Cross-amplification of EST-derived markers among 16 grass species

Field Crops Research

Volumn 118, Issue 1, 2010, Pages 28-35

  Zeid, M ^a   Yu, J K ^a,b   Goldowitz, I ^a   Denton, M E ^a   Costich, Denise E ^a,d   Jayasuriya, C T ^a   Saha, M ^c   Elshire, R ^a   Benscher, D ^a   Breseghello, F ^e   Munkvold, J ^a,f   Varshney, R K ^g   Belay, G ^h   Sorrells, M E ^a  

^a Department of Obstetrics Gynecology   (United States)

^b SYNGENTA CROP PROTECTION   (United States)

^c PLANT BIOLOGY DIVISION   (United States)

^d ROBERT W HOLLEY CENTER FOR AGRICULTURE AND HEALTH   (United States)

^e EMBRAPA ARROZ E FEIJÃO   (Brazil)

^f United States Department of Agriculture Agricultural Research Service and Boyce Thompson Institute for Plant Research   (United States)

^g INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (India)

^h DEBRE ZEIT AGRICULTURAL RESEARCH CENTER   (Ethiopia)

Author keywords

CISP; Comparative mapping; EST SSR; Expressed sequence tag (EST); Homology; Poaceae; Sequence conservation

Indexed keywords

CONSERVATION GENETICS; FORAGE; GENETIC MARKER; GENOME; GRASS; HOMOLOGY; MILLET; MITOCHONDRIAL DNA; POLYMERASE CHAIN REACTION; RICE; SORGHUM;

FESTUCA ARUNDINACEA; PENNISETUM GLAUCUM; PHALARIS; PHALARIS ARUNDINACEA; POACEAE;

EID: 77956877432     PISSN: 03784290     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fcr.2010.03.014     Document Type: Article

References (35)

1. Asp T., Frei U.K., Didion T., Nielsen K.K., Lubberstedt T. Frequency, type, and distribution of EST-SSRs from three genotypes of Lolium perenne, and their conservation across orthologous sequences of Festuca arundinacea, Brachypodium distachyon, and Oryza sativa. BMC Plant Biol. 2007, 7:36.
2. Casler M.D., Phillips M.M., Krohn A.L. DNA polymorphisms reveal geographic races of reed canarygrass. Crop Sci. 2009, 49:2139-2148.
3. Chalhoub B.A., Thibault S., Laucou V., Rameau C., Hofte H., Cousin R. Silver staining and recovery of AFLP (TM) amplification products on large denaturing polyacrylamide gels. Biotechniques 1997, 22:216-220.
4. Feltus F.A., Singh H.P., Lohithaswa H.C., Schulze S.R., Silva T.D., Paterson A.H. A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops. Plant Physiol. 2006, 140:1183-1191.
5. Gaut B.S. Evolutionary dynamics of grass genomes. New Phytologist 2002, 154:15-28.
6. Gimenes M.A., Hoshino A.A., Barbosa A.V.G., Palmieri D.A., Lopes C.R. Characterization and transferability of microsatellite markers of the cultivated peanut (Arachis hypogaea). BMC Plant Biol. 2007, 7:1471-2229.
7. Gupta P.K., Rustgi S., Sharma S., Singh R., Kumar N., Balyan H.S. Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol. Genet. Genom. 2003, 270:315-323.
8. Gupta P.K., Varshney R.K. The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 2000, 113:163-185.
9. Hsiao C., Chatterton N.J., Asay K.H., Jensen K.B. Molecular phylogeny of the Pooideae (Poaceae) based on nuclear rDNA (ITS) sequences. Theor. Appl. Genet. 1995, 90:389-398.
10. Ishikawa G., Nakamura T., Ashida T., Saito M., Nasuda S., Endo T.R., Wu J., Matsumoto T. Localization of anchor loci representing five hundred annotated rice genes to wheat chromosomes using PLUG markers. Theor. Appl. Genet. 2009, 118:499-514.
11. Jensen L.B., Holm P.B., Lubberstedt T. Cross-species amplification of 105 Lolium perenne SSR loci in 23 species within the Poaceae. Mol. Ecol. Notes 2007, 7:1155-1161.
12. Kellogg E.A. Evolutionary history of the grasses. Am. Soc. Plant Biol. 2001, 1198-1205.
13. Khlestkina E.K., Than M.H.M., Pestsova E.G., Röder M.S., Malyshev S.V., Korzun V., Börner A. Mapping of 99 new microsatellite-derived loci in rye (Secale cereale L.) including 39 expressed sequence tags. Theor. Appl. Genet. 2004, 109:725-732.
14. Kindiger B. Cross-species amplification of Lolium microsatellites in Poa ssp. Grassland Sci. 2006, 52:105-115.
15. La Rota M., Kantety R.V., Yu J.K., Sorrells M.E. Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genom. 2005, 6:23.
16. Lavergne S., Molofsky J. Reed canary grass (Phalaris arundinacea) as a biological model in the study of plant invasions. Critical Rev. Plant Sci. 2004, 23:415-429.
17. Mian M.A.R., Saha M.C., Hopkins A.A., Wang Z.Y. Use of tall fescue EST-SSR markers in phylogenetic analysis of cool-season forage grasses. Genome 2005, 48:637-647.
18. Nei M., Li W.H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. 1979, 76:5269-5273.
19. Opanowicz M., Vain P., Draper J., Parker D., Doonan J.H. Brachypodium distachyon: making hay with a wild grass. Trends Plant Sci. 2008, 13:172-177.
20. Parida S.K., Anand Raj Kumar K., Dalal V., Singh N.K., Mohapatra T. Unigene derived microsatellite markers for the cereal genomes. Theor. Appl. Genet. 2006, 112:808-817.
21. Roa A.C., Chavarriaga-Aguirre P., Duque M.C., Maya M.M., Bonierbale M.W., Iglesias C., Tohme J. Cross-species amplification of cassava (Manihot esculenta) (Euphorbiaceae) microsatellites: allelic polymorphism and degree of relationship. Am. J. Bot. 2000, 87:1647-1655.
22. Rohlf F.J. NTSYS-pc, Version 2.10 z 2002, Exeter Software, Setauket, New York.
23. Saha M.C., Mian M.A.R., Eujayl I., Zwonitzer J.C., Wang L., May G.D. Tall fescue EST-SSR markers with transferability across several grass species. Theor. Appl. Genet. 2004, 109:783-791.
24. Sim S.C., Yu J.K., Jo Y., Sorrells M.E., Jung G. Transferability of cereal EST-SSR markers to ryegrass. Genome 2009, 52:431-437.
25. Squirrell J., Hollingsworth P.M., Woodhead M., Russell J., Lowe A.J., Gibby M., Powell W. How much effort is required to isolate nuclear microsatellites from plants?. Mol. Ecol. 2003, 12:1339-1348.
26. Tai T.H., Tanksley S.D. A rapid and inexpensive method for isolation of total DNA from dehydrated plant tissue. Plant Mol. Biol. Rep. 1990, 8:297-303.
27. Temnykh S., Park W.D., Ayres N., Cartinhour S., Hauck N., Lipovich L., Cho Y.G., Ishii T., McCouch S.R. Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 2000, 100:697-712.
28. Thiel T., Michalek W., Varshney R., Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 2003, 106:411-422.
29. Varshney R.K., Graner A., Sorrells M.E. Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 2005, 23:48-55.
30. Wang M.L., Barkley N.A., Yu J.K., Dean R.E., Newman M.L., Sorrells M.E., Pederson G.A. Transfer of simple sequence repeat (SSR) markers from major cereal crops to minor grass species for germplasm characterization and evaluation. Plant Genet. Resour. 2005, 3:45-57.
31. Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., Zeng C., et al. The genomes of Oryza sativa: a history of duplications. PLoS Biol. 2005, 3:e38.
32. Yu J.K., Dake T.M., Singh S., Benscher D., Li W.L., Gill B., Sorrells M.E. Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat. Genome 2004, 47:805-818.
33. Yu J.K., Kantety R.V., Graznak E., Benscher D., Tefera H., Sorrells M.E. A genetic linkage map for tef [Eragrostis tef (Zucc.) Trotter]. Theor. Appl. Genet. 2006, 113:1093-1102.
34. Zhang L.Y., Bernard M., Leroy P., Feuillet C., Sourdille P. High transferability of bread wheat EST-derived SSRs to other cereals. Theor. Appl. Genet. 2005, 111:677-687.
35. Zhu W., Buell C.R. Improvement of whole-genome annotation of cereals through comparative analyses. Genome Res. 2007, 17:299-310.