Tall fescue genomic SSR markers: Development and transferability across multiple grass species

Theoretical and Applied Genetics

Volumn 113, Issue 8, 2006, Pages 1449-1458

  Saha, Malay C ^a   Cooper, John D ^a   Mian, M A Rouf ^a,b   Chekhovskiy, Konstantin ^a   May, Gregory D ^a,c  

^a PLANT BIOLOGY DIVISION   (United States)

^b OHIO STATE UNIVERSITY   (United States)

^c NATIONAL CENTER FOR GENOME RESOURCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENES; MAPPING; PLANTS (BOTANY); POPULATION STATISTICS; SET THEORY;

LINKAGE MAPPING; LOCI SEGREGATING; PRIMER PAIRS (PP);

GENETIC ENGINEERING;

PRIMER DNA;

ARTICLE; DNA SEQUENCE; FESCUE; GENE LIBRARY; GENETIC MARKER; GENETIC POLYMORPHISM; GENETICS; GENOME; HORIZONTAL GENE TRANSFER; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; VARIABLE NUMBER OF TANDEM REPEAT;

BASE SEQUENCE; DNA PRIMERS; FESTUCA; GENE TRANSFER, HORIZONTAL; GENETIC MARKERS; GENOME, PLANT; GENOMIC LIBRARY; MINISATELLITE REPEATS; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

FESTUCA ARUNDINACEA; LOLIUM; TRITICUM AESTIVUM;

EID: 33750686637     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-006-0391-2     Document Type: Article

References (46)

1. Ayers NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD (1997) Microsatellite and single nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germplasm. Theor Appl Genet 94:773-781
2. Brunner S, Fengler K, Morgante M, Tingey S, Rafalski A (2005) Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 17:343-360
3. Cai H-W, Yuyama N, Tamaki H, Yoshizawa A (2003) Isolation and characterization of simple sequence repeat markers in the hexaploid forage grass timothy (Phleum pretense L). Theor Appl Genet 107:1337-1349
4. Cho YG, Ishii T, Temnykh S, Chen X, Lopovich L, McCouch SR, Park WD, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713-722
5. Cipriani G, Lot G, Huang W-G, Marrazzo MT, Peterlunger E, Testolin R (1999) AC/GT and AG/CT microsatellite repeats in peach [Prunus persica (L) Batsch]: isolation, characterization and cross-species amplification in Prunus. Theor Appl Genet 99:65-72
6. Cordeiro GM, Maguire TL, Edwards KJ, Henry RJ (1999) Optimisation of a microsatellite enrichment technique in Saccharum spp. Plant Mol Biol Rep 17:225-229
7. Dayanandan S, Bawa KS, Kesseli RV (1997) Conservation of microsatellites among tropical trees (Leguminosae). Am J Bot 84:1658-1663
8. Depeiges A, Goubely C, Lenoir A, Cocherel S, Picard G, Raynal M, Grellet F, Delseny M (1995) Identification of the most represented repeated motifs in Arabidopsis thaliana microsatellite loci. Theor Appl Genet 91:160-168
9. Dirlewanger E, Cosson P, Tavaud M, Aranzana MJ, Poizat C, Zanetto A, Arús P, Laigret F (2002) Development of microsatellite markers in peach [Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry (Prunus avium L). Theor Appl Genet 105:127-138
10. Edwards KJ, Barker JHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 20:758-759
11. Fu H, Dooner HK (2002) Intraspecific violation of genetic colinearity and its implications in maize. Proc Natl Acad Sci USA 99:9573-9578
12. Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci USA 95:1971-1974
13. Gaitán-Solís E, Duque MC, Edwards KJ, Tohme J (2002) Microsatellite repeats in common bean (Phaseolus vulgaris): isolation, characterization, and cross-species amplification in Phaseolus ssp. Crop Sci 42(6):2128-2136
14. Hamilton MB, Pincus EL, DiR=Fiore A, Fleischer RC (1999) A universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. Biotechniques 27(3):500-507
15. Hernández P, Oorado G, Laurie D, Martin A, Snape J (2001) Microsatellites and RFLP probes from maize are efficient sources of molecular markers for the biomass energy crop Miscanthus. Theor Appl Genet 102:616-622
16. Jones ES, Dupal MP, Kölliker R, Drayton MC, Forster JW (2001) Development and characterization of simple sequence repeat (SSR) markers for perennial ryegrass (Lolium perenne L.). Theor Appl Genet 102:405-415
17. Kantety RV, Rota ML, Matthews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501-510
18. Kijas JMH, Flower JCS, Garbett CA, Thomas MR (1994) Enrichment of microsatellites from the citrus genome using biotinylated oligonucleotide sequences bound to streptavidin-coated magnetic particles. Biotechniques 16:656-662
19. Kölliker R, Jones ES, Drayton MC, Dupal MP, Forster JW (2001) Development and characterization of simple sequence repeat (SSR) markers for white clover (Trifolium repens L.). Theor Appl Genet 102:416-424
20. Kubik C, Meyer WA, Gaut BS (1999) Assessing the abundance and polymorphism of simple sequence repeats in perennial ryegrass. Crop Sci 39:1136-1141
21. Kuleung C, Baenziger PS, Dweikat I (2004) Transferability of SSR markers among wheat, rye, and triticale. Theor Appl Genet 108:1147-1150
22. La Rota M, Kantety RV, Yu JK, Sorrells ME (2005) Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice wheat and barley. BMC Genomics 6:23-35
23. Lee JM, Nahm SH, Kim YM, Kim BD (2004) Characterization and molecular genetic mapping of microsatellite loci in pepper. Theor Appl Genet 108:619-627
24. Liu Z-W, Jarret RL, Kresovich S, Duncan RR (1995) Characterization and analysis of simple sequence repeat (SSR) loci in seashore paspalum (Paspalum vaginatum Swartz). Theor Appl Genet 91:47-52
25. Mian MAR, Saha MC, Hopkins AA, Wang Z (2005) Use of tall fescue EST-SSR markers in phylogenetic analysis of cool-season forage grasses. Genome 48:637-647
26. Paterson AH, Lin YR, Li S, Schertz KF, Doebley JF, Pinson SRM, Liu SC, Stansel JW, Irvine JE (1995) Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 269:1714-1717
27. Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A (1998) Cross species amplification of soybean (Glycine max) simple sequence repeat (SSRs) within the genus and other legume genera: Implication for transferability of SSRs in plants. Mol Biol Evol 15(10):1275-1287
28. Pfeiffer A, Olivieri AM, Morgante M (1997) Identification and characterization of microsatellites in Norway spruce (Picea abies K). Genome 40:411-419
29. Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225-238
30. Rafalski JA, Vogel JM, Morgante M, Powell W, Andre C, Tingey SV (1996) Generating and using DNA markers in plants. In: Birren B, Lai E (eds) Non-mammalian genomic analysis: a practical guide. Academic, San Diego, pp 75-135
31. Rallo P, Dorado G, Martin A (2000) Development of simple sequence repeats (SSRs) in olive tree (Olea europaea L). Theor Appl Genet 101:984-989
32. Roa AC, Chavarriaga-Aguirre P, Duque MC, Maya MM, Bonierbale MW, Iglesias C, Tohme J (2000) Cross-species amplification of cassava (Manihot esculenta) (Euphorbiaceae) microsatellites: allelic polymorphism and degree of relationship. Am J Bot 87:1647-1655
33. Saha MC, Mian MAR, Eujayl I, Zwonitzer JC, Wang L, May GD (2004) Tall fescue EST-SSR markers with transferability across several grass species. Theor Appl Genet 109:783-791
34. Saha MC, Mian MAR, Zwonitzer JC, Chekhovskiy K, Hopkins AA (2005) An SSR- and AFLP-based genetic linkage map of tall fescue (Festuca arundinacea Schreb.). Theor Appl Genet 110:323-336
35. Sefc KM, Regner F, Turetschek E, Glössl J, Steinkellner H (1999) Identification of microsatellite sequences in Vitis riparia and their applicability for genotyping of different Vitis species. Genome 42:367-373
36. Sharma AD, Gill PK, Singh P (2002) DNA isolation from dry and fresh samples for polysaccharide-rich plants. Plant Mol Biol Rep 20:415a-415f
37. Sorrells ME, La Rota M, Bermudez-Kandianis CE, Greene RA, Kantety RV, Munkvold JD, Miftahudin , Mahmoud A, Ma X, Gustafson PJ, Qi LL, Echalier B, Gill BS, Matthews DE, Lazo GR, Chao S, Anderson OD, Edwards H, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvorak J, Zhang D, Nguyen HT, Peng J, Lapitan NLV, Gonzalez-Hernandez JL, Anderson JA, Hossain K, Kalavacharla V, Kianian SF, Choi DW, Close TJ, Dilbirligi M, Gill KS, Steber C, Walker-Simmons MK, McGuire PE, Qualset CO (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13:1818-27
38. Taramino G, Tarchini R, Ferrario S, Lee M, Pe' ME (1997) Characterization and mapping of simple sequence repeats (SSRs) in Sorghum bicolor. Theor Appl Genet 95:66-72
39. Temnykh S, Park WD, Ayers N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697-712
40. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411-422
41. Van Deynze AE, Ducovsky J, Gill KS, Nelson JC, Sorrells ME, Dvorak J, Gill BS, Lagudah ES, McCouch SR, Apples R (1995a) Molecular-genetic maps for chromosome 1 in Triticeae species and their relation to chromosomes in rice and oats. Genome 38:45-59
42. Van Deynze AE, Nelson JC, O'Donoughue LS, Ahn SN, Siripoonwiwat W, Harrington SE, Yglesias ES, Braga DP, McCouch SR, Sorrells ME (1995b) Comparative mapping in grasses. Oat relationships. Mol Gen Genet 249:349-356
43. Varshney RK, Sigmund R, Boerner A, Korzun V, Stein N, Sorrells ME, Langridge P, Graner A (2005) Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Sci 168:195-202
44. Warnke SE, Barker RE, Jung G, Sim S-C, Mian MAR, Saha MC, Brilman LA, Dupal MP, Forster JW (2004) Genetic linkage mapping of an annual x perennial ryegrass population. Thero Appl Genet 109:294-304
45. Yu J-K, Dake TM, Singh S, Benscher D, Li W, Gill B, Sorrells ME (2004a) Development and mapping of EST-Derived simple sequence repeat (SSR) markers for hexaploid wheat. Genome 47:805-818
46. Yu J-K, La Rota CM, Kantety RV, Sorrells ME (2004b) EST-derived SSR markers for comparative mapping in wheat and rice. Mol Gen Genet 271:742-751