Development, Validation and Characterization of Genic Microsatellite Markers in <i>Urochloa</i> Species

Abstract

Urochloa (syn. Brachiaria) cultivars represent 85% of tropical pastures occupying 114 million hectares of cultivated grasslands in Brazil. Despite the commercial importance of the Urochloa species, low molecular information is available and is far from saturating the genome. Investigating and obtaining more markers associated to characteristics of difficult and late expression can benefit in accelerating breeding programs of more important species. Aiming to increase the number of molecular markers, genic microsatellite markers were obtained from transcriptome of U. decumbens and analyzed for their cross-amplification to U. brizantha, U. humidicola and U. ruziziensis. Genic microsatellite markers were isolated from a transcriptome obtained of U. decumbens "Basilisk" roots. Specific primers were designed for one hundred loci, and 32 were polymorphic presenting polymorphism informative content values ranging of 0.12 to 0.81 (mean 0.54). Amplified microsatellite regions yield an average of 4.44 alleles per locus (ranging of 1 to 13). Cross-amplification to U. brizantha, U. humidicola and U. ruziziensis were successfully performed, although the number of the loci transferred varied among them. Multiple Correspondence Analysis revealed three distinct groups separating accessions and species. Four genetic markers presented high potential to distinguish sexual and apomictic accessions of Urochloa and must be further investigated. The genic markers identified in this study are the first set of expressed sequence tagged molecular markers for Urochloa species.

An Overview of the Genetics and Genomics of the Urochloa Species Most Commonly Used in Pastures

“…In addition, the analysis showed that U. brizantha , U. decumbens , and U. ruziziensis were genetically closer to each other than to U. humidicola . This finding has also been observed in later studies using SSR markers ( Jungmann et al, 2009a ; Silva et al, 2013 ; Santos et al, 2015a ; Ferreira et al, 2016 ; Triviño et al, 2017 ; Pessoa-Filho et al, 2017 ; Souza et al, 2018 ).…”

“…The Embrapa collection has been evaluated in terms of morphological and agronomic characteristics, reproductive mode (apomictic or sexual), cytogenetics, and genetic diversity, this one mainly involving the use of molecular markers. (e.g., Valle and Savidan, 1996 ; Mendes-Bonato et al, 2002a , b ; Boldrini et al, 2006 ; Risso-Pascotto et al, 2006 ; Nielen et al, 2009 ; Ambiel et al, 2010 ; Jungmann et al, 2010 ; Azevedo et al, 2011 ; Boldrini et al, 2011a ; Vigna et al, 2011a ; Garcia et al, 2013 ; Pessoa-Filho et al, 2015 ; Santos et al, 2015a ; de Paula et al, 2017 ; Souza et al, 2018 ; Corrêa et al, 2020 ; Moraes et al, 2021 ). Based on morphological and agronomic traits, U. brizantha exhibited the greatest variation, which reflects the larger number of accessions and the greater inherent genetic variability.…”

“…These studies revealed significant genetic diversity between and within the main Urochloa species, and this finding has also been observed phenotypically. Hundreds of SSR markers are available specifically for Urochloa species, and many of these markers are transferable to different species ( Jungmann et al, 2009a , b ; Vigna et al, 2011b ; Silva et al, 2013 ; Santos et al, 2015a ; Ferreira et al, 2016 ; Souza et al, 2018 ; Table 4 ). Therefore, further studies must be carried out with the available molecular markers, mainly involving characterization of the entire germplasms.…”

Genetic Mapping With Allele Dosage Information in Tetraploid Urochloa decumbens (Stapf) R. D. Webster Reveals Insights Into Spittlebug (Notozulia entreriana Berg) Resistance

“…In this scenario, the number of currently available molecular genetic resources is limited. Previous molecular studies have increased knowledge of U. decumbens genetics, including the development of sets of microsatellite markers (Ferreira et al, 2016; Souza et al, 2018) and the first transcriptome (Salgado et al, 2017) of the species as well as linkage maps from the interspecific progeny of U. decumbens × U. ruziziensis (Worthington et al, 2016). Other studies with molecular markers have analyzed the genetic relationships of this species to other species in the Urochloa genus (Almeida et al, 2011; Pessoa-Filho et al, 2017; Triviño et al, 2017).…”