Diagnostic Markers for Apospory derived from Saturated Genetic Linkage Maps of a Brachiaria ruziziensis x Brachiaria decumbens Hybrid Population

The availability of new tools such as genotyping-by-sequencing (GBS) and bioinformatics pipelines for species lacking reference genomes makes the construction of dense maps possible in Brachiaria and other polyploid, apomict grass genera. The objectives of this study were to develop saturated linkage maps for the maternal and paternal genomes of an interspecific B. ruziziensis x B. decumbens F₁ mapping population, assess synteny between Brachiaria and foxtail millet and identify diagnostic markers linked to the apospory specific genetic region (ASGR) in B. decumbens. A total of 1920 GBS-derived single dose allele markers were mapped to 70 linkage groups across the maternal and paternal genetic maps. Linkage groups were assigned to chromosomes based on conservation of genome structure between Brachiaria and foxtail millet and shared linkages to double dose allele markers in synthetic autotetraploid B. ruziziensis. Parental GBS read ratios and marker segregation ratios in F₁ progeny support segmental allopolyploidy in B. decumbens, with strong preferential pairing of homeologs across the genome and multisomic segregation most common in chromosome 8. The ASGR was mapped to an 8.3 cM region on B. decumbens linkage group 5c. Six GBS markers linked to the ASGR were converted to diagnostic Kompetitive allele specific PCR (KASP) assays for marker assisted selection. The linkage maps presented in this study provide novel insights on the ploidy and genomic complexity of B. decumbens and make basic and applied research on apomixis in an exciting possibility in Brachiaria.