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 .
Valle, C.B., Jank, L. and Resende, R.M.S. (2008) Brachiaria Breeding. In: Resende, R.M.S., Jank, L. and Valle, C.B., Eds., Tropical Forages Breeding, Embrapa Gado de Corte, Campo Grande, 13-53.
Pessoa-Filho, M., Azevedo, A.L.S., Sobrinho, F.S., Gouvea, E.G., Martins, A.M. and Ferreira, M.E. (2015) Genetic Diversity and Structure of Ruzigrass Germplasm Collected in Africa and Brazil. Crop Science, 55, 2736-3745. https://doi.org/10.2135/cropsci2015.02.0096
Miles, J.W. (2007) Apomixis for Cultivar Development in Tropical Forage Grasses. Crop Science, 47, S238-S249. https://doi.org/10.2135/cropsci2007.04.0016IPBS
Jank, L., Barrios, S.C., Valle, C.B., Simeao, R.M. and Alves, G.F. (2014) The Value of Improved Pastures to Brazilian Beef Production. Crop and Pasture Science, 65, 1132-1137. https://doi.org/10.1071/CP13319
Valle, C.B. and Savidan, Y. (1996) Genetics, Cytogenetics, and Reproductive Biology of Brachiaria. In: Miles, J.W., Maass, B.L. and Valle, C.B., Eds., Brachiaria: Biology, Agronomy, and Improvement, EMBRAPA/CIAT, Cali, 147-163.
Lutts, S., Ndikumana, J. and Louant, B.P. (1991) Fertility of Brachiaria ruziziensis in Interspecific Crosses with Brachiaria decumbens and Brachiaria brizantha—Meiotic Behavior, Pollen Viability and Seed Set. Euphytica, 57, 267-274. https://doi.org/10.1007/BF00039673
Ferreira, R.C.U., Cancado, L.J., Valle, C.B., Chiari, L. and de Souza, A.P. (2016) Microsatellite Loci for Urochloa decumbens (Stapf) R.D. Webster and Cross-Amplification in Other Urochloa Species. BMC Research Notes, 9, 152. https://doi.org/10.1186/s13104-016-1967-9
Silva, P.I.T., Martins, A.M., Gouvea, E.G., Pessoa-Filho, M. and Ferreira, M.E. (2013) Development and Validation of Microsatellite Markers for Brachiaria ruziziensis Obtained by Partial Genome Assembly of Illumina Single-End Reads. BMC Genomics, 14, 17. https://doi.org/10.1186/1471-2164-14-17
Worthington, M.L., Heffelfinger, C., Bernal, D., Quintero, C., Zapata, Y.P., Perez, J.G., Vega, J.D., Miles, J., Dellaporta, S. and Tohme, J. (2016) A Parthenogenesis Gene Candidate and Evidence for Segmental Allopolyploidy in Apomictic Brachiaria decumbens. Genetics, 203, 1117-1132. https://doi.org/10.1534/genetics.116.190314
Ishigaki, G., Gondo, T., Ebina, M., Suenaga, K. and Akashi, R. (2010) Estimation of Genome Size in Brachiaria Species. Grassland Science, 56, 240-242. https://doi.org/10.1111/j.1744-697X.2010.00200.x
Bouck, A. and Vision, T. (2007) The Molecular Ecologist’s Guide to Expressed Sequence Tags. Molecular Ecology, 16, 907-924. https://doi.org/10.1111/j.1365-294X.2006.03195.x
Salgado, L.R., Lima, R., Santos, B.F., Shirakawa, K.T., Vilela, M.A., Almeida, N.F., Pereira, R.M., Nepomuceno, A.L. and Chiari, L. (2017) De Novo RNA Sequencing and Analysis of the Transcriptome of Signalgrass (Urochloa decumbens) Roots Exposed to Aluminum. Plant Growth Regulation, 83, 157-170. https://doi.org/10.1007/s10725-017-0291-2
Thiel, T. (2001) MISA: MIcroSAtellite Identification Tool. Version 1.0. In: MISA: MicroSAtellite Identification Tool. Leibniz Institute of Plant Genetics and Crop Plant Research. http://pgrc.ipk-gatersleben.de/misa/
Untergasser, A., Nijveen, H., Rao, X., Bisseling, T., Geurts, R. and Leunissen, J.A.M. (2007) Primer3Plus, an Enhanced Web Interface to Primer3. Nucleic Acids Research, 35, W71-W74. https://doi.org/10.1093/nar/gkm306
Lyons, E., Pedersen, B., Kane, J., Alam, M., Ming, R., et al. (2008) Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids. Plant Physiology, 148, 1772-1781. https://doi.org/10.1104/pp.108.124867
Doyle, J.J. and Doyle, J.L. (1987) A Rapid DNA Isolation Procedure for Small Quantities of Fresh Leaf Tissue. Phytochemical Bulletin, 19, 11-15.
Creste, S., Tulmann Neto, A. and Figueira, A. (2001) Detection of Single Sequence Repeat Polymorphisms in Denaturing Polyacrylamide Sequencing Gels by Silver Staining. Plant Molecular Biology Reporter, 19, 299-306. https://doi.org/10.1007/BF02772828
Finn, R.D., Coggill, P., Eberhardt, R.Y., Eddy, S.R., Mistry, J., Mitchell, A.L., Potter, S.C., Punta, M., Qureshi, M., Sangrador-Vegas, A., Salazar, G.A., Tate, J. and Bateman, A. (2016) The Pfam Protein Families Database: Towards a More Sustainable Future. Nucleic Acids Research, 44, D279-D285. https://doi.org/10.1093/nar/gkv1344
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. and Madden, T. (2009) BLAST+: Architecture and Applications. BMC Bioinformatics, 10, 421. https://doi.org/10.1186/1471-2105-10-421
Goodstein, D.M., Shu, S., Howson, R., Neupane, R., Hayes, R.D., Fazo, J., Mitros, T., Dirks, W., Hellsten, U., Putnam, N. and Rokhsar, D.S. (2012) Phytozome: A Comparative Platform for Green Plant Genomics. Nucleic Acids Research, 40, D1178-D1186. https://doi.org/10.1093/nar/gkr944
R Development Core Team (2016) R: A Language and Environment for Statistical Computing. Version 3.3.4. R Foundation for Stat. Comput., Vienna.
Conner, J.A., Goel, S., Gunawan, G., Cordonnier-Pratt, M.M., Johnson V.E., et al. (2008) Sequence Analysis of Bacterial Artificial Chromosome Clones from the Apospory-Specific Genomic Region of Pennisetum and Cenchrus. Plant Physiology, 147, 1396-1411. https://doi.org/10.1104/pp.108.119081
Eujayl, I., Sorrells, M.E., Baum, M., Wolters, P. and Powell, W. (2002) Isolation of EST-Derived Microsatellite Markers for Genotyping the A and B Genomes of Wheat. Theoretical and Applied Genetics, 104, 399-407. https://doi.org/10.1007/s001220100738
Varshney, R.K., Sigmund, R., Borner, A., Korzun, V., Stein, N., Sorrels, M.E., Langridge, P. and Graner, A. (2005) Interspecific Transferability and Comparative Mapping of Barley EST-SSR Markers in Wheat, Rye and Rice. Plant Science, 168, 195-202. https://doi.org/10.1016/j.plantsci.2004.08.001
Kaur, S., Cogan, N.O., Pembleton, L.W., Shinozuka, M., Savin, K.W., Materne, M. and Forster, J.W. (2011) Transcriptome Sequencing of Lentil Based on Second-Generation Technology Permits Large-Scale Unigene Assembly and SSR Marker Discovery. BMC Genomics, 12, 265. https://doi.org/10.1186/1471-2164-12-265
Jungmann, L., Sousa, A.C.B., Paiva, J., Francisco, P.M., Vigna, B.B.Z., Valle, C.B., Zucchi, M.I. and Souza, A.P. (2009) Isolation and Characterization of Microsatellite Markers for Brachiaria brizantha (Hochst. ex A. Rich.) Stap. Conservation Genetics, 10, 1873-1876. https://doi.org/10.1007/s10592-009-9839-7
Jungmann, L., Vigna, B.B.Z., Paiva, J., Sousa, A.C.B., Valle, C.B., Laborda, P.R., Zucchi, M.I. and Souza, A.P. (2009) Development of Microsatellite Markers for Brachiaria humidicola (Rendle) Schweick. Conservation Genetics Resources, 1, 475-479. https://doi.org/10.1007/s12686-009-9111-y
Vigna, B.B., Alleoni, G.C., Jungmann, L., Valle, C.B. and Souza, A.P. (2011) New Microsatellite Markers Developed from Urochloa humidicola (Poaceae) and Cross Amplification in Different Urochloa Species. BMC Research Notes, 4, 523. https://doi.org/10.1186/1756-0500-4-523
Santos, J.C.S., Barreto, M.A., Oliveira, F.A., Vigna, B.B.Z. and Souza, A.P. (2015) Microsatellite Markers for Urochloa humidicola (Poaceae) and Their Transferability to Other Urochloa Species. BMC Research Notes, 8, 83-95. https://doi.org/10.1186/s13104-015-1044-9
Chabane, K., Ablett, G.A., Cordeiro, G.M., Valkoun, J. and Henry, R.J. (2005) EST versus Genomic Derived Microsatellite Markers for Genotyping Wild and Cultivated Barley. Genetic Resources and Crop Evolution, 52, 903-909. https://doi.org/10.1007/s10722-003-6112-7
Chagné, D., Chaumeil, P., Ramboer, A., Collada, C., Guevara, A., Cervera, M.T., et al. (2004) Cross-Species Transferability and Mapping of Genomic and cDNA SSRs in Pines. Theoretical and Applied Genetics, 109, 1204-1214. https://doi.org/10.1007/s00122-004-1683-z
Jungmann, L., Vigna, B.B., Boldrini, K.R., Sousa, A.C., Valle, C.B., Resende, R.M., Pagliarini, M.S., Zucchi, M.I. and Souza, A.P. (2010) Genetic Diversity and Population Structure Analysis of the Tropical Pasture Grass Brachiaria humidicola Based on Microsatellites, Cytogenetics, Morphological Traits, and Geographical Origin. Genome, 53, 698-709. https://doi.org/10.1139/G10-055
Boldrini, K.R., Pagliarini, M.S. and Valle, C.B. (2009) Meiotic Behavior of a Nonaploid Accession Endorses x = 6 for Brachiaria humidicola (Poaceae). Genetics and Molecular Research, 8, 1444-1450. https://doi.org/10.4238/vol8-4gmr679
Worthington, M.L. and Miles, J.W. (2015) Reciprocal Full-Sib Recurrent Selection and Tools for Accelerating Genetic Gain in Apomictic Brachiaria. In: Budak, H. and Spangenberg, G., Eds., Molecular Breeding of Forage and Turf, Springer International, Cham, 19-30. https://doi.org/10.1007/978-3-319-08714-6_3
Akiyama, Y., Goel, S., Conner, J.A., Hanna, W.W., Yamada-Akiyama, H. and Ozias-Akins, P. (2011) Evolution of the Apomixis Transmitting Chromosome in Pennisetum. BMC Evolutionary Biology, 11, 289. https://doi.org/10.1186/1471-2148-11-289
Zorzatto, C., Chiari, L., Araújo Bitencourt, G., Valle, C.B., Leguizamón, G.O.C., Schuster, I. and Pagliarini, M.S. (2010) Identification of a Molecular Marker Linked to Apomixis in Brachiaria humidicola (Poaceae). Plant Breeding, 129, 734-736. https://doi.org/10.1111/j.1439-0523.2010.01763.x
Pedraza Garcia, F.P. (1995) Genetic Mapping of Apomixis Gene using RAPD Makers. PhD Thesis, Universidad Nacional de Colombia, Palmira, Valle del Cauca.
Ozias-Akins, P., Roche, D. and Hanna, W.W. (1998) Tight Clustering and Hemizygosity of Apomixis-Linked Molecular Markers in Pennisetum squamulatum Implies Genetic Control of Apospory by a Divergent Locus That May Have No Allelic Form in Sexual Genotypes. Proceedings of the National Academy of Sciences, 95, 5127-5132. https://doi.org/10.1073/pnas.95.9.5127
Zhao, K., Aranzana, M.J., Kim, S., Lister, C., Shindo, C., Tang, C., Toomajian, C., Zheng, H., Dean, C., Marjoram, P. and Nordborg, M. (2007) An Arabidopsis Example of Association Mapping in Structured Samples. PLOS Genetics, 3, e4. https://doi.org/10.1371/journal.pgen.0030004