Development of microsatellite markers for Brachiaria humidicola (Rendle) Schweick

Abstract

We describe the first panel of nuclear simple sequence repeats (SSRs) loci for Brachiaria humidicola (Rendle) Schweick., a warmseason grass with facultative apomixis, variation in ploidy levels (6X-9X), and important forage grass species in the Tropics. Of 38 pairs of primers obtained by using an enriched-library methodology, 27 revealed polymorphism in 58 accessions of the Germplasm Collection of B. humidicola held at Embrapa Beef Cattle, Brazil. Eleven loci amplified in B. dictyoneura, a closely related species with unclear taxonomic boundaries with B. humidicola. Transferability to other three Brachiaria species was also evaluated. The developed microsatellites are potentially useful for genetic studies of B. humidicola, as well as phylogenetic evaluations, conservation and breeding applications.Keywords Urochloa humidicola Á Koroviniagrass Á SSRs Á Taxonomy Á Genetic diversity Brachiaria (Trin.) Griseb. is a large genus of grasses that belongs to the tribe Paniceae, in the subfamily Panicoideae of the family Poaceae. It contains about 100 species distributed throughout the Tropics. Many aspects of taxonomic relationships among Brachiaria species and the related genera Urochloa, Eriochloa and Panicum remain unclear. Such taxonomic issues have been largely discussed since Brachiaria was elevated to the category of genus by Grisebach (1853).Brachiaria humidicola (Rendle) Schweick. is an African perennial stoloniferous species that aposporous pseudogamus apomixis is the predominant reproduction mode. Although apomixes is facultative, in most genotypes it prevails over sexuality.

Molecular Characterizations of Kenyan Brachiaria Grass Ecotypes with Microsatellite (SSR) Markers

“…The PIC value in this study is within the range reported by Silva et al [14], Jungmann et al [15], and Vigan et al [16], but was lower than that found by Jungmann et al [17] and Pessoa-Filho et al [18]. Similarly, the average numbers of allele detected per loci (5.45) was in the range reported by Silva et al [14], Jungmann et al [15], and Vigan et al [16], but was about half and one-third of that reported by Jungmann et al [17] and Pessoa-Filho et al [18], respectively. However, these comparisons between studies may not be conclusive due to differences in types and number of germplasms and markers used among studies.…”

Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes

“…Indeed, while most accessions of U. brizantha and U. decumbens are tetraploid and predominantly apomict, a few diploid sexual accessions of U. decumbens can be found in germplasm collections [89–91] and at least one sexual diploid accession of U. brizantha is available [92, 93]. One hexaploid sexual accession of U. humidicola has also been reported [94]. …”

Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas

“…SSR markers play an important role in germplasm characterization, linkage and QTL map construction, gene flow and mating system evaluations, and marker-assisted selection [85, 86]. In U. humidicola , the currently available SSR markers [11, 21–23] were all developed from enriched genomic libraries.…”

“…The objectives of the present study were to provide novel genetic resources for the species through the de novo assembly of RNA-seq data from the leaves of two divergent genotypes, assess the transcriptomic differences between the genotypes and identify potential functional molecular markers because the genomic single sequence repeat (SSR) developed for U. humidicola [11, 21–23] displays amplification issues in the sexual genotype BH031.…”