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Background  The apomictic reproductive mode of  Brachiaria  (syn.  Urochloa ) forage species allows breeders to faithfully propagate heterozygous genotypes through seed over multiple generations. In  Brachiaria , reproductive mode segregates as single dominant locus, the apospory-specific genomic region (ASGR). The AGSR has been mapped to an area of reduced recombination on  Brachiaria decumbens  chromosome 5. A primer pair designed within  ASGR-BABY BOOM-like  ( BBML ), the candidate gene for the parthenogenesis component of apomixis in  Pennisetum squamulatum,  was diagnostic for reproductive mode in the closely related species  B. ruziziensis ,  B. brizantha , and  B. decumbens . In this study, we used a mapping population of the distantly related commercial species  B. humidicola  to map the ASGR and test for conservation of  ASGR-BBML  sequences across  Brachiaria  species.    Results  Dense genetic maps were constructed for the maternal and paternal genomes of a hexaploid (2n = 6x = 36)  B. humidicola  F 1  mapping population ( n  = 102) using genotyping-by-sequencing, simple sequence repeat, amplified fragment length polymorphism, and transcriptome derived single nucleotide polymorphism markers. Comparative genomics with  Setaria italica  provided confirmation for x = 6 as the base chromosome number of  B. humidicola . High resolution molecular karyotyping indicated that the six homologous chromosomes of the sexual female parent paired at random, whereas preferential pairing of subgenomes was observed in the apomictic male parent. Furthermore, evidence for compensated aneuploidy was found in the apomictic parent, with only five homologous linkage groups identified for chromosome 5 and seven homologous linkage groups of chromosome 6. The ASGR mapped to  B. humidicola  chromosome 1, a region syntenic with chromosomes 1 and 7 of  S. italica . The  ASGR-BBML  specific PCR product cosegregated with the ASGR in the F 1  mapping population, despite its location on a different carrier chromosome than  B. decumbens .    Conclusions  The first dense molecular maps of  B. humidicola  provide strong support for cytogenetic evidence indicating a base chromosome number of six in this species. Furthermore, these results show conservation of the ASGR across the Paniceae in different chromosomal backgrounds and support postulation of the  ASGR-BBML  as candidate genes for the parthenogenesis component of apomixis.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5392-4) contains supplementary material, which is available to authorized users.

Translocation of a parthenogenesis gene candidate to an alternate carrier chromosome in apomictic Brachiaria humidicola