Skip Navigation

DNA Research 2002 9(6):199-207; doi:10.1093/dnares/9.6.199
© 2002 by Kazusa DNA Research Institute
This Article
Right arrow FREE Full Text (PDF) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (300)
Right arrow Request Permissions
Google Scholar
Right arrow Articles by McCouch, S. R.
Right arrow Articles by Stein, L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by McCouch, S. R.
Right arrow Articles by Stein, L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Development and Mapping of 2240 New SSR Markers for Rice (Oryza sativa L.)

Susan R. McCouch1,*, Leonid Teytelman2, Yunbi Xu3, Katarzyna B. Lobos3, Karen Clare3, Mark Walton3, Binying Fu4, Reycel Maghirang4, Zhikang Li4, Yongzhong Xing5, Qifa Zhang5, Izumi Kono6, Masahiro Yano7, Robert Fjellstrom8, Genevieve DeClerck9, David Schneider9, Samuel Cartinhour9, Doreen Ware2 and Lincoln Stein2

1Plant Breeding Dept, Cornell University Ithaca, NY 14853-1901, USA
2Cold Spring Harbor Lab P.O. Box 100, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
3RiceTec, Inc. P.O. Box 1305, Alvin, Texas 77512, USA
4International Rice Research Institute P.O. Box 933, Manila 1099, Philippines
5National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University Wuhan 430070, China
6Institute of the Society for Tecno-innovation of Agriculture, Forestry and Fisheries (STAFF) 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
7Applied Genomics Laboratory, Department of Molecular Genetics, National Institute of Agrobiological Sciences 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
8USDA-ARS, Rice Research Unit 1509 Aggie Dr., Beaumont, TX 77713, USA
9USDA Center for Agricultural Bioinformatics, Theory Center, Cornell University Ithaca, NY 14850-1901, USA

* To whom correspondence should be addressed. 240 Emerson Hall, Ithaca, NY 14853-1901. Tel. +1-607-255-0420, Fax. +1-607-255-6683, E-mail: SRM4{at}cornell.edu

A total of 2414 new di-, tri- and tetra-nucleotide non-redundant SSR primer pairs, representing 2240 unique marker loci, have been developed and experimentally validated for rice (Oryza sativa L.). Duplicate primer pairs are reported for 7% (174) of the loci. The majority (92%) of primer pairs were developed in regions flanking perfect repeats ≥ 24 bp in length. Using electronic PCR (e-PCR) to align primer pairs against 3284 publicly sequenced rice BAC and PAC clones (representing about 83% of the total rice genome), 65% of the SSR markers hit a BAC or PAC clone containing at least one genetically mapped marker and could be mapped by proxy. Additional information based on genetic mapping and "nearest marker" information provided the basis for locating a total of 1825 (81%) of the newly designed markers along rice chromosomes. Fifty-six SSR markers (2.8%) hit BAC clones on two or more different chromosomes and appeared to be multiple copy. The largest proportion of SSRs in this data set correspond to poly(GA) motifs (36%), followed by poly(AT) (15%) and poly(CCG) (8%) motifs. AT-rich microsatellites had the longest average repeat tracts, while GC-rich motifs were the shortest. In combination with the pool of 500 previously mapped SSR markers, this release makes available a total of 2740 experimentally confirmed SSR markers for rice, or approximately one SSR every 157 kb.

Key words: simple sequence repeats (SSR); rice (Oryza sativa L.); electronic PCR (e-PCR)


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Plant Cell PhysiolHome page
Y. Makita, N. Kobayashi, Y. Mochizuki, Y. Yoshida, S. Asano, N. Heida, M. Deshpande, R. Bhatia, A. Matsushima, M. Ishii, et al.
PosMed-plus: An Intelligent Search Engine that Inferentially Integrates Cross-Species Information Resources for Molecular Breeding of Plants
Plant Cell Physiol., July 1, 2009; 50(7): 1249 - 1259.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
J.-i. Yonemaru, T. Ando, T. Mizubayashi, S. Kasuga, T. Matsumoto, and M. Yano
Development of Genome-wide Simple Sequence Repeat Markers Using Whole-genome Shotgun Sequences of Sorghum (Sorghum bicolor (L.) Moench)
DNA Res, June 1, 2009; 16(3): 187 - 193.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
Y. Monden, K. Naito, Y. Okumoto, H. Saito, N. Oki, T. Tsukiyama, O. Ideta, T. Nakazaki, S. R. Wessler, and T. Tanisaka
High Potential of a Transposon mPing as a Marker System in japonica x japonica Cross in Rice
DNA Res, April 1, 2009; 16(2): 131 - 140.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
A. Sharma, A. M. McClung, S. R. M. Pinson, J. L. Kepiro, A. R. Shank, R. E. Tabien, and R. Fjellstrom
Genetic Mapping of Sheath Blight Resistance QTLs within Tropical Japonica Rice Cultivars
Crop Sci., January 28, 2009; 49(1): 256 - 264.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
E. M. Septiningsih, A. M. Pamplona, D. L. Sanchez, C. N. Neeraja, G. V. Vergara, S. Heuer, A. M. Ismail, and D. J. Mackill
Development of submergence-tolerant rice cultivars: the Sub1 locus and beyond
Ann. Bot., January 1, 2009; 103(2): 151 - 160.
[Abstract] [Full Text] [PDF]

Home page
 Mol PlantHome page
J.-J. Luo, W. Hao, J. Jin, J.-P. Gao, and H.-X. Lin
Fine Mapping of Spr3, a Locus for Spreading Panicle from African Cultivated Rice (Oryza glaberrima Steud.)
Mol Plant, September 1, 2008; 1(5): 830 - 838.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
X. Wan, J. Weng, H. Zhai, J. Wang, C. Lei, X. Liu, T. Guo, L. Jiang, N. Su, and J. Wan
Quantitative Trait Loci (QTL) Analysis For Rice Grain Width and Fine Mapping of an Identified QTL Allele gw-5 in a Recombination Hotspot Region on Chromosome 5
Genetics, August 1, 2008; 179(4): 2239 - 2252.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
X.-Y. Gu, E. B. Turnipseed, and M. E. Foley
The qSD12 Locus Controls Offspring Tissue-Imposed Seed Dormancy in Rice
Genetics, August 1, 2008; 179(4): 2263 - 2273.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
K. K. Jena and D. J. Mackill
Molecular Markers and Their Use in Marker-Assisted Selection in Rice
Crop Sci., July 1, 2008; 48(4): 1266 - 1276.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
C. Chen, Q. Yu, S. Hou, Y. Li, M. Eustice, R. L. Skelton, O. Veatch, R. E. Herdes, L. Diebold, J. Saw, et al.
Construction of a Sequence-Tagged High-Density Genetic Map of Papaya for Comparative Structural and Evolutionary Genomics in Brassicales
Genetics, December 1, 2007; 177(4): 2481 - 2491.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
G. Hu, E.W. Jackson, and J. M. Bonman
Expansion of PCR-based Marker Resources in Oat by Surveying Genome-Derived SSR Markers from Barley and Wheat
Crop Sci., September 1, 2007; 47(5): 2004 - 2012.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
Z. Wu, X. Zhang, B. He, L. Diao, S. Sheng, J. Wang, X. Guo, N. Su, L. Wang, L. Jiang, et al.
A Chlorophyll-Deficient Rice Mutant with Impaired Chlorophyllide Esterification in Chlorophyll Biosynthesis
Plant Physiology, September 1, 2007; 145(1): 29 - 40.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
Z. Zhang, Y. Deng, J. Tan, S. Hu, J. Yu, and Q. Xue
A Genome-wide Microsatellite Polymorphism Database for the Indica and Japonica Rice
DNA Res, April 23, 2007; (2007) dsm005v1.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
J. Bernier, A. Kumar, V. Ramaiah, D. Spaner, and G. Atlin
A Large-Effect QTL for Grain Yield under Reproductive-Stage Drought Stress in Upland Rice
Crop Sci., March 1, 2007; 47(2): 507 - 516.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
L. E. Giarrocco, M. A. Marassi, and G. L. Salerno
Assessment of the Genetic Diversity in Argentine Rice Cultivars with SSR Markers
Crop Sci., March 1, 2007; 47(2): 853 - 858.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
P. Jayamani, S. Negrao, M. Martins, B. Macas, and M. M. Oliveira
Genetic Relatedness of Portuguese Rice Accessions from Diverse Origins as Assessed by Microsatellite Markers
Crop Sci., March 1, 2007; 47(2): 879 - 884.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
P. Rajendrakumar, A. K. Biswal, S. M. Balachandran, K. Srinivasarao, and R. M. Sundaram
Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions
Bioinformatics, January 1, 2007; 23(1): 1 - 4.
[Abstract] [Full Text] [PDF]

Home page
 J BiochemHome page
Y. Sato, K. Mitomi, T. Sunami, J. Kondo, and A. Takenaka
DNA Octaplex Formation with an I-Motif of Water-Mediated A-Quartets: Reinterpretation of the Crystal Structure of d(GCGAAAGC)
J. Biochem., December 1, 2006; 140(6): 759 - 762.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
G. C. Eizenga, H. A. Agrama, F. N. Lee, W. Yan, and Y. Jia
Identifying Novel Resistance Genes in Newly Introduced Blast Resistant Rice Germplasm
Crop Sci., July 25, 2006; 46(5): 1870 - 1878.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
G. He, X. Luo, F. Tian, K. Li, Z. Zhu, W. Su, X. Qian, Y. Fu, X. Wang, C. Sun, et al.
Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice
Genome Res., May 1, 2006; 16(5): 618 - 626.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J.-H. Mun, D.-J. Kim, H.-K. Choi, J. Gish, F. Debelle, J. Mudge, R. Denny, G. Endre, O. Saurat, A.-M. Dudez, et al.
Distribution of Microsatellites in the Genome of Medicago truncatula: A Resource of Genetic Markers That Integrate Genetic and Physical Maps
Genetics, April 1, 2006; 172(4): 2541 - 2555.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
M. T. Sweeney, M. J. Thomson, B. E. Pfeil, and S. McCouch
Caught Red-Handed: Rc Encodes a Basic Helix-Loop-Helix Protein Conditioning Red Pericarp in Rice
PLANT CELL, February 1, 2006; 18(2): 283 - 294.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
B. Yue, W. Xue, L. Xiong, X. Yu, L. Luo, K. Cui, D. Jin, Y. Xing, and Q. Zhang
Genetic Basis of Drought Resistance at Reproductive Stage in Rice: Separation of Drought Tolerance From Drought Avoidance
Genetics, February 1, 2006; 172(2): 1213 - 1228.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
X.-Y. Gu, S. F. Kianian, and M. E. Foley
Phenotypic Selection for Dormancy Introduced a Set of Adaptive Haplotypes From Weedy Into Cultivated Rice
Genetics, October 1, 2005; 171(2): 695 - 704.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
J. M. Wan, Y. J. Cao, C. M. Wang, and H. Ikehashi
Quantitative Trait Loci Associated with Seed Dormancy in Rice
Crop Sci., February 23, 2005; 45(2): 712 - 716.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
H. Lu, M. A. Redus, J. R. Coburn, J. N. Rutger, S. R. McCouch, and T. H. Tai
Population Structure and Breeding Patterns of 145 U.S. Rice Cultivars Based on SSR Marker Analysis
Crop Sci., January 1, 2005; 45(1): 66 - 76.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
S. Sato, S. Isobe, E. Asamizu, N. Ohmido, R. Kataoka, Y. Nakamura, T. Kaneko, N. Sakurai, K. Okumura, I. Klimenko, et al.
Comprehensive Structural Analysis of the Genome of Red Clover (Trifolium pratense L.)
DNA Res, January 1, 2005; 12(5): 301 - 364.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J. Li, M. Thomson, and S. R. McCouch
Fine Mapping of a Grain-Weight Quantitative Trait Locus in the Pericentromeric Region of Rice Chromosome 3
Genetics, December 1, 2004; 168(4): 2187 - 2195.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
Y. Xu, H. Beachell, and S. R. McCouch
A Marker-Based Approach to Broadening the Genetic Base of Rice in the USA
Crop Sci., November 1, 2004; 44(6): 1947 - 1959.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
J. F. Ma, N. Mitani, S. Nagao, S. Konishi, K. Tamai, T. Iwashita, and M. Yano
Characterization of the Silicon Uptake System and Molecular Mapping of the Silicon Transporter Gene in Rice
Plant Physiology, October 1, 2004; 136(2): 3284 - 3289.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
R. Fjellstrom, C. A. Conaway-Bormans, A. M. McClung, M. A. Marchetti, A. R. Shank, and W. D. Park
Development of DNA Markers Suitable for Marker Assisted Selection of Three Pi Genes Conferring Resistance to Multiple Pyricularia grisea Pathotypes
Crop Sci., September 1, 2004; 44(5): 1790 - 1798.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
Y.-J. Shen, H. Jiang, J.-P. Jin, Z.-B. Zhang, B. Xi, Y.-Y. He, G. Wang, C. Wang, L. Qian, X. Li, et al.
Development of Genome-Wide DNA Polymorphism Database for Map-Based Cloning of Rice Genes
Plant Physiology, July 1, 2004; 135(3): 1198 - 1205.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
X.-Y. Gu, S. F. Kianian, and M. E. Foley
Multiple Loci and Epistases Control Genetic Variation for Seed Dormancy in Weedy Rice (Oryza sativa)
Genetics, March 1, 2004; 166(3): 1503 - 1516.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
C. A. Whitelaw, W. B. Barbazuk, G. Pertea, A. P. Chan, F. Cheung, Y. Lee, L. Zheng, S. van Heeringen, S. Karamycheva, J. L. Bennetzen, et al.
Enrichment of Gene-Coding Sequences in Maize by Genome Filtration
Science, December 19, 2003; 302(5653): 2118 - 2120.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
V. C. Andaya and D. J. Mackill
Mapping of QTLs associated with cold tolerance during the vegetative stage in rice
J. Exp. Bot., November 1, 2003; 54(392): 2579 - 2585.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
F. Y. Hu, D. Y. Tao, E. Sacks, B. Y. Fu, P. Xu, J. Li, Y. Yang, K. McNally, G. S. Khush, A. H. Paterson, et al.
Convergent evolution of perenniality in rice and sorghum
PNAS, April 1, 2003; 100(7): 4050 - 4054.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.