Rye

RYE-SELECT: Genome-based precision breeding strategies for rye

Persons ins charge: Eva Bauer, Manfred Schönleben, Wiltrud Erath, Chris-Carolin Schön 
Project duration: 01.10.2011 - 30.09.2014 
Project partners: 
KWS-LOCHOW GMBH, Peer Wilde, Viktor Korzun
IPK Gatersleben, Uwe Scholz
Universität Hohenheim, Karl Schmid, Hans-Peter Piepho, Thomas Miedaner
Julius-Kühn Institut in Groß-Lüsewitz, Bernd Hackauf
Project management agency: Project Management Jülich (PTJ)
Funding: Federal Ministry of Education and Research (BMBF)

Project description:

Aims of the project:
Recent developments in high-throughput sequencing and genotyping techniques open new possibilities for genome-wide and target-specific improvement of elite material in rye. One of the most promising genome-based breeding concepts developed during the last decade is genomic selection. The key feature of genomic selection (GS) is the estimation of genomic breeding values (GBVs) from genotypic and phenotypic data in a training population and the subsequent prediction of breeding values of untested individuals with maximum accuracy. In rye, test units are highly heterozygous, breeding populations have low levels of linkage disequilibrium (LD) and an unknown linkage phase of SNPs. In comparison to maize, these factors introduce additional complexity in the estimation of GBVs, underlining the need for a rye-specific optimization of the concept. Recent developments in population genetic methods will help to adapt this highly innovative concept to the specific situation in rye breeding. In addition to genome-wide approaches, the efficient management of “must-have” alleles for traits of agronomic relevance, such as frost tolerance, quality, and efficient pollen-fertility restoration, is of importance for the target-specific improvement of elite hybrid breeding material for German and European markets.
RYE-SELECT aims at developing genome-based breeding strategies by i) improving the molecular toolbox for rye with a high-density SNP genotyping array and target-specific gene-based markers, ii) comprehensively characterising diversity patterns in rye breeding pools using population genetic methods as a prerequisite for the choice of appropriate breeding strategies and germplasm management, iii) evaluating the potential of GS for improving yield and yield stability in rye by adapting and developing state-of-the-art methodology, and iv) identifying and validating genomic regions involved in frost tolerance and fertility restoration as well as yield and quality traits in hybrid rye. 

Organisation:
The project is organized in three work packages (WP). In WP1 we will sequence various rye inbred lines and detect polymorphisms for the development of a high-density genotyping array. In WP2 strategies for Genomic Selection will be developed and implemented in rye breeding, supported by population genetic analyses. WP3 focuses on specific genomic regions harbouring genes for frost tolerance, quality, fertility, and yield components.