Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat (original) (raw)
References
Akhunov ED, et al (2003) The organization and rate of evolution of the wheat genome are correlated with recombination rates along chromosome arms. Genome Res (http://www.genome.org/cgi/doi/10.1101/gr.808603)
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic Local Alignment Search Tool. J Mol Biol 215:403–410 ArticleCASPubMed Google Scholar
Bachem CWB, Van der Hoeven RS, de Brujin SM, Vreugdenhill D, Zabeau M, Visser RGF (1996) Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J 9:745–753 CASPubMed Google Scholar
Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331 CASPubMed Google Scholar
Brown GR, Kadel EE III, Bassoni DL, Kiehne KL, Temesgen B, van Buijtenen JP, Sewell MM, Marshall KA, Neale DB (2001) Anchor reference loci in loblolly pine ( Pinus taeda L.) for integrating pine genomics. Genetics 159:799–809 Google Scholar
Burstin J, Deniot G, Potier J, Winachter C, Aubert G, Baranger A (2001) Microsatellite polymorphism in Pisum sativum. Plant Breed 120:311–317 Article Google Scholar
Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156:847–854 CASPubMed Google Scholar
Cho YG, Ishii T, Temnykh S, Chen X, Lipovich 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 CAS Google Scholar
Cordeiro GM, Casu R, McIntyre CL, Manners JM, Henry RJ (2001) Microsatellite markers from sugarcane ( Saccharum spp.) ESTs cross transferable to Erianthus and sorghum. Plant Sci 160:1115–1123 CASPubMed Google Scholar
Edwards KJ, Mogg R (2001) Plant genotyping by analysis of single nucleotide polymorphisms. In: Henry RJ (ed) Plant genotyping: the DNA fingerprinting of plants. CABI, Wallingford, UK, pp 1–13
Eujayl I, Sorrells ME, Baum M, Wolters P, Powell W (2002) Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor Appl Genet 104:339–407 Article Google Scholar
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 Google Scholar
Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185 ArticleCAS Google Scholar
Gupta PK, et al (2002) Genetic mapping of 66 new microsatellite (SSR) loci in bread wheat. Theor Appl Genet 105:413–422 Article Google Scholar
Holton TA, Christopher JT, McClure L, Harker N, Henry RJ (2002) Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat. Mol Breed 9:63–71 CAS Google Scholar
International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860–920 CASPubMed Google Scholar
Jaccard P (1908) Nouvelles recherches sur la distribution florale. Bull Soc Vand Sci Nat 4:223–270 Google Scholar
Kantety RV, La Rota M, 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 ArticleCASPubMed Google Scholar
Maestri E, Malcevschi A, Massari A, Marmiroli N (2002) Genome analysis of cultivated barley ( Hordeum vulgare) using sequence-tagged molecular markers. Estimates based on divergence based on RFLP and PCR markers derived from stress-responsive genes, and simple sequence repeats (SSRs). Mol Genet Genomics 267:186–201 ArticleCASPubMed Google Scholar
Metzgar D, Bytof J, Wills C (2000) Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res 10:72–80 CASPubMed Google Scholar
Mogg R, Batley J, Hanley S, Edwards D, O'Sullivan H, Edwards KJ (2002) Characterization of the flanking regions of Zea mays microsatellites reveals a large number of useful sequence polymorphisms. Theor Appl Genet 105:532–543 Article Google Scholar
Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with non-repetitive DNA in plant genomes. Nature Genet 30:194–200 CASPubMed Google Scholar
Prasad M, Varshney RK, Kumar A, Balyan HS, Sharma PC, Edwards KJ, H-Singh, Dhaliwal HS, Roy JK, Gupta PK (1999) A microsatellite marker associated with a QTL for grain protein content on chromosome arm 2DL of bread wheat. Theor Appl Genet 99:341–345 Article Google Scholar
Prasad M, Varshney RK, Roy JK, Balyan HS, Gupta PK (2000) The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat. Theor Appl Genet 100:584–592 CAS Google Scholar
Roy JK, Prasad M, Varshney RK, Balyan HS, Blake TK, Dhaliwal HS, Singh H, Edwards KJ, Gupta PK (1999) Identification of microsatellite on chromosome 6B and a STS on 7D of bread wheat showing an association with preharvest sprouting tolerance. Theor Appl Genet 99:336–340 Article Google Scholar
Roy JK, Balyan HS, Prasad M, Gupta PK (2002) Use of SAMPL for a study of polymorphism, genetic diversity and possible gene tagging. Theor Appl Genet 104:465–472 Article Google Scholar
Roy JK, Lakshmikumaran M, Balyan HS, Gupta PK (2004) AFLP-based genetic diversity and its comparison with diversity based on SSR, SAMPL and phenotypic traits in bread wheat. Biochem Genet, in press
Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726 CAS Google Scholar
Sneath PHA, Sokol RR (1973) Numerical taxonomy. WH Freeman, San Francisco
Somers DJ, Kirkpatrick R, Moniwa M, Walsh A (2003) Mining single nucleotide polymorphisms from hexaploid wheat ESTs. Genome 49:431–437 Article Google Scholar
Stack S, Campbell L, Henderson K, Eujayl I, Hanafey M, Powell W, Wolter P (2000) Development of EST-derived microsatellite markers for mapping and germplasm analysis in wheat. In: Abstracts of Plant and Animal Genome VIII, January 9–12, 2000, San Diego
Suarez MC, Bernal A, Gutierrez, Tohme J, Fregene M (2000) Developing expressed sequence tags (ESTs) from polymorphic transcript-derived fragments (TDFs) in cassava ( Manihot esculenta Crantz). Genome 43:62–67 ArticleCASPubMed Google Scholar
Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST database for the development and characterization of gene derived SSR-markers in barley ( Hordeum vulgare L.). Theor Appl Genet 106:411–422 CASPubMed Google Scholar
Varshney RK, Kumar A, Balyan HS, Roy JK, Prasad M, Gupta PK (2000) Characterization of microsatellites and development of chromosome specific STMS markers in bread wheat. Plant Mol Biol Rep 18:5-16 CAS Google Scholar
Varshney RK, Thiel T, Stein N, Langridge P, Graner A (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 7:537–546 CASPubMed Google Scholar