PotatoMASH · Potato Multi-Allele Scanning Haplotags – a low cost, genome-scanning marker system for use in potato breeding
Horizon 2020 — Marie Skłodowska-Curie Actions
- Duration
- 2018-09-24 → 2020-09-23
- EU contribution
- €175,866
- Participants
- 1
- Scheme
- MSCA-IF-EF-ST
Lines connect the coordinator with its partners.
Results in brief
Potato Multi-Allele Scanning Haplotags – a low cost, genome-scanning marker system for use in potato breeding
The goal of potato breeders is to produce varieties that have improved sustainability, utilisation and consumer characteristics. Parent varieties with characteristics that the breeder wishes to combine are crossed to produce a population, from which individual lines that outperform the parents and exhibit desirable combinations of characteristics, are selected, and advanced as new varieties. This process takes over 10 years, and is challenging due to the fact that up to 40 characteristics have to be combined (including yield, resistance to pests, diseases and stress conditions, and quality characteristics). Marker assisted selection (MAS) and genomic selection (GS) use genetic fingerprinting (genotyping) to help make the process of selection more efficient by allowing the genes controlling the characteristics under selection to be tracked during crossing and selection, allowing better selection of parents and the identification of progeny with good trait combinations. Unfortunately, these approaches can be too expensive for breeders to implement, especially for characteristics controlled by multiple genes, which require genotyping approaches that scan the whole genome to track all of these genes simultaneously. The goal of PotatoMASH (Potato Multi-Allele Scanning Haplotags) is to develop a novel, affordable, genotyping test for use in GS and MAS for multiple important traits in potato breeding.
Data: CORDIS, © European Union
Project objective
Potato breeding is a 10-year process that involves combining over 40 characteristics to produce varieties that have improved sustainability, utilisation and consumer characteristics. Genomic and marker assisted selection (GS and MAS) can make breeding faster/more efficient, increasing the rate of genetic gain and the ability to combine multiple traits. Strategies for GS to date have tended to employ many thousands of markers; however, the economic burden of deploying such approaches on thousands of plants annually in a breeding programme may restrict the adoption of GS. The objective of this action is to develop a novel, low cost, genome-scanning marker platform for use in simultaneous GS and MAS for multiple traits in potato breeding, by combining existing knowledge on the patterns of linkage disequilibrium in potato with recent advances in genotyping-by-sequencing approaches based on massively multiplex PCR. The marker system will target clusters of SNPs whose aggregate profile over distances covered by paired-end next generation sequencing (NGS) reads will allow them to be used as haplotags. Unlike bi-allelic SNPs, haplotags can discriminate multiple allelic variants in tetraploid potato. Approximately 400 loci at placed at 1Mb spacing throughout the euchromatic portion of the genome, and a further 100 SNPs linked to specific traits, will be targeted and assayed using an approach called GT-Seq, which uses combinatorial barcoding to allow multiplexing of thousands of samples in a single NGS run. The sequencing platform will be utilised in conjunction with 2 training populations to develop genomic prediction equations for yield and fry colour of potato. Subsequently, it will be deployed for combined GS and MAS on 1000 plants from the second field generation of a commercial potato breeding programme. The research and training activities in the fellowship proposal will equip a young postdoctoral researcher with the skills of a ""next generation plant breeder"".""
Original text from CORDIS.
Participants
- TEAGASC - AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY · CarlowCoordinatorIreland
Links
Data: CORDIS, © European Union