Genotyping-by-sequencing based cytoplasmic markers underpin population structural variation of perennial ryegrass

Abstract Chloroplast and mitochondrial genomes provide unique information in studying plant populations because cytoplasmic genes exhibit a different mode of inheritance and a different rate of gene mutation compared to nuclear genes. Despite this, cytoplasmic genomic contributions to plant population performance are largely unexplored because few methods are available to characterize and evaluate cytoplasmic genome-wide variations. Here we have developed cytoplasmic markers based on genotyping-by-sequencing (GBS), which enable us to characterize thousands of samples, to survey gene variants across cytoplasmic genomes, and to monitor within-population variations of chloroplast or mitochondrial origin. Using these cytoplasmic genome-wide markers we have found that within-population differentiations are evident in ryegrass ( Lolium perenne ), beyond the explanation of nuclear markers. Moreover, chloroplast and mitochondrial variations exhibit different patterns, with mitochondrial markers more readily reflecting the maternal origins. Application of GBS-based cytoplasmic markers should facilitate quantifying the contribution of cytoplasmic inheritance to plant performance through selective breeding or under natural selection pressure.