Charlotte Jones

Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement.

Red clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems. It is an attractive component of grassland farming, because of its high yield and protein content, nutritional value and ability to fix atmospheric nitrogen. Enhancing its role further in sustainable agriculture requires genetic improvement of persistency, disease resistance, and tolerance to grazing. To help address these challenges, we have assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with Medicago truncatula and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. Genotyping by sequencing of a synthetic population of 86 genotypes show that the number of markers required for genomics-based breeding approaches is tractable, making red clover a suitable candidate for association studies and genomic selection.

The genetic location of the self-incompatibility locus in white clover (Trifolium repens L.)

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 F1 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.

Predicting future biomass yield in Miscanthus using the carbohydrate metabolic profile as a biomarker

In perennial energy crop breeding programmes, it can take several years before a mature yield is reached when potential new varieties can be scored. Modern plant breeding technologies have focussed on molecular markers, but for many crop species, this technology is unavailable. Therefore, prematurity predictors of harvestable yield would accelerate the release of new varieties. Metabolic biomarkers are routinely used in medicine, but they have been largely overlooked as predictive tools in plant science. We aimed to identify biomarkers of productivity in the bioenergy crop, Miscanthus, that could be used prognostically to predict future yields. This study identified a metabolic profile reflecting productivity in Miscanthus by correlating the summer carbohydrate composition of multiple genotypes with final yield 6 months later. Consistent and strong, significant correlations were observed between carbohydrate metrics and biomass traits at two separate field sites over 2 years. Machine‐learning feature selection was used to optimize carbohydrate metrics for support vector regression models, which were able to predict interyear biomass traits with a correlation (R) of >0.67 between predicted and actual values. To identify a causal basis for the relationships between the glycome profile and biomass, a 13C‐labelling experiment compared carbohydrate partitioning between high‐ and low‐yielding genotypes. A lower yielding and slower growing genotype partitioned a greater percentage of the 13C pulse into starch compared to a faster growing genotype where a greater percentage was located in the structural biomass. These results supported a link between plant performance and carbon flow through two rival pathways (starch vs. sucrose), with higher yielding plants exhibiting greater partitioning into structural biomass, via sucrose metabolism, rather than starch. Our results demonstrate that the plant metabolome can be used prognostically to anticipate future yields and this is a method that could be used to accelerate selection in perennial energy crop breeding programmes.

Could Miscanthus replace maize as the preferred substrate for anaerobic digestion in the United Kingdom? : Future breeding strategies

Fodder maize is the most commonly used crop for biogas production owing to its high yields, high concentrations of starch and good digestibility. However, environmental concerns and possible future conflict with land for food production may limit its long‐term use. The bioenergy grass, Miscanthus, is a high‐yielding perennial that can grow on marginal land and, with ‘greener’ environmental credentials, may offer an alternative. To compete with maize, the concentration of non‐structural carbohydrates (NSC) and digestibility may need to be improved. Non‐structural carbohydrates were quantified in 38 diverse genotypes of Miscanthus in green‐cut biomass in July and October. The aim was to determine whether NSC abundance could be a target for breeding programmes or whether genotypes already exist that could rival maize for use in anaerobic digestion systems. The saccharification potential and measures of N P and K were also studied. The highest concentrations of NSC were in July, reaching a maximum of 20% DW. However, the maximum yield was in October with 300–400 g NSC plant−1 owing to higher biomass. The digestibility of the cell wall was higher in July than in October, but the increase in biomass meant yields of digestible sugars were still higher in October. Nutrient concentrations were at least twofold higher in July compared to November, and the abundance of potassium showed the greatest degree of variation between genotypes. The projected maximum yield of NSC was 1.3 t ha−1 with significant variation to target for breeding. Starch accumulated in the highest concentrations and continued to increase into autumn in some genotypes. Therefore, starch, rather than sugars, would be a better target for breeding improvement. If harvest date was brought forward to autumn, nutrient losses in non‐flowering genotypes would be comparable to an early spring harvest.

QTL Analysis and Gene Expression Studies in White Clover

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.

Population structure of red clover ecotypes collected from Europe and Asia

Red clover (Trifolium pratense L.) is a highly adaptable species, with a wide geographic distribution. At the genetic level, wild ecotypes possess high variability, which enables them to adapt rapidly to diverse environments. This variation can be identified, via molecular techniques, and used to determine the differences between populations that may otherwise be indistinguishable. The results presented here are part of a wider study undertaken with a view to assess the available genetic diversity and use it to facilitate future introgression of useful traits into red clover breeding populations.