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Anchoring of rice BAC clones to the rice genetic map in silico
Published on Sep 15, 2000in Nucleic Acids Research 11.56
· DOI :10.1093/nar/28.18.3636
Qiaoping Yuan10
Estimated H-index: 10
(J. Craig Venter Institute),
Feng Liang8
Estimated H-index: 8
(J. Craig Venter Institute)
+ 5 AuthorsRobin Buell1
Estimated H-index: 1
(J. Craig Venter Institute)
Abstract
A wealth of molecular resources have been developed for rice genomics, including dense genetic maps, expressed sequence tags (ESTs), yeast artificial chromosome maps, bacterial artificial chromosome (BAC) libraries and BAC end sequence databases. Integration of genetic and physical maps involves labor-intensive empirical experiments. To accelerate the integration of the bacterial clone resources with the genetic map for the International Rice Genome Sequencing Project, we cleaned and filtered the available EST and BAC end sequences for repetitive sequences and then searched all available rice genetic markers with our filtered databases. We identified 418 genetic markers that aligned with at least one BAC end sequence with >95% sequence identity, providing a set of large insert clones with an average separation of 1 Mb that can serve as nucleation points for the sequencing phase of the International Rice Genome Sequencing Project.
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References1
Published on Jan 1, 1989
Joseph Sambrook29
Estimated H-index: 29
,
Edward F. Fritsch6
Estimated H-index: 6
,
Tom Maniatis26
Estimated H-index: 26
Molecular Cloning has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential. Molecular Cloning, Fourth Edition, by the celebrated founding author Joe Sambrook and new co-author, the distinguished HHMI investigator Michael Green, preserves the highly praised detail and clarity of previous editions and includes specific chapters and protocols commissioned for the book from expert practitioners at Yale, U Mass, Rockefe...
141k Citations
Cited By38
Published on Jan 1, 2004
Yeisoo Yu37
Estimated H-index: 37
(University of Arizona),
Rod A. Wing80
Estimated H-index: 80
(University of Arizona)
2 Citations Source Cite
Published on Jan 1, 2001
Rod A. Wing80
Estimated H-index: 80
,
Yeisoo Yu37
Estimated H-index: 37
+ 23 AuthorsTeri Rambo8
Estimated H-index: 8
The CCW Rice Genome Sequencing Consortium is funded to sequence and annotate the short arms of rice chromosomes 10 and 3—approximately 30 Mb of DNA. To efficiently sequence the rice genome, the Clemson University Genomics Institute has developed a framework consisting of two deep-coverage bacterial artificial chromosome (BAC) libraries and BAC fingerprint, genome-anchoring, and sequence-tagged connector databases. These resources have been provided to the International Rice Genome Sequencing Pro...
Published on Jan 1, 2007in Methods of Molecular Biology
Jong-Seong Jeon28
Estimated H-index: 28
(Kyung Hee University),
Pamela C. Ronald64
Estimated H-index: 64
(University of California, Davis)
Nipponbare BAC Clones for Physical Mapping of RGL Use of Nipponbare BAC Clones for Physical Mapping of an R Gene Locus in Rice Jong-Seong Jeon and Pamela C. Ronald Summary Major advances in rice genomics during the last few years have made positional clon- ing in rice much more efficient. Nipponbare is a model rice genotype being sequenced by the International Rice Genome Sequencing Project Consortium. Here, we describe an efficient procedure of the construction of physical map for positional cl...
1 Citations Source Cite
Published on Mar 20, 2008
Isobel A. P. Parkin34
Estimated H-index: 34
,
Stephen J. Robinson12
Estimated H-index: 12
+ 3 AuthorsDerek J. Lydiate39
Estimated H-index: 39
Source Cite
Published on Sep 27, 2005in BMC Biology 5.77
Nathalie Choisne12
Estimated H-index: 12
,
Nadia Demange2
Estimated H-index: 2
+ 96 AuthorsPatrick Wincker78
Estimated H-index: 78
135 Citations Source Cite
Published on Jan 1, 2004
Rajeev K. Varshney72
Estimated H-index: 72
,
Viktor Korzun43
Estimated H-index: 43
,
A. Börner42
Estimated H-index: 42
Cereals provide for our major food crops, and therefore have been a subject of detailed genetic and cytogenetic studies during major part of the last century. These studies led to the preparation of linkage maps, which were also assigned to individual chromosomes, thus leading to the construction of chromosome maps in all major cereals. In some cases, the availability of cytogenetic stocks (e.g. deletion stocks in bread wheat) also allowed construction of physical maps. In the past, a major limi...
22 Citations Source Cite
Published on Aug 1, 2001in Genome Biology 13.21
Natalia Volfovsky15
Estimated H-index: 15
,
Brian J. Haas64
Estimated H-index: 64
,
Steven L. Salzberg118
Estimated H-index: 118
Background A computational system for analysis of the repetitive structure of genomic sequences is described. The method uses suffix trees to organize and search the input sequences; this data structure has been used previously for efficient computation of exact and degenerate repeats.
118 Citations Source Cite
Published on Jul 15, 2004
Pablo D. Rabinowicz28
Estimated H-index: 28
(Cold Spring Harbor Laboratory),
Robert A. Martienssen87
Estimated H-index: 87
(Cold Spring Harbor Laboratory)
Since the Human Genome Project started in 1990 numerous large-scale genomic sequencing projects have been conducted by different consortia of laboratories. As a result, the complete genetic information of an ever growing number of higher eukaryotes is now available in the public databases, which constitute an invaluable resource for biological research. Although eukaryote genomes are very large, most of their DNA is repetitive and do not code for genes. This is particularly true for plants, wher...
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Published on Jan 1, 2004
Jong-Seong Jeon28
Estimated H-index: 28
(Kyung Hee University),
D. Chen + 3 AuthorsPamela C. Ronald12
Estimated H-index: 12
(University of California)
AFLP-derived markers linked to Pi5(t)-mediated resistance were isolated using bulked segregant analysis of F2 populations generated by crossing three recombinant inbred lines (RILs), RIL125, RIL249, and RIL260 with the susceptible line CO39. The most tightly linked AFLP marker, S04G03, was positioned on chromosome 9 of the fingerprint-based physical map of Nipponbare, a well-characterized rice genotype. Flanking BAC-based Nipponbare markers were generated for saturation mapping using four popula...
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Published on Jan 1, 2006
Meredith Diane Carter1
Estimated H-index: 1
Under certain environmental conditions, some varieties of wheat synthesize the enzyme alpha amylase late in grain ripening, even in the absence of rain or sprouting. The resulting grain has a sound appearance but can be unsuitable for end-product applications due to the presence of late maturity alpha amylase (LMA) activity. Reduction of LMA and the development of cultivars tolerant to boron toxic soils are high priority traits in the WA wheat breeding program and the use of molecular markers cl...
2 Citations
View next paperA High-Density Rice Genetic Linkage Map with 2275 Markers Using a Single F2 Population