Project properties

Title Domestication of diploid potato (in close collaboration with Solynta)
Group Plant Breeding, Laboratory of
Project type thesis
Credits 36-39
Supervisor(s) Richard Visser, Ronald Hutten & Richard Finkers (PBR-WUR) and Ate van der Burgt & James Adams (Solynta)
Examiner(s) Richard Visser
Contact info Richard.visser@wur.nl
Begin date 2020/01/01
End date 2020/12/31
Description Introduction

Diploid hybrid potato breeding is a new paradigm. Already for many decades diploid potato germplasm has been generated, partially by producing di-haploids from tetraploid cultivars and partially by crosses with crossable diploid wild Solanum species. The previous Institute for Plant Breeding (IVP, nowadays Plant Breeding of Wageningen University & Research) has played an active role by collecting, recombining and selecting diploid germplasm that eventually resulted in the PhD thesis of Ronald Hutten in 1994: “Basic aspects of potato breeding via the diploid level”.
Diploid potato is self-incompatible controlled by so-called S-alleles. However, the wild crossable diploid species S. chacoense carries the Sli-gene that induces self-compatibility that is dominant over these S-genes. This gene has been crossed with three diploid clones from the PBR-WUR diploid collection and further crosses and selves have been made among a subset of 16 diploid clones of this collection. This has been developed into a practical hybrid potato breeding programme operated by the potato breeding company Solynta. Thus, we refer to these 16 diploid clones as being founders (of the Solynta breeding programme)
Structural pedigree information from the initial crosses made in the previous century is lacking. Some scattered information on these initial generations, eventually resulting in the founders, is available at PBR-WUR. Recently, these diploid founders have been sequenced (GBS and/or WGS), and genetic commonalities became evident, suggesting overlapping origin(s). Reliable pedigree information is available at Solynta since the first cross (of founders) with S. chacoense and subsequent crosses and selfings in the Solynta breeding programme. Moreover, detailed genetic information is available from the recent breeding populations.

Aim: To follow the genetic variation, shifts and drifts since the onset of diploid potato breeding in Wageningen.
Research project:
1. Historic study of the generation of the diploid germplasm since 1970s till 1990s. This is based on old reports, brochures and bulletins available at PBR-WUR.
2. Interpretation of the GBS/WGS data of the 16 founders with respect to the genetic variation that is present in these founders and comparisons with genetic variation in tetraploid cultivars and wild species.
3. For this, a large(r) and diverse panel of GBS/WGS datasets is available.
4. Analysis of genetic variation in present breeding germplasm.
5. Synthesis on genetic shift and drifts during domestication and breeding of diploid potato.
Used skills • genomics software programmes and programming
o Python, JAVA and/or UNIX
o samtools, variant calling & filtering
Requirements • Knowledge on statistics, plant genetics, genomics and breeding
• Preferably skilled in (genomics software programmes and) programming
o More specific, being familiar to Python, JAVA and/or UNIX
o More specific, being familiar to using samtools, variant calling & filtering