Velmurugan J, Milbourne D, Connolly V, Heslop-Harrison JS, Anhalt UC, Lynch MB, Barth S. 2018. An immortalized genetic mapping population for perennial ryegrass: a resource for phenotyping and complex trait mapping. Frontiers in Plant Science 9: article 717. https://doi.org/10.3389/fpls.2018.00717

To address the lack of a truly portable, universal reference mapping population
for perennial ryegrass, we have been developing a recombinant inbred line (RIL)
mapping population of perennial ryegrass derived via single seed descent from a
well-characterized F2 mapping population based on genetically distinct inbred parents
in which the natural self-incompatibility (SI) system of perennial ryegrass has been
overcome. We examined whether it is possible to create a genotyping by sequencing
(GBS) based genetic linkage map in a small population of the F6 generation of this
population. We used 41 F6 genotypes for GBS with PstI/MspI-based libraries. We
successfully developed a genetic linkage map comprising 6074 SNP markers, placing a
further 22080 presence and absence variation (PAV) markers on the map. We examined
the resulting genetic map for general and RIL specific features. Overall segregation
distortion levels were similar to those experienced in the F2 generation, but segregation
distortion was reduced on linkage group 6 and increased on linkage group 7. Residual
heterozygosity in the F6 generation was observed at a level of 5.4%. There was a high
proportion of chromosomes (30%) exhibiting the intact haplotype of the original inbred
parents of the F1 genotype from which the population is derived, pointing to a tendency
for chromosomes to assort without recombining. This could affect the applicability
of these lines and might make them more suitable for situations where repressed
recombination is an advantage. Inter- and intra-chromosomal linkage disequilibrium
(LD) analysis suggested that the map order was robust. We conclude that this RIL
population, and subsequent F7 and F8 generations will be useful for genetic analysis
and phenotyping of agronomic and biological important traits in perennial ryegrass.

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https://doi.org/10.3389/fpls.2018.00717

Keywords: perennial ryegrass, Lolium perenne, recombinant inbred lines (RIL), genotyping by sequencing, mapping population, phenotyping