) markers and construction of an SSR-based linkage map in Italian ryegrass (Lolium multiflorum Lam.)

In order to develop simple sequence repeat (SSR) markers in Italian ryegrass, we constructed a genomic library enriched for (CA)n-containing SSR repeats. A total of 1,544 clones were sequenced, of which 1,044 (67.6%) contained SSR motifs, and 395 unique clones were chosen for primer design. Three hundred and fifty-seven of these clones amplified products of the expected size in both parents of a two-way pseudo-testcross F₁ mapping population, and 260 primer pairs detected genetic polymorphism in the F₁ population. Genetic loci detected by a total of 218 primer pairs were assigned to locations on seven linkage groups, representing the seven chromosomes of the haploid Italian ryegrass karyotype. The SSR markers covered 887.8 cM of the female map and 795.8 cM of the male map. The average distance between two flanking SSR markers was 3.2 cM. The SSR markers developed in this study will be useful in cultivar discrimination, linkage analysis, and marker-assisted selection of Italian ryegrass and closely related species.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

The effect of frit fly Oscinella frit on the yield and persistence of Italian and hybrid ryegrasses in the laboratory

Three cultivars of Italian or hybrid ryegrass were exposed to frit fly attack at varying frequency in the laboratory. Initially a Westerwolds and a hybrid cultivar showed greater yield reductions than an Italian ryegrass cultivar, although they did not usually suffer a higher proportion of damaged tillers. The differing effect on yield appeared to be due mainly to greater impact of first or infrequent attacks on cultivars producing fewer tillers. After two to six attacks in approximately 7 months the Westerwolds and hybrid cultivars appeared to become tolerant to attack and were subsequently the least affected, although continuing to suffer tiller damage at a rate at least as high as the Italian ryegrass. All cultivars recovered fully when attack ceased, and their exclusion from attack did not improve their persistence.     

Genetic variation and cultivar identification in Cymbidium ensifolium

As a popular flowering species with many cultivars, Cymbidium ensifolium (L.) is commercially important in horticulture. However, so far little has been known about genetic diversity and conservation genetics of this species. Understanding of the genetic variation and relationships in cultivars of C.?ensifolium is a prerequisite for development of future germplasm conservation and cultivar improvement. Here we report assessment of genetic variations in C.?ensifolium cultivars using the DNA fingerprinting technique of inter-simple sequence repeats (ISSR). A total of 239 ISSR loci were identified and used for evaluation of genetic variation with a selection of 19 ISSR primers. Among these ISSR loci, 99.16% were polymorphic with wide genetic variation as shown by Nei??s gene diversity (H?=?0.2431) among 85 tested cultivars. ISSR fingerprinting profiles showed that each cultivar had its characteristic DNA pattern, indicating unequivocal cultivar identification at molecular level. Eighteen cultivar-specific ISSR markers were identified in seven cultivars. The cultivar Sijiwenhan was confirmed as hybrid by four ISSR primers. Several cultivars with same name but different geographical origins were distinguished based on their ISSR profiles. A dendrogram generated with ISSR markers could group 73 of 85 cultivars into four major clusters. Further analysis of ISSR variation revealed that about 69% of total genetic variation in this species is due to genetic divergence inside geographical groups. Our results suggest that both germplasm collection and in?situ conservation are important for future planning of C.?ensifolium species conservation.     

Instability during storage of phosphogluco-isomerase isoenzymes from ryegrasses (Lolium spp.)

The stability during storage of phosphogluco-isomerase (D-glucose-6-phosphate ketol isomerase EC 5.3.1.9) isoenzymes coded for at the PGI/2 locus has been examined. Extracts were prepared from leaves of several diploid and tetraploid Italian ( Lolium multiflorum Lam.) and perennial ( Lolium perenne . L.) ryegrass cultivars, as well as from interspecific hybrids. It was clearly demonstrated that extracts from plants homozygous for a specific PGI/2 allele could quickly generate new band forms upon storage. The novel forms were not due to aggregation or disintegration of the original enzyme molecule, and some of the generated bands electrophoresed to gel positions characteristic of other alleles of the same locus. An assessment was also made of the effects of a range of compounds added to the storage buffer. The most likely explanation was that the observed changes were due to the action of proteases, and the implications, especially for those using isoenzymes as genetic markers, are discussed.     

Infection Biology of Bacterial Wilt of Forage Grasses

Infection of perennial ryegrass (Lolium perenne L.), Italian ryegrass (Loliummultiflorum L.), and timothy (Phleum pratense L.) by Xanthomonas campestris pv. graminis and Xanthomonas campestris pv. phlei occurred mainly via wounds rather than natural openings. Nevertheless, bacteria were detected by isolation and immunofluorescence in plants sprayed with the pathogen without prior wounding and in plants in which intact ears had been dipped in inocula. High concentrations of bacteria were observed around the stomata of perennial ryegrass and timothy by scanning electron microscopy 48 h after inoculation. Perennial ryegrass and Italian ryegrass and individual plants of ryegrass and timothy differedin susceptibility to the pathogens.     

The effect of 2,4-dichlorophenoxyacetic acid and donor plant environment on plant regeneration from immature inflorescence-derived callus of Lolium perenne L. and Lolium multiflorum L.

Callus cultures were obtained from immature inflorescences of perennial ryegrass (Lolium perenne) and Italian ryegrass (Lolium multiflorum). Inflorescence segments were cultured on Murashige and Skoog medium (MS) supplemented with 2,4-dichlorophenoxyacetic acid (2,4-D). The response in culture with regard to compact callus induction, embryogenesis and plant regeneration was determined for different varieties. The in vitro response was compared for explants from field-grown plants and explants from greenhouse-grown plants. The effect of different 2,4-D concentrations on the in vitro response was also investigated in one L. perenne variety and one L. multiflorum variety. The percentage of explants that formed compact callus and embryogenic callus differed strongly with the cultivar. There was no consistent effect of the growth conditions of the donor plants or the 2,4-D concentration of the medium on this response. Green plants were regenerated from all the cultivars tested. Explants from field-grown plants showed a higher tendency to form albino shoots than explants from greenhouse-grown plants. In the L. perenne variety tested higher 2,4-D concentrations (up to 15 mg/l) resulted in a lower regeneration frequency of green shoots and a higher regeneration frequency of albino shoots (up to 12.5 mg/l). In the L. multiflorum variety tested the effect of 2,4-D on regeneration was less pronounced.     

Serological detection of ryegrass mosaic virus and ryegrass seed-borne virus

Ryegrass mosaic virus (RMV) was reliably detected in both perennial (S24) and Italian (S22) ryegrass, by enzyme-linked immunosorbent assay (ELISA) when plants had been infected for 8 wk. ELISA detected more infections in field-grown perennial ryegrass cv. Premo than either visual assessment or electron microscopy. However, with plants of Italian ryegrass cultivars only recently infected with RMV, positive reactions were more difficult to separate from the reactions of RMV-free plants, which varied considerably with cultivar, some giving high absorbance values. Immunosorbent electron microscopy showed that the RMV antiserum also contained antibodies to ryegrass seed-borne virus (RGSV), suggesting that these high values were caused by RGSV infection in the material tested.