Abstract
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.
Highlights
Most breeding methods rely heavily on phenotypic selection for germplasm improvement with little importance on genotypic selection at the molecular level
An average of 3,108,151 reads per sample was generated from the 181 cultivars, with >79% of all cultivars having over 1M reads and over 89% of the high-quality reads aligned to the reference genome
With the release of the potato genome sequence (The Potato Genome Sequencing Consortium, 2011), reducing sequencing costs and an increase in computational power and analysis tools, the extensive application of Genomic selection (GS) to potato will become the modern era of breeding
Summary
Most breeding methods rely heavily on phenotypic selection for germplasm improvement with little importance on genotypic selection at the molecular level. Marker-assisted selection (MAS) has been incorporated into the potato breeding cycle for several traits which has resulted in selection of individuals a few years earlier when compared to traditional phenotypic selection and is cost effective (Slater et al, 2013). Other more complex traits like most tuber and plant morphological traits, cooking characteristics and yield can be selected for under this scheme (van Eck, 2007; Ramakrishnan et al, 2015). Due to their polygenic nature, it is more difficult and extremely slow (Hospital, 2009; Slater, 2013)
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