A Parthenogenesis Gene Candidate and Evidence for Segmental Allopolyploidy in Apomictic Brachiaria decumbens

Abstract

Apomixis, asexual reproduction through seed, enables breeders to identify and faithfully propagate superior heterozygous genotypes by seed without the disadvantages of vegetative propagation or the expense and complexity of hybrid seed production. The availability of new tools such as genotyping by sequencing and bioinformatics pipelines for species lacking reference genomes now makes the construction of dense maps possible in apomictic species, despite complications including polyploidy, multisomic inheritance, self-incompatibility, and high levels of heterozygosity. In this study, we developed saturated linkage maps for the maternal and paternal genomes of an interspecific Brachiaria ruziziensis (R. Germ. and C. M. Evrard) × B. decumbens Stapf. F1 mapping population in order to identify markers linked to apomixis. High-resolution molecular karyotyping and comparative genomics with Setaria italica (L.) P. Beauv provided conclusive evidence for segmental allopolyploidy in B. decumbens, with strong preferential pairing of homologs across the genome and multisomic segregation relatively more common in chromosome 8. The apospory-specific genomic region (ASGR) was mapped to a region of reduced recombination on B. decumbens chromosome 5. The Pennisetum squamulatum (L.) R.Br. PsASGR-BABY BOOM-like (psASGR–BBML)-specific primer pair p779/p780 was in perfect linkage with the ASGR in the F1 mapping population and diagnostic for reproductive mode in a diversity panel of known sexual and apomict Brachiaria (Trin.) Griseb. and P. maximum Jacq. germplasm accessions and cultivars. These findings indicate that ASGR–BBML gene sequences are highly conserved across the Paniceae and add further support for the postulation of the ASGR–BBML as candidate genes for the apomictic function of parthenogenesis.

Genetic Diversity and Population Structure of Brachiaria Species and Breeding Populations

“…Conclusive evidence of segmental allopolyploidy was recently documented in a tetraploid apomictic accession of B. decumbens (CIAT 606, cv. Basilisk) (Worthington et al, 2016). The admixture with B. brizantha observed in the tetraploid apomictic B. decumbens accessions in the STRUCTURE analysis suggests that one subgenome of B. decumbens may be closely related to B. ruziziensis , whereas the other is more similar to B. brizantha .…”

“…CIAT 26179 was classified as an apomictic tetraploid accession of B. brizantha in the EMBRAPA genebank, and this assignment was subsequently confirmed by studies of reproductive mode (Vigna et al, 2011) and chromosome counts (Mendes‐Bonato et al, 2002). However, CIAT 26179 is listed as B. ruziziensis in the CIAT genetic resources database and was classified as sexually reproducing by the diagnostic apomixis marker p779/p780 (Worthington et al, 2016). Similarly, the B. decumbens accession CIAT 26186 was classified as sexually reproducing by marker analysis with p779/p780 but was described as a tetraploid apomict by EMBRAPA (Penteado et al, 2000; Valle et al, 2008).…”

“…Identifying information including species, taxonomic group (Renvoize et al, 1996), geographic coordinates of the collection site, and reproductive mode is provided for the 261 genotypes included in the study in Supplemental Table S1. Reproductive mode was assessed with the primer pair p779/p780, a diagnostic marker for apomixis in Brachiaria , following Worthington et al (2016).…”

Diplosporous development in Boehmeria tricuspis: Insights from de novo transcriptome assembly and comprehensive expression profiling

“…Recently, a study revealed that the PsASGR-BBML gene, which is in perfect linkage with the ASGR of both Pennisetum and Cenchrus , could induce parthenogenesis or the initiation of embryo development from an unfertilised egg cell38. ASGR-BBML was strongly supported as a candidate gene for the apomictic function of parthenogenesis60. In contrast to their function at the stage of parthenogenesis in Pennisetum, AP2 genes are expected to have important functions in diplosporous development in B. tricuspis .…”

Genetic mapping in polyploids

“…This would combine the advantages of true seed production while avoiding the numerous disadvantages of vegetative clones as already discussed. Apomixis has been shown to be under genetic control in multiple species (reviewed in (Bicknell and Catanach, 2015)), with a number of recent genetic mapping studies in tropical polyploid forage grasses such as the tetraploid Brachiaria decumbens or the hexaploid Urochloa humidicola revealing major QTL underlying the trait (Vigna et al, 2016;Worthington et al, 2016). A nice example of where apomixis is actively used in polyploid breeding is in Kentucky bluegrass (Poa pratensis) (Huff, 2010).…”