Genetics, Vol. 148, 479-494, January 1998, Copyright © 1998, Genetics Society of America

A High-Density Rice Genetic Linkage Map with 2275 Markers Using a Single F2 Population

Yoshiaki Harushimaa, Masahiro Yanoa, Ayahiko Shomuraa, Mikiko Satoa, Tomotoshi Shimanoa, Yoshihide Kubokia, Toshio Yamamotoa, Shao Yang Lina, Baltazar A. Antonioa, Arnold Parcob, Hiromi Kajiyaa, Ning Huangb, Kimiko Yamamotoa, Yoshiaki Nagamuraa, Nori Kurataa, Gurdev S. Khushb, and Takuji Sasakia
a Rice Genome Research Program, National Institute of Agrobiological Resources/Institute of Society for Techno-Innovation of Agriculture, Forestry, and Fisheries, Tsukuba, Ibaraki 305, Japan,
b International Rice Research Institute, Manila, Philippines

Corresponding author: Masahiro Yano, Rice Genome Research Program, National Institute of Agrobiological Resources, 2-1-2 Kannondai, Tsukuba, Ibaraki 305, Japan, myano{at}abr.affrc.go.jp (E-mail).

Communicating editor: J. A. BIRCHLER

A 2275-marker genetic map of rice (Oryza sativa L.) covering 1521.6 cM in the Kosambi function has been constructed using 186 F2 plants from a single cross between the japonica variety Nipponbare and the indica variety Kasalath. The map provides the most detailed and informative genetic map of any plant. Centromere locations on 12 linkage groups were determined by dosage analysis of secondary and telotrisomics using >130 DNA markers located on respective chromosome arms. A limited influence on meiotic recombination inhibition by the centromere in the genetic map was discussed. The main sources of the markers in this map were expressed sequence tag (EST) clones from Nipponbare callus, root, and shoot libraries. We mapped 1455 loci using ESTs; 615 of these loci showed significant similarities to known genes, including single-copy genes, family genes, and isozyme genes. The high-resolution genetic map permitted us to characterize meiotic recombinations in the whole genome. Positive interference of meiotic recombination was detected both by the distribution of recombination number per each chromosome and by the distribution of double crossover interval lengths.




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H. Itoh, M. Ueguchi-Tanaka, N. Sentoku, H. Kitano, M. Matsuoka, and M. Kobayashi
Cloning and functional analysis of two gibberellin 3beta -hydroxylase genes that are differently expressed during the growth of rice
PNAS, June 28, 2001; (2001) 141239398.
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Z. Cheng, G. G. Presting, C. R. Buell, R. A. Wing, and J. Jiang
High-Resolution Pachytene Chromosome Mapping of Bacterial Artificial Chromosomes Anchored by Genetic Markers Reveals the Centromere Location and the Distribution of Genetic Recombination Along Chromosome 10 of Rice
Genetics, April 1, 2001; 157(4): 1749 - 1757.
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Y.-D. Tan, C. Wan, Y. Zhu, C. Lu, Z. Xiang, and H.-W. Deng
An Amplified Fragment Length Polymorphism Map of the Silkworm
Genetics, March 1, 2001; 157(3): 1277 - 1284.
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Q. Yuan, J. Quackenbush, R. Sultana, M. Pertea, S. L. Salzberg, and C. R. Buell
Rice Bioinformatics. Analysis of Rice Sequence Data and Leveraging the Data to Other Plant Species
Plant Physiology, March 1, 2001; 125(3): 1166 - 1174.
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N. C. Collins, T. Lahaye, C. Peterhänsel, A. Freialdenhoven, M. Corbitt, and P. Schulze-Lefert
Sequence Haplotypes Revealed by Sequence-Tagged Site Fine Mapping of the Ror1 Gene in the Centromeric Region of Barley Chromosome 1H
Plant Physiology, March 1, 2001; 125(3): 1236 - 1247.
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J. Dubcovsky, W. Ramakrishna, P. J. SanMiguel, C. S. Busso, L. Yan, B. A. Shiloff, and J. L. Bennetzen
Comparative Sequence Analysis of Colinear Barley and Rice Bacterial Artificial Chromosomes
Plant Physiology, March 1, 2001; 125(3): 1342 - 1353.
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Z. Cheng, H. Yan, H. Yu, S. Tang, J. Jiang, M. Gu, and L. Zhu
Development and Applications of a Complete Set of Rice Telotrisomics
Genetics, January 1, 2001; 157(1): 361 - 368.
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M. Yano, Y. Katayose, M. Ashikari, U. Yamanouchi, L. Monna, T. Fuse, T. Baba, K. Yamamoto, Y. Umehara, Y. Nagamura, et al.
Hd1, a Major Photoperiod Sensitivity Quantitative Trait Locus in Rice, Is Closely Related to the Arabidopsis Flowering Time Gene CONSTANS
PLANT CELL, December 1, 2000; 12(12): 2473 - 2484.
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Q. Yuan, F. Liang, J. Hsiao, V. Zismann, M.-I. Benito, J. Quackenbush, R. Wing, and R. Buell
Anchoring of rice BAC clones to the rice genetic map in silico
Nucleic Acids Res., September 15, 2000; 28(18): 3636 - 3641.
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B. S. Gaut, M. Le Thierry d'Ennequin, A. S. Peek, and M. C. Sawkins
Maize as a model for the evolution of plant nuclear genomes
PNAS, June 20, 2000; 97(13): 7008 - 7015.
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R. Tarchini, P. Biddle, R. Wineland, S. Tingey, and A. Rafalski
The Complete Sequence of 340 kb of DNA around the Rice Adh1-Adh2 Region Reveals Interrupted Colinearity with Maize Chromosome 4
PLANT CELL, March 1, 2000; 12(3): 381 - 392.
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T. Yamamoto, H. Lin, T. Sasaki, and M. Yano
Identification of Heading Date Quantitative Trait Locus Hd6 and Characterization of Its Epistatic Interactions With Hd2 in Rice Using Advanced Backcross Progeny
Genetics, February 1, 2000; 154(2): 885 - 891.
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K. Sakata, B. A. Antonio, Y. Mukai, H. Nagasaki, Y. Sakai, K. Makino, and T. Sasaki
INE: a rice genome database with an integrated map view
Nucleic Acids Res., January 1, 2000; 28(1): 97 - 101.
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K. M. Devos, J. Beales, Y. Nagamura, and T. Sasaki
Arabidopsis-Rice: Will Colinearity Allow Gene Prediction Across the Eudicot-Monocot Divide?
Genome Res., September 1, 1999; 9(9): 825 - 829.
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W. A. Wilson, S. E. Harrington, W. L. Woodman, M. Lee, M. E. Sorrells, and S. R. McCouch
Inferences on the Genome Structure of Progenitor Maize Through Comparative Analysis of Rice, Maize and the Domesticated Panicoids
Genetics, September 1, 1999; 153(1): 453 - 473.
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M. Ashikari, J. Wu, M. Yano, T. Sasaki, and A. Yoshimura
Rice gibberellin-insensitive dwarf mutant gene Dwarf 1 encodes the alpha -subunit of GTP-binding protein
PNAS, August 31, 1999; 96(18): 10284 - 10289.
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G. L. Davis, M. D. McMullen, C. Baysdorfer, T. Musket, D. Grant, M. Staebell, G. Xu, M. Polacco, L. Koster, S. Melia-Hancock, et al.
A Maize Map Standard With Sequenced Core Markers, Grass Genome Reference Points and 932 Expressed Sequence Tagged Sites (ESTs) in a 1736-Locus Map
Genetics, July 1, 1999; 152(3): 1137 - 1172.
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Y. Fujisawa, T. Kato, S. Ohki, A. Ishikawa, H. Kitano, T. Sasaki, T. Asahi, and Y. Iwasaki
Suppression of the heterotrimeric G protein causes abnormal morphology, including dwarfism, in rice
PNAS, June 22, 1999; 96(13): 7575 - 7580.
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J. Wu, N. Kurata, H. Tanoue, T. Shimokawa, Y. Umehara, M. Yano, and T. Sasaki
Physical Mapping of Duplicated Genomic Regions of Two Chromosome Ends in Rice
Genetics, December 1, 1998; 150(4): 1595 - 1603.
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J. Xu, D. Yang, J. Domingo, J. Ni, and N. Huang
Screening for overlapping bacterial artificial chromosome clones by PCR analysis with an arbitrary primer
PNAS, May 12, 1998; 95(10): 5661 - 5666.
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H. Itoh, M. Ueguchi-Tanaka, N. Sentoku, H. Kitano, M. Matsuoka, and M. Kobayashi
Cloning and functional analysis of two gibberellin 3beta -hydroxylase genes that are differently expressed during the growth of rice
PNAS, July 17, 2001; 98(15): 8909 - 8914.
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