[Show abstract][Hide abstract] ABSTRACT: Red clover (Trifolium pratense L.) is a versatile forage crop legume, which can tolerate a variety of soils and is suitable for silage production for winter feed and for grazing. It is one of the most important forage legumes in temperate livestock agriculture. Its beneficial attributes include ability to fix nitrogen, improve soil and provide protein rich animal feed. It is however, a short-lived perennial providing good biomass yield for two or three years. Improved persistency is thus a major breeding target. Better water-stress tolerance is one of the key factors influencing persistency, but little is known about how red clover tolerates water stress.
[Show abstract][Hide abstract] ABSTRACT: BACKGROUND:Red clover (Trifolium pratense L.) is a versatile forage crop legume, which can tolerate a variety of soils and is suitable for silage production for winter feed and for grazing. It is one of the most important forage legumes in temperate livestock agriculture. Its beneficial attributes include ability to fix nitrogen, improve soil and provide protein rich animal feed. It is however, a short-lived perennial providing good biomass yield for two or three years. Improved persistency is thus a major breeding target. Better water-stress tolerance is one of the key factors influencing persistency, but little is known about how red clover tolerates water stress.RESULTS:Plants from a full sib mapping family were used in a drought experiment, in which the growth rate and relative water content (RWC) identified two pools of ten plants contrasting in their tolerance to drought. Key metabolites were measured and RNA-Seq analysis was carried out on four bulked samples: the two pools sampled before and after drought. Massively parallel sequencing was used to analyse the bulked RNA samples. A de novo transcriptome reconstruction based on the RNA-Seq data was made, resulting in 45181 contigs, representing 'transcript tags'. These transcript tags were annotated with gene ontology (GO) terms. One of the most striking results from the expression analysis was that the drought sensitive plants were characterised by having approximately twice the number of differentially expressed transcript tags than the tolerant plants after drought. This difference was evident in most of the major GO terms. Before onset of drought the sensitive plants overexpressed a number of genes annotated as senescence-related. Furthermore, the concentration of three metabolites, particularly pinitol, but also proline and malate increased in leaves after drought stress.CONCLUSIONS:This de novo assembly of a red clover transcriptome from leaf material of droughted and non-droughted plants provides a rich source for gene identification, single nucleotide polymorphisms (SNP) and short sequence repeats (SSR). Comparison of gene expression levels between pools and treatments identified candidate genes for further analysis of the genetic basis of drought tolerance in red clover.
[Show abstract][Hide abstract] ABSTRACT: BACKGROUND: White clover (Trifolium repens L.) is an allotetraploid species possessing two highly collinear ancestral sub-genomes. The apparent existence of highly similar homeolog copies for the majority of genes in white clover is problematic for the development of genome-based resources in the species. This is especially true for the development of genetic markers based on single nucleotide polymorphisms (SNPs), since it is difficult to distinguish between homeolog-specific and allelic variants. Robust methods for categorising single nucleotide variants as allelic or homeolog-specific in large transcript datasets are required. We illustrate one potential approach in this study. RESULTS: We used 454-pyrosequencing sequencing to generate ~760,000 transcript sequences from an 8th generation white clover inbred line. These were assembled and partially annotated to yield a reference transcript set comprising 71,545 sequences. We subsequently performed Illumina sequencing on three further white clover samples, generating 14 million transcript reads from a mixed sample comprising 24 divergent white clover genotypes, and 50 million reads on two further eighth generation white clover inbred lines. Mapping these reads to the reference transcript set allowed us to develop a significant SNP resource for white clover, and to partition the SNPs from the inbred lines into categories reflecting allelic or homeolog-specific variation. The potential for using haplotype reconstruction and progenitor genome comparison to assign haplotypes to specific ancestral sub-genomes of white clover is demonstrated for sequences corresponding to genes encoding dehydration responsive element binding protein and acyl-coA oxidase. CONCLUSIONS: In total, 208,854 independent SNPs in 31,715 reference sequences were discovered, approximately three quarters of which were categorised as representing allelic or homeolog-specific variation using two inbred lines. This represents a significant resource for white clover genomics and genetics studies. We discuss the potential to extend the analysis to identify a "core set" of ancestrally derived homeolog specific variants in white clover.
[Show abstract][Hide abstract] ABSTRACT: Clovers (Trifolium species) are a large and widespread genus of legumes. Recent work supports the Mediterranean origin of the genus in the Early Miocene period, and centres of diversity for clovers occur in the Eastern Mediterranean, East Africa and South America. A number of clovers are of agricultural importance as forage species in grassland agriculture around the world, particularly in temperate areas. White clover (Trifolium repens L.) is the most important legume of grazed pastures, and red clover (T. pratense) is widely cut and conserved as a winter feed. We consider the current state of collected resources in clovers, which have been collated in the most important databases. These are European Internet Search Catalogue (EURISCO), germplasm resources information network and system-wide information network for genetic resources together with the collection held at AgResearch, New Zealand. In total, collections have been made of 204 species with 48 species having more than 100 accessions in these databases. As expected, the majority of accessions are of the agriculturally important species. The geographical origin of collected material is outlined and, for the major species, accessions are broken down according to their status, e.g. wild population, breeders' lines. We then describe some of the ways in which genetic resources of white and red clovers and their relatives have been used in the breeding of these species. These include introgression of stress tolerance traits, targetting improvements in resource use efficiency and increasing seed yield.
[Show abstract][Hide abstract] ABSTRACT: Ruminant farming is an important component of the human food chain. Ruminants can use offtake from land unsuitable for cereal crop cultivation via interaction with the diverse microbial population in their rumens. The rumen is a continuous flow fermenter for the digestion of ligno-cellulose, with microbial protein and fermentation end-products incorporated by the animal directly or during post-ruminal digestion. However, ruminal fermentation is inefficient in capturing the nutrient resource presented, resulting in environmental pollution and generation of greenhouse gases. Methane is generated as a consequence of ruminal fermentation and poor retention of ingested forage nitrogen causes nitrogenous pollution of water and land and contributes to the generation of nitrous oxide. One possible cause is the imbalanced provision of dietary substrates to the rumen micro-organisms. Deamination of amino acids by ammonia-producing bacteria liberates ammonia which can be assimilated by the rumen bacteria and used for microbial protein synthesis. However, when carbohydrate is limiting, microbial growth is slow, meaning low demand for ammonia for microbial protein synthesis and excretion of the excess. Protein utilisation can therefore be improved by increasing the availability of readily fermentable sugars in forage or by making protein unavailable for proteolysis through complexing with plant secondary products. Alternatively, realisation that grazing cattle ingest living cells has led to the discovery that plant cells undergo endogenous, stress-mediated protein degradation due to the exposure to rumen conditions. This presents the opportunity to decrease the environmental impact of livestock farming by using decreased proteolysis as a selection tool for the development of improved pasture grass varieties.
Proceedings of The Nutrition Society 11/2010; 69(4):613-20. · 3.67 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In white clover (Trifolium repens L.) plant persistence, overwintering and grazing tolerance are to a significant extent determined by the presence of a dense
network of horizontal stems or stolons. At IGER, we have developed new linkage maps of white clover specifically to facilitate
the identification of quantitative trait loci (QTLs) for important components of stolon morphology. The parents of the F1 mapping family were derived following two generations of divergent selection for stolon traits, in particular length and
thickness. One parental genotype had thick, sparse stolons and one parent had thin profuse stolons. Two linkage maps were
generated for each parental clone: one consisted of 16 linkage groups with 154 markers covering 710 cM and the other consisted
13 linkage groups with 86 markers covering 524 cM. There are 31 shared markers across the two maps. A total of nine QTLs were
identified on the maps for the following traits: stolon width, internode length, petiole length, leaf length and width, plant
spread and height. Potential QTLs associated with water use efficiency (WUE) have also been identified.
[Show abstract][Hide abstract] ABSTRACT: White clover (Trifolium repens L.) is a forage legume of considerable economic importance in temperate agricultural systems. It has a strong self-incompatibility system. The molecular basis of self-incompatibility in T. repens is unknown, but it is under the control of a single locus, which is expressed gametophytically. To locate the self-incompatibility locus (S locus) in T. repens, we carried out cross-pollination experiments in an F(1) mapping population and constructed a genetic linkage map using amplified fragment length polymorphism and simple sequence repeat markers. As the first step in a map-based cloning strategy, we locate for the first time the S locus in T. repens on a genetic linkage map, on the homoeologous linkage group pair 1 (E), which is broadly syntenic to Medicago truncatula L. chromosome 1. On the basis of this syntenic relationship, the possibility that the S locus may or may not possess an S-RNase gene is discussed.
Theoretical and Applied Genetics 04/2010; 121(3):567-76. · 3.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: White clover (Trifolium repens L.) is the most widely grown temperate forage legume and the most common forage legume in pastures grazed by sheep or cattle.
A detailed overview of all aspects of white clover was given by Baker and Williams (1987). The agronomy of this species and
its performance in mixtures with grasses has been previously reviewed (Frame and Newbould 1986, Frame et al. 1998, Laidlaw
and Teuber 2001). Recent reviews outline the objectives of white clover breeding programmes in both the rain fed and irrigated
regions of Australia (Lane et al. 1997, Jahufer et al. 2002), in the USA (Taylor 2008) and in New Zealand (Williams et al.
2007). In the UK, breeding of white clover was discussed by Rhodes and Ortega (1996).
[Show abstract][Hide abstract] ABSTRACT: Island populations are often thought to be more susceptible to the loss of genetic diversity as a consequence of limited population
size and genetic drift, greater susceptibility to detrimental stochastic events and low levels of immigration. However the
geographic isolation of islands may create refuges for native crop species whose genetic diversity is threatened from the
genetic erosion occurring in mainland areas as a result of crop-wild gene flow and genetic swamping. Many UK islands remain
uncharacterised in terms of plant genetic diversity. In this study we compared the genetic diversity of mainland populations
and landraces of Trifolium repens with wild populations collected from the islands surrounding the UK, including the island of Hirta in the St Kildan archipelago.
Individuals from St Kilda represent a unique conservation resource, with populations both highly differentiated from UK mainland
populations and genetically distinct from cultivated varieties, whilst able to retain diversity through limited human influence
on the islands. In contrast, there is relative genetic similarity of wild UK populations to cultivated forms highlighted in
mainland populations, but with geographic barriers preventing complete homogenisation of the mainland UK genepool. We underline
the need for conservation priorities to include common species that are threatened by gene flow from cultivation, and draw
attention to the potential of islands to preserve natural levels of genetic diversity.
[Show abstract][Hide abstract] ABSTRACT: Interspecific hybrids have been developed between white clover and the annual, profuse flowering diploid species Trifolium nigrescens Viv.(ball clover) as a strategy to improve the seed yield of white clover. Third generation backcross hybrids have now been
developed in different leaf size categories that have the agronomic performance of white clover. Assessment of the seed yield
of the hybrids in field experiments conducted over two harvest years showed that the medium and large leaved hybrids produced
significantly more inflorescences and had a higher seed yield potential than control varieties of comparable leaf size improving
the commercial potential of this material. Introgression of the rhizomatous trait from Caucasian clover (Trifolium ambiguum M. Bieb) into white clover has been used to improve persistence and tolerance of moisture stress. Advanced hybrids are now
at the stage of development where they will be submitted to official variety trials.
-Seed yield-Moisture stress
[Show abstract][Hide abstract] ABSTRACT: The model legume species Medicago truncatula is a potentially useful tool for gene discovery in white clover using translational genomics strategies. A prerequisite to
the practical implementation of this approach is a good understanding of the extent of conservation of gene order between
the species. Previous studies have demonstrated conservation at the macrosyntenic level, but no published information exists
on the extent of conserved microsynteny between these species. In a previously published study, we reported the construction
of a BAC library of white clover, the end sequencing of approximately 700 clover BACs, and the comparison of these BAC-end
sequences to the M. truncatula genome. We found that 14 paired BAC-ends were shown to have the equivalent pairs of M. truncatula sequence on the same M. truncatula BAC clone or contig sequence within a span of 25–200Kb, suggesting they represent orthologous regions in the two species.
In this follow-up analysis, we have chosen five of these BACs, sequenced them to approximately six-fold coverage, and compared
the resulting assembled contigs to their putatively equivalent regions of M. truncatula. Highly conserved gene content and almost complete conservation of gene order and orientation for all five sequences were
found, suggesting that translational genomics approaches for gene discovery using Medicago could be successful.
[Show abstract][Hide abstract] ABSTRACT: Proceedings of the 5th International Symposium on the Molecular Breeding of Forage Turf, Sapporo, Japan, 2-6 July 2007. This book includes papers from plenary lectures and selected oral presentations of the 5th International Symposium on the Molecular Breeding of Forage and Turf. A wide variety of themes are addressed in a collection that provides authoritative reports on the recent progress and understanding of molecular technologies and their application in plant breeding. The book covers almost all relevant areas in molecular breeding of forage and turf as well as biofuel crops, from gene discovery to the development of improved cultivars.
[Show abstract][Hide abstract] ABSTRACT: Proceedings of the University of Nottingham 42nd Feed Conference, September 2-4 2008. This book contains the proceedings of the 42nd University of Nottingham Feed Conference held in September 2008. Authors of all chapters are international experts in their fields and have provided comprehensive analyses of the issues together with practical applications. This book is essential reading for all involved in animal production science/practice, including researchers, consultants, animal science students, legislators and practitioners.
[Show abstract][Hide abstract] ABSTRACT: Home grown forages offer the livestock farmer high quality and traceable feeds for his or her animals. As animal genetics change to give faster growth rates and higher milk yields, the genetics of forage crops also need to improve to match animal requirements. Breeding is essentially a process of exploitation of genetic variation. This has to be either selected or created and then incorporated into genetic stock that already contains a number of desirable characteristics, combining new genes while maintaining other required traits. For forage improvement, this genetic variation must then be fixed into new plant varieties. This is a more complex task in out-breeding species that have incompatibility mechanisms, such as most forage grasses and legumes, compared with inbreeding species such as most cereal crops.
Recent Advances in Animal Nutrition. 12/2008; 2008(1):39-65.
[Show abstract][Hide abstract] ABSTRACT: Hybrids between white clover (Trifolium repens L.) and Caucasian clover (or Kura clover, Trifolium ambiguum M. Bieb) are a potential route for the improvement of drought tolerance and persistence in white clover. However, to be agronomically viable they must show no significant reduction in their potential for nitrogen fixation relative to white clover. A comparative study of growth rate and nitrogen fixation was carried out in flowing solution culture without a supply of mineral nitrogen to the plants. The two parental species and two generations of backcross hybrids, with white clover as the recurrent parent, were assessed. The growth rate and N content of T. ambiguum were significantly lower than those of the other lines. However, dry matter production, nodule biomass per plant and rates of fixation were similar in second-generation backcross plants and white clover. The results suggest that the agronomic potential of this novel germplasm is not compromised by limitations with respect to nitrogen fixation.ZusammenfassungHybriden zwischen Weißklee (Trifolium repens L.) und Kaukasischen Klee (Trifolium ambiguum M. Bieb) ermöglichen die Verbesserung der Dürretoleranz und der Ausdauer von Weissklee. Um jedoch agronomisch nützlich zu sein, dürfen die Hybriden keine bedeuende Verringerung ihrer Fähigkeiten der Stickstoffgewinnung gegenüber dem Weißklee zeigen. Eine vergleichbare Studie der Wachstumsrate und der Stickstoffgewinnung wurde mit Pflanzen in flüssiger Kultur Lösung ohne Zugabe von Mineralstickstoff durchgeführt. In dieser Studie wurden die zwei elterlichen Sorten unter zwei Generationen von Rückkreuzungshybriden mit Weißklee als rücklaufigen Eltern gemessen. Die Wachstumsrate und der Stickstoffgehalt waren erheblich niedriger in T. anbiguum als in den anderen Abkömmlingen. Totaltrockensubstanz, Knötchenlebendmasse pro Pflanze und die spezifische Kinetik der Stickstoffixierung waren ähnlich zwischen Pflanzen der zweiten Generation von Rückkreuzungen und von Weißkleepflanzen. Die Ergebnisse deuten darauf hin, daß dieses neuartige Germplasma bezüglich der Stickstoffgewinnung nicht begrenzt ist.
Journal of Agronomy and Crop Science 07/2008; 185(4):241 - 247. · 2.15 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Seven varieties or advanced breeding lines of white clover (Trifolium repens L.), all of small leaf size, were grown separately in mixtures with perennial ryegrass (Lolium perenne L.) in an experiment encompassing three harvest years. Harvestable dry-matter (DM) yield measurements were taken of these mixtures and of perennial ryegrass monocultures under two management regimes: cutting and continuous sheep grazing. Considerable differences were observed in the harvestable DM yields of white clover, perennial ryegrass and total yields of the mixtures between plots containing different white clover varieties. White clover yields were generally higher under cutting, and perennial ryegrass yields were higher under grazing. The difference between perennial ryegrass yield in monoculture and in mixture was variable. In the second harvest year, a significant interaction effect was seen between management and white clover variety for white clover yield but not for perennial ryegrass yield. The relationship between clover yield and grass yield differed between the two management regimes. Under cutting, a negative correlation was observed, indicative of competitive effects. However, under grazing, no such correlation was seen. Possible mechanisms underlying these outcomes are discussed.
[Show abstract][Hide abstract] ABSTRACT: An experiment investigated the hypothesis that incorporating lupins ( Lupinus spp.) into lamb finishing diets would not alter lamb productivity and carcass characteristics when compared with a soya bean ( Glycine max ) meal concentrate or a commercial concentrate diet. The 4 dietary treatments were: narrow-leaf lupin (cv. Prima), yellow lupin (cv. Wodjil), soya bean meal and a commercial (control) lamb finisher diet. Eighty male Suffolk-cross castrated lambs were used. Diets were formulated so as to be iso-nitrogenous (160 g kg DM -1) and iso-energetic (ME 11.0 MJ kg DM -1). The experiment comprised of 3 phases: a 14-d covariate period, a 14-d adaptation period (14 days prior to day 0) and an 8-week measurement period (Day 0-56). During the covariate period, lambs were kept as one group on pasture. During the adaptation period, lambs were housed and offered increasing amounts of their treatment diets. Each blocking group was allocated at random to a set of four adjacent pens within 4 treatment blocks. During the measurement period, animals were offered straw and concentrate ad libitum , with refusal margins of 0.10 to 0.15 d-1. Lambs were weighed and condition scored every 7-d throughout the experiment. The measurement period was split into two phases. From Day 0-28, live weight data from all lambs was collected to determine liveweight gain, with the mean of each replicate pen of 5 lambs used in the data analysis. The mean liveweight gain of lambs offered concentrates incorporating soya, narrow-leaf lupin, yellow lupin or a commercial control diet were 185, 229, 193 and 166 g d-1, respectively. There was no significant effect (P > 0.05) of dietary treatment on the liveweight gain of lambs offered the different dietary treatments. From Day 29 onwards, lambs were selected-out for slaughter and their carcass characteristics determined. The killing out percentage of lambs offered the soya, narrow-leaf lupin, yellow lupin or commercial control concentrate diet was 50.1, 50.7, 51.3 and 50.1%, respectively. Lambs offered a commercial control concentrate or concentrates containing yellow lupin took, on average, 31 days to finish for slaughter, with lambs offered narrow-leaf lupin and soya diets taking 29 and 32 days, respectively.