Genetic linkage mapping in Megathyrsus maximus (Jacq.) with multiple dosage markers

Megathyrsus maximus (Jacq.), commonly known as guinea grass, is a forage crop widely used to form pastures and feed livestock. The species stands out for presenting high yield and nutritional quality in the leaves and its ability to be clonally propagated by seeds. In this work, we construct a dense and informative genetic linkage map for M. maximus using multiple dosage markers. We sequenced DNA from leaf samples of 224 individuals from a biparental cross between two tetraploid genotypes, then analyzed the raw sequencing data to find variants and call dosage-based genotypes using four related reference genomes. With the multiple dosage genotypes for both parents and all individuals, we constructed a highly informative genetic linkage map using state-of-the-art methods coupled with the multipoint Hidden Markov Model approach. We present the densest and most informative genetic linkage map to date for the species, with 7,095 markers distributed across eight homology groups, spanning 1573.31 cM of the genome. Both parents and all individuals in the mapping population were phased according to the species' ploidy level. There was no evidence of double-reduction or preferential pairing in the studied population. The linkage analysis provided in this work can help unravel the evolutionary pathway of the species, understand the genetic behavior of quantitative traits, assist in the assembly of reference genomes, and support the adoption of genomics-assisted selection strategies in M. maximus breeding programs.