Abstract
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.
Highlights
Genetic linkage mapping in segregating populations is one of the classic approaches to gain insights into the genetic control of key characteristics in a species, and can form the basis of molecular marker-assisted selection in plant breeding
Family-based linkage (FBL) studies continue to be extremely important in genetic analysis of perennial ryegrass
This has been driven by a mixture of the continuously dropping costs associated with saturating genomes with markers, and the precision of genome wide association (GWAS), combined with the fact that the use of diverse germplasm panels allows the discovery of a greater number of QTLs relative to biparentally derived populations
Summary
Genetic linkage mapping in segregating populations is one of the classic approaches to gain insights into the genetic control of key characteristics in a species, and can form the basis of molecular marker-assisted selection in plant breeding. Seed propagated, immortalized populations for perennial ryegrass would be very useful for trait dissection. In addition to immortalization, RILs offer an advantage in that the additional number of recombination events experienced per genotype during recurrent rounds of selfpollination/inbreeding required to produce them increases the resolving power of the resulting mapping populations and allows fine mapping of QTL with fewer individuals (Takuno et al, 2012). In addition to increasing the genetic map resolution for detecting QTLs, RILs are fixed and thereby provide an immortalized reference mapping population which can be genotyped once and can be phenotyped multiple times for different traits under different environments
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