Development and validation of microsatellite markers for Brachiaria ruziziensis obtained by partial genome assembly of Illumina single-end reads

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Silva, Pedro I T ^a,b,d   Martins, Alexandre M ^a,b   Gouvea, Ediene G ^a   Pessoa Filho, Marco ^c   Ferreira, Márcio E ^a  

^a EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

^b UNIVERSITY OF BRASILIA   (Brazil)

^c EMBRAPA CERRADOS   (Brazil)

^d DUPONT COMPANY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BRACHIARIA; BRACHIARIA RUZIZIENSIS; DNA SEQUENCE; DNA STRUCTURE; GENE LOCUS; GENE TRANSFER; GENETIC ANALYSIS; GENETIC POLYMORPHISM; MICROSATELLITE MARKER; NUCLEOTIDE SEQUENCE; PLANT GENOME; UNINDEXED SEQUENCE; VALIDATION STUDY;

BRACHIARIA; BREEDING; CHROMOSOME MAPPING; DNA PRIMERS; GENOME, PLANT; GENOMICS; MICROSATELLITE REPEATS; QUANTITATIVE TRAIT LOCI; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

BRACHIARIA; UROCHLOA BRIZANTHA;

EID: 84872187815     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-17     Document Type: Article

References (31)

1. de Lima M, Pessoa M, Neves M, de Carvalho E. Emissões de metano por fermentação entérica e manejo de dejetos de animais. Segundo inventário brasileiro de emissões e remoções antrópicas de gases de efeito estufa 2012, 120. Ministério da Ciência e Tecnologia, Brasília.
2. Barcellos AO, Vilela L, Lupinacci AV. Produção animal e pasto: desafios e oportunidades. Encontro Nacional do Boi Verde - A Pecuária Sustentável: 2001 2001, 29-64. Sindicato Rural de Uberlândia, Uberlândia.
3. Barbosa RA. Morte de pastos de braquiárias 2006, Embrapa Gado de Corte, Campo Grande.
4. Ishigaki G, Gondo T, Ebina M, Suenaga K, Akashi R. Estimation of genome size in Brachiaria species. Grassl Sci 2010, 56(4):240-242.
5. Billotte N, Lagoda PJL, Risterucci AM, Baurens FC. Microsatellite-enriched libraries: applied methodology for the development of SSR markers in tropical crops. Fruits 1999, 54(4):277-288.
6. Ostrander EA, Jong PM, Rine J, Duyk G. Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences. Proceedings Of The National Academy Of Sciences Of The United States Of America 1992, 89(8):3419-3423. 10.1073/pnas.89.8.3419, 48879, 1314388.
7. Paetkau D. Microsatellites obtained using strand extension: an enrichment protocol. Biotechniques 1999, 26(4):690-692. 694-697.
8. Abdelkrim J, Robertson B, Stanton J-A, Gemmell N. Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. Biotechniques 2009, 46(3):185-192. 10.2144/000113084, 19317661.
9. Castoe TA, Poole AW, Gu W, de Koning AP J, Daza JM, Smith EN, Pollock DD. Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Mol Ecol Resour 2010, 10(2):341-347. 10.1111/j.1755-0998.2009.02750.x, 21565030.
10. Csencsics D, Brodbeck S, Holderegger R. Cost-effective, species-specific microsatellite development for the endangered Dwarf Bulrush (Typha minima) using next-generation sequencing technology. J Hered 2010, 101(6):789-793. 10.1093/jhered/esq069, 20562212.
11. Tangphatsornruang S, Somta P, Uthaipaisanwong P, Chanprasert J, Sangsrakru D, Seehalak W, Sommanas W, Tragoonrung S, Srinives P. Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek). BMC Plant Biol 2009, 9:137. 10.1186/1471-2229-9-137, 2788553, 19930676.
12. Zhu H, Senalik D, McCown BH, Zeldin EL, Speers J, Hyman J, Bassil N, Hummer K, Simon PW, Zalapa JE. Mining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.). Theor Appl Genet 2012 Jan, 124(1):87-96.
13. Castoe TA, Poole AW, de Koning APJ, Jones KL, Tomback DF, Oyler-McCance SJ, Fike JA, Lance SL, Streicher JW, Smith EN, et al. Rapid microsatellite identification from illumina paired-end genomic sequencing in two birds and a snake. PLoS One 2012, 7(2):e30953. 10.1371/journal.pone.0030953, 3279355, 22348032.
14. Cançado LJ. Caracterização da diversidade genética molecular em germoplasma de Brachiaria spp 2009, Universidade Estadual de Campinas, Campinas.
15. Jungmann L, Sousa ACB, Paiva J, Francisco PM, Vigna BBZ, do Valle CB, Zucchi MI, DE Souza AP. Isolation and characterization of microsatellite markers for Brachiaria brizantha (Hochst. ex A. Rich.) Stap. Conserv Genet 2009, 10(6):1873-1876.
16. Vigna BBZ, Jungmann L, Francisco PM, Zucchi MI, Valle CB, Souza AP. Genetic diversity and population structure of the Brachiaria brizantha germplasm. Tropical Plant Biology 2011, 4(3-4):157-169.
17. Jungmann L, Vigna BBZ, Paiva J, Sousa ACB, do Valle CB, Laborda PR, Zucchi MI, DE Souza AP. Development of microsatellite markers for Brachiaria humidicola (Rendle) Schweick. Conserv Genet Resour 2009, 1(1):475-479.
18. Vigna BB, Alleoni GC, Jungmann L, do Valle CB, de Souza AP. New microsatellite markers developed from Urochloa humidicola (Poaceae) and cross amplification in different Urochloa species. BMC research notes 2011, 4:523. 10.1186/1756-0500-4-523, 3251623, 22142493.
19. Santana Q, Coetzee M, Steenkamp E, Mlonyeni O, Hammond G, Wingfield M, Wingfield B. Microsatellite discovery by deep sequencing of enriched genomic libraries. Biotechniques 2009, 46(3):217-223. 10.2144/000113085, 19317665.
20. Garg R, Patel RK, Tyagi AK, Jain M. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA research: an international journal for rapid publication of reports on genes and genomes 2011, 18(1):53-63.
21. Wei W, Qi X, Wang L, Zhang Y, Hua W, Li D, Lv H, Zhang X. Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 2011, 12:451. 10.1186/1471-2164-12-451, 3184296, 21929789.
22. O'Bryhim J, Chong JP, Lance SL, Jones KL, Roe KJ. Development and characterization of sixteen microsatellite markers for the federally endangered species: Leptodea leptodon (Bivalvia: Unionidae) using paired-end Illumina shotgun sequencing. Conservation Genetics Resources 2012, 4(3):787-789.
23. Squirrell J, Hollingsworth P, Woodhead M, Russell J, Lowe A, Gibby M, Powell W. How much effort is required to isolate nuclear microsatellites from plants?. Mol Ecol 2003, 12(6):1339-1348. 10.1046/j.1365-294X.2003.01825.x, 12755865.
24. Mayer C. Phobos 2006-2010, 3.3.11 edn.
25. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JAM. Primer3Plus, An enhanced web interface to Primer3. Nucleic Acids Res 2007, 35(Web Server issue):W71-W74. 1933133, 17485472.
26. Keller-Grein G, Maas BL. Natural variation in Brachiaria and existing germplasm collections. Brachiaria: biology, agronomy and improvement 1996, 16-42. CIAT, Cali, Miles J, Maas BL, Valle CB.
27. Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 1987, 19(1):11-15.
28. Ferreira ME, Grattapaglia D. Introdução ao uso de marcadores moleculares em análise genética 1998, Embrapa-SPI, Brasilia.
29. Holleley CE, Geerts PG. Multiplex Manager 1.0: a cross-platform computer program that plans and optimizes multiplex PCR. Biotechniques 2009, 46(7):511-517. 10.2144/000113156, 19594450.
30. Idury RM, Cardon LR. A simple method for automated allele binning in microsatellite markers. Genome Res 1997, 7(11):1104-1109. 310687, 9371746.
31. Liu K, Muse SV. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 2005, 9(21):2128-2129.