Developing an integrated genomic selection approach beyond biomass for varietal protection and nutritive traits in perennial ryegrass (Lolium perenne L.).

KEY MESSAGE: Breeding target traits can be broadened to include nutritive value and plant breeder's rights traits in perennial ryegrass by using in-field regression-based spectroscopy phenotyping and genomic selection. Perennial ryegrass breeding has focused on biomass yield, but expansion into a broader set of traits is needed to benefit livestock industries whilst also providing support for intellectual property protection of cultivars. Numerous breeding objectives can be targeted simultaneously with the development of sensor-based phenomics and genomic selection (GS). Of particular interest are nutritive value (NV), which has been difficult and expensive to measure using traditional phenotyping methods, resulting in limited genetic improvement to date, and traits required to obtain varietal protection, known as plant breeder's rights (PBR) traits. In order to assess phenotyping requirements for NV improvement and potential for genetic improvement, in-field reflectance-based spectroscopy was assessed and GS evaluated in a single population for three key NV traits, captured across four timepoints. Using three prediction approaches, the possibility of targeting PBR traits using GS was evaluated for five traits recorded across three years of a breeding program. Prediction accuracy was generally low to moderate for NV traits and moderate to high for PBR traits, with heritability highly correlated with GS accuracy. NV did not show significant or consistent correlation between timepoints highlighting the need to incorporate seasonal NV into selection indexes and the value of being able to regularly monitor NV across seasons. This study has demonstrated the ability to implement GS for both NV and PBR traits in perennial ryegrass, facilitating the expansion of ryegrass breeding targets to agronomically relevant traits while ensuring necessary varietal protection is achieved.

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.