Jean-Paul Sampoux

Genetic diversity in red clover (Trifolium pratense L.) revealed by morphological and microsatellite (SSR) markers

The NPGS-USDA core collection with 85 accessions of red clover, an important forage species, is little described. The goal of the present study was to evaluate the diversity of a set of accessions from the core collection at the morphological and molecular level in order to extract some valuable accessions for Brazilian red clover breeding programs. Twenty-one morphological traits, collected in field and greenhouse in South Brazil, and seven SSR markers were used to describe 57 accessions from the U.S. core collection and one population cultivated in Southern Brazil. Variation between accessions was large for most of the 21 morphological traits. A cluster analysis based on the morphological traits revealed five distinct clusters that separated the populations according to flowering earliness, as already described, but also according to persistency, growth habit and dry matter productivity. Over seven SSR loci, the number of alleles averaged 11.1 alleles per locus. Genetic diversity measured with SSR markers was high, with a mean expected heterozygosity of 0.86. An analysis of molecular variance revealed that the largest proportion of variation (83.6%) resided at the within population level. Although the molecular markers also separated accessions into five clusters, there was no coincidence between the composition of groups found with morphological and molecular data. Use of genetic diversity in breeding programs requires to use the most promising populations, to combine positive traits such as persistency and forage yield, and probably to use within population variation to detect valuable genotypes that could be used as parents of synthetic varieties.

Genetic Improvement in Ryegrass (Lolium perenne) from Turf and Forage Breeding Over the Four Past Decades

In order to assess the efficiency of breeding in ryegrass (Lolium perenne), we tested the agronomic performances of a set of diploid cultivars including turf and forage cultivars registered on European national lists from 1965 to 2004. Seven ecotypes, originating from the main European climatic areas were also tested. Linear regressions fitting agronomic traits to the year of registration enabled to test the genetic improvement in turf and forage breeding through time. The genetic improvement in turf breeding was highly significant (p value of regression slope < 0.001) for most target traits (aesthetic aspect, disease resistance, wear tolerance, summer aspect, persistency). In forage breeding, the genetic improvement was highly significant (p value < 0.001) for autumn dry matter yield, rust resistance, and persistency, and was significant (p value < 0.05) for summer dry matter yield and reduction of aftermath heading. The rate of improvement of annual dry matter yield reached 0.29 ton per 10 years. Forage breeding was additionally associated with a highly significant decrease of lignin and crude protein content, and with a highly significant increase of soluble carbohydrate content. No significant change in grain production was noted either in forage or turf breeding, but conversely a large range of seed production was pointed out in both ancient and recent cultivars.

Empirical Niche Modelling of the Spontaneous Diversity of Forage and Turf Species to Improve Collection and Ex Situ Conservation

Rational sampling of the spontaneous diversity of forage and turf species requires an a priori knowledge of the range of environmental conditions suitable for these species. We introduce some concepts and methods for investigating the environmental range of species by empirical modelling of species ecological niche, and we suggest how such investigations could help to plan collection campaigns and to improve the choice of core-collections. The empirical modelling of the ecological niche of a species consists of building a function of environmental parameters predicting the presence of the species from a calibration dataset including observed presence-absence or abundance records of the species and environmental data at observation sites. We emphasize that data from collection campaigns of plant breeders are valuable information for niche modelling. We introduce two methods for investigating the environmental distribution of species and for niche modelling based on presence-absence data: the canonical correlation analysis and the logistic regression. We give examples combining niche model and GIS software that may contribute to organize collection campaigns. We suggest that models predicting probability of presence of species may be useful for the selection of core-collections. Such models may help to delineate geographically isolated areas of presence of species that should be sampled separately for selecting a core-collection. In each isolated area of presence, we propose to stratify the accessions in clusters according to the predicted probability of presence of the species in collection sites, and to select accessions in each cluster.

Pleistocene climate changes explain large-scale genetic variation in a dominant grassland species, Lolium perenne L.

Aim Grasslands have been pivotal in the development of herbivore breeding since the Neolithic and are still nowadays the most widespread agricultural land-use across Europe. However, it remains unclear whether the current large-scale genetic variation of plant species found in natural grasslands of Europe is the result of human activities or natural processes. Location Europe. Taxon Lolium perenne L (perennial ryegrass). Methods We reconstructed the phylogeographic history of L. perenne, a dominant grassland species, using 481 natural populations including 11 populations from closely related taxa. We combined the Genotyping-by-Sequencing (GBS) and Pool-sequencing (Pool-seq) methods to obtain high-quality allele frequency calls of ~ 500 k SNP loci. We performed genetic structure analyses and demographic reconstructions based on the site frequency spectrum (SFS). We additionally used the same genotyping protocol to assess the genomic diversity of a set of 32 cultivars representative of the L. perenne cultivars widely used for forage purposes. Results Expansion across Europe took place during the Würm glaciation (12-110 kya), a cooling period that decreased the dominance of trees in favour of grasses. Splits and admixtures in L. perenne fit historical sea level changes in the Mediterranean basin. The development of agriculture in Europe (7-3.5 kya), that caused an increase in the abundance of grasslands, did not have an effect on the demographic patterns of L. perenne. We found little differentiation between modern cultivars and certain natural variants. However, modern cultivars do not represent the wide genetic variation found in natural populations. Main conclusions Demographic events in L. perenne can be explained by the changing climatic conditions during the Pleistocene. Natural populations maintain a wide genomic variability at continental scale that has been underused by recent breeding activities. This variability constitutes valuable standing genetic variation for future adaptation of grasslands to climate change, safeguarding the agricultural services they provide.

Patterns of Spring Growth and Phenology in Natural Populations of Lolium perenne Under Contrasting Field Conditions

The ecotypic diversity of perennial ryegrass (Lolium perenne L.) is a major genetic resource for breeding programs. In three replicated micro-sward trials in France, Belgium and Germany, we measured spring growth and recorded heading date of round 400 genebank accessions from the natural diversity of L. perenne that were selected as to represent the wide range of variability in this species. We observed marked differences between trial locations as well as interaction between accessions and locations in the timing of spring growth rates along growing-degree-days (GDDs). These preliminary results are part of a wider project aiming to investigate the natural adaptation of perennial ryegrass to various regional climates across its spontaneous area of presence in Europe.

Report of the Breeding Debate

Based on a questionnaire with 11 questions, 5 breeding institutes and 4 breeding companies defined their 2035 horizon for grass and forage crops breeding. Visions and opinions differed a lot regarding targeted species, breeding goals, importance of plant physiology, breeding techniques, testing environments, the use of molecular tools and the influence of regulations and sustainability drivers. The report can be considered as a joint reference document for future debates.

Comparison of Lucerne Genotypes and Varieties in Pure and Mixed Stands

Grasslands sown with grass/legume mixtures combine agricultural and environmental advantages, but genetic progress is still needed. Current breeding and evaluation of alfalfa varieties is conducted in monoculture, which may not allow for the creation of varieties that perform well in mixture with grasses (such as tall fescue or cocksfoot). We report on recent results on lucerne–grass mixtures which reveal that the ranking of lucerne genotypes or varieties for biomass production is substantially different in mixture and in monoculture. Biomass production of a mixture mainly resulted in additive effects of the varieties of each species, without statistically significant interaction. We suggest that the performance in mixture for lucerne variety breeding and evaluation should be taken into account.

Genetic Response to Climate Scenarios in Dactylis and Festuca of Temperate Versus Mediterranean Origin

Climate change stresses the importance of exploring the genetic adaptation of plants to an increase of both temperature and water deficit. To this end, dense swards of Mediterranean and temperate cultivars of Dactylis and Festuca were seed harvested after 2 years under artificial climate scenarios (range of summer drought) in two environments (Mediterranean and temperate). To assess possible genetic changes, all populations of the next generation were assessed and compared with their parent population having not been subjected to these climate scenarios. The experiment was a spaced plant design in the temperate location. The results showed that a drought escape strategy through earlier heading time and reduced total plant yield was enhanced by scenarios of greater summer drought. However, the direction and the intensity of the response of the main measured traits suggested that the physiological plant adaptation to water stress differs between species. In Dactylis, the phenology appeared to be a very responsive trait in the late heading temperate cultivar and induced a plant size reduction, while no genetic variability seems to be still available for selection within the early flowering Mediterranean cultivar. By contrast, the balance between both traits was not found so crucial in Festuca which suggests a possible greater role of the rooting system in drought resistance for this species.

Impact of Four Decades of Breeding on Molecular Differentiation Between Forage and Turf Cultivars of Lolium Perenne

How much differentiated are forage and turf type cultivars within L. perenne? To estimate this, we used 10 SSR/STS markers for genotyping a collection of 7 natural populations, 50 forage and turf cultivars and 4 old cultivars of dual usage registered since 1965–2004. We showed that differentiation between usage types has steadily increased since the opening of a turf national list in France and that it has mostly involved 3 markers, among which 2 were mapped onto linkage group 1 in L. perenne. Relative to natural populations, assumed to sample genetic diversity in perennial ryegrass when breeding started, turf cultivars were found to be more distantly related than forage cultivars, especially those which were recently registered. However, genetic differentiation remained primarily between cultivars whatsoever type they were. Differentiation between cultivars has increased to be about twice higher on average than between natural populations, even of quite distant geographical origin. Loss of genetic variability after 40 years of breeding was found to be very low. All alleles present in natural populations were sampled again in the collection of cultivars we investigated. The results are briefly discussed in conclusion as respect to phenotypic differentiation and efficiency of breeding methods in the grasses.