QTL Analysis of Mineral Content in Perennial Ryegrass (\u3cem\u3eLolium Perenne\u3c/em\u3e L.)

Variation in mineral content of grasses can be strongly influenced by genetic factors. Grass tetany (hypomagnesemia) of cattle and sheep is due to disturbances in serum magnesium levels. In Southern Australia, resultant levels of mortality in cattle vary between 0.5-1.5% of total stock numbers. Serum magnesium variation may be due to feed deficits, or dietary imbalances that interfere with magnesium metabolism. High levels of potassium appear to exert negative effects on the levels of magnesium in the blood. Italian ryegrass genotypes with high levels of magnesium can alleviate the incidence of grass tetany. The genetic control of mineral content, including magnesium, in perennial ryegrass has been investigated using molecular marker-based analysis

Validation of Genotyping by Sequencing Using Transcriptomics for Diversity and Application of Genomic Selection in Tetraploid Potato

Potato is an important food crop due to its increasing consumption, and as a result, there is demand for varieties with improved production. However, the current status of breeding for improved varieties is a long process which relies heavily on phenotypic evaluation and dated molecular techniques and has little emphasis on modern genotyping approaches. Evaluation and selection before a cultivar is commercialized typically takes 10–15 years. Molecular markers have been developed for disease and pest resistance, resulting in initial marker-assisted selection in breeding. This study has evaluated and implemented a high-throughput transcriptome sequencing method for dense marker discovery in potato for the application of genomic selection. An Australian relevant collection of commercial cultivars was selected, and identification and distribution of high quality SNPs were examined using standard bioinformatic pipelines and a custom approach for the prediction of allelic dosage. As a result, a large number of SNP markers were identified and filtered to generate a high-quality subset that was then combined with historic phenotypic data to assess the approach for genomic selection. Genomic selection potential was predicted for highly heritable traits and the approach demonstrated advantages over the previously used technologies in terms of markers identified as well as costs incurred. The high-quality SNP list also provided acceptable genome coverage which demonstrates its applicability for much larger future studies. This SNP list was also annotated to provide an indication of function and will serve as a resource for the community in future studies. Genome wide marker tools will provide significant benefits for potato breeding efforts and the application of genomic selection will greatly enhance genetic progress

SNP Discovery and Haplotypic Variation in Full-Length Herbage Quality Genes of Perennial Ryegrass (Lolium Perenne L.)

The development of forages with enhanced nutritive value through improvements of herbage quality (digestibility, carbohydrate content) is potentially capable of increasing both meat and milk production by up to 25%. However, the expense and time-consuming nature of the relevant biochemical and biophysical assays has limited breeding improvement for forage quality. The development of accurate high-throughput molecular marker-based selection systems such as single nucleotide polymorphisms (SNPs) permits evaluation of genetic variation and selection of favourable variants to accelerate the production of elite new varieties

Genetic Analysis of the Interaction Between the Host Perennial Ryegrass and the Crown Rust Pathogen (\u3cem\u3ePuccinia Coronata\u3c/em\u3e F.SP. \u3cem\u3eLolii\u3c/em\u3e)

Crown rust (Puccinia coronata f.sp lolii) is the most important fungal pathogen of perennial ryegrass (L.perenne L.). The physiological effects associated with infection include reduction of water soluble carbohydrate (WSC) reserves, causing decreased dry matter yield, digestibility and palatability for herbivores reared for meat, milk and wool production. Phenotypic variability of rust-infection in perennial ryegrass is likely to be due to environmental effects, as well as the interaction of defence and resistance genes in the grass and virulence genes in the pathogen. Classical and molecular genetic marker-based studies have previously detected both qualitative and quantitative resistance, due respectively to major genes and quantitative trait loci (QTL). In addition, evidence for physiological race variation has been demonstrated for P. coronata f.sp. avenae, the causative organisms of crown rust in oat, and has been inferred for P. coronata f.sp. lolii. Evaluation of genotypic variation in both the host and pathogen is consequently important for the analysis of the interaction

Integration of Perennial Ryegrass (L. Perenne) Genetic Maps using Gene-Associated SNPs

The reference genetic map of perennial ryegrass was developed by the International Lolium Genome Initiative (ILGI), using the p150/112 one-way pseudo-testcross population. A selection of public domain genetic markers including RFLPs, detected by wheat, barley, oat and rice cDNA probes, and AFLPs were mapped, allowing studies of comparative relationships between perennial ryegrass and other Poaceae species. The map was enhanced through the addition of unique perennial ryegrass genomic DNA-derived SSR (LPSSR) markers, providing the basis of framework genetic mapping in other populations. In addition, a small number of RFLP loci detected by candidate genes involved in herbage quality traits were added to the map. A second-generation reference genetic mapping family was developed based on the F1(NA6 x AU6) two-way pseudo-testcross family, generating two parental genetic maps. These maps were populated by genomic SSR loci, EST-RFLP loci and EST-SSR loci (corresponding to multiple functional categories of agronomic importance). A third genetic mapping population based on an interspecific cross between perennial and annual ryegrass genotypes [F1(Andrea1246 x Lincoln1133)] generated a map based on LPSSR and EST-SSR markers. Linkage groups in the two latter maps were inferred using common LPSSR loci with the p150/112 genetic map

Application of Molecular Technologies in Forage Plant Breeding

Key points A range of molecular breeding technologies have been developed for forage plant species including both transgenic and non-transgenic methodologies. The application of these technologies has the potential to greatly increase the range of genetic variation that is available for incorporation into breeding programs and subsequent delivery to producers in the form of improved germplasm. Further developments in detailing the phenotypic effect of genes and alleles both through research in target species and through inference from results from model species will further refine the delivery of new forage cultivars

Evaluation of Genetic Diversity in White Clover (\u3cem\u3eTrifolium Repens\u3c/em\u3e L.) Through Measurement of Simple Sequence Repeat (SSR) Polymorphism

White clover (Trifolium repens L.) is a key important temperate pasture legume. Due to the obligate outbreeding nature of white clover, individual genotypes within cultivars are highly genetically heterogeneous. Genetic diversity has been assessed within and between 16 elite cultivars derived from Europe, North and South America, New Zealand and Australia

Genetic Analysis of the Interaction Between Perennial Ryegrass and the Fungal Endophyte \u3cem\u3eNeotyphodium Lolii\u3c/em\u3e

The fungal endophyte Neotyphodium lolii is widely distributed in perennial ryegrass pastures, especially in Australia and New Zealand. The presence of the endophyte is associated with improved tolerance to water and nutrient stress and resistance to insect pests, but is accompanied by reduced herbivore feeding. The molecular mechanisms responsible for these endophyte-related traits are in general poorly understood. Comparisons of different grass-endophyte associations show that endophyte-related traits are affected by both endophyte and host genotype, and environmental interactions

Gene-Associated Single Nucleotide Polymorphism Discovery in White Clover (\u3cem\u3eT. Repens\u3c/em\u3e L.)

Single nucleotide polymorphism (SNP) discovery permits the discovery of molecular marker variation associated with functionally-defined genes. SNP markers have been developed for the temperate pasture legume crop white clover (Trifolium repens) using public and proprietary genic sequences correlated with key agronomic traits of interest

Gene-Associated Single Nucleotide Polymorphism (SNP) Discovery in Perennial Ryegrass (\u3cem\u3eLolium Perenne\u3c/em\u3e L.)

Perennial ryegrass (Lolium perenne L.) is the most important grass species for temperate pasture systems world-wide. Varietal improvement programs for this obligate outbreeding species are based on polycrossing of multiple parents to produce heterogeneous synthetic populations. The complexity of breeding systems creates challenges and opportunities for molecular marker technology development and implementation. Previous research has led to: the generation of a comprehensive suite of simple sequence repeat (SSR) markers, reference genetic map construction, comparative genetic studies, QTL identification, and population structure analysis. Emphasis has now shifted from the use of anonymous genetic markers linked to trait-specific genes to the development of functionally-associated genetic markers based on candidate genes. The successful implementation of this approach will allow effective selection of parental plants in germplasm collections based on superior allele content