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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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  • Citations (38)
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References1
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Published on Jan 1, 1989
Joseph Sambrook29
Estimated H-index: 29
,
Edward F. Fritsch16
Estimated H-index: 16
,
Tom Maniatis126
Estimated H-index: 126
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...
145k Citations
Cited By38
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Published on Jun 3, 2019in bioRxiv
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Published on Nov 24, 2015
Allah Bakhsh12
Estimated H-index: 12
,
Faheem Shehzad Baloch12
Estimated H-index: 12
+ 1 AuthorsH.akan. Özkan
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Published on Nov 24, 2015
C.engiz. Kazak1
Estimated H-index: 1
,
K.amil. Karut1
Estimated H-index: 1
,
İsmail Döker5
Estimated H-index: 5
1 Citations Source Cite
Published on Jul 22, 2014in Frontiers in Genetics 4.15
Yanliang Jiang19
Estimated H-index: 19
(Chinese Academy of Fishery Sciences),
Peng Xu31
Estimated H-index: 31
(Chinese Academy of Fishery Sciences),
Zhanjiang Liu56
Estimated H-index: 56
(Auburn University)
Rapid advances of the next-generation sequencing technologies have allowed whole genome sequencing of many species. However, with the current sequencing technologies, the whole genome sequence assemblies often fall in short in one of the four quality measurements: accuracy, contiguity, connectivity, and completeness. In particular, small-sized contigs and scaffolds limit the applicability of whole genome sequences for genetic analysis. To enhance the quality of whole genome sequence assemblies, ...
1 Citations Source Cite
Published on Jan 1, 2014
Rekha Dixit , Durg Vijay Rai7
Estimated H-index: 7
+ 1 AuthorsAditya Pundhir
Mapping genome of an organism is an important tool to provide a guide for the sequencing experiments by showing the exact positions of genes and other distinctive features in the chromosomal DNA. Whole genome sequencing of eukaryotic genomes is greatly facilitated by high- density genome maps. The highdensity maps serve as foundation during organizing and assembling the nucleotide sequences of genomes. Reference to the map ensures that regions containing repetitive DNA are assembled correctly. D...
Published on Oct 1, 2012in G3: Genes, Genomes, Genetics 2.74
Parichart Ninwichian5
Estimated H-index: 5
(Auburn University),
Eric Peatman34
Estimated H-index: 34
(Auburn University)
+ 15 AuthorsLudmilla Kaltenboeck10
Estimated H-index: 10
(Auburn University)
Construction of high-density genetic linkage maps is crucially important for quantitative trait loci (QTL) studies, and they are more useful when integrated with physical maps. Such integrated maps are valuable genome resources for fine mapping of QTL, comparative genomics, and accurate and efficient whole-genome assembly. Previously, we established both linkage maps and a physical map for channel catfish, Ictalurus punctatus , the dominant aquaculture species in the United States. Here we added...
35 Citations Source Cite
Published on Jan 1, 2012in BioMed Research International 2.58
Ruvini Ariyadasa13
Estimated H-index: 13
,
Nils Stein58
Estimated H-index: 58
In the advent of next-generation sequencing (NGS) platforms, map-based sequencing strategy has been recently suppressed being too expensive and laborious. The detailed studies on NGS drafts alone indicated these assemblies remain far from gold standard reference quality, especially when applied on complex genomes. In this context the conventional BAC-based physical mapping has been identified as an important intermediate layer in current hybrid sequencing strategy. BAC-based physical map constru...
28 Citations Source Cite
Published on Jan 21, 2011
Michael Pillay7
Estimated H-index: 7
,
A. Tenkouano14
Estimated H-index: 14
3 Citations Source Cite
Published on Jun 30, 2010in Journal of Plant Biotechnology
류학승 ( Hak Seung Ryu )1
Estimated H-index: 1
,
류나연1
Estimated H-index: 1
+ 2 Authors전종성 ( Jong Seong Jeon )1
Estimated H-index: 1
【Rice (Oryza sativa) is a major cereal crop that has been developed as a monocot model species. In past decades rice researchers have established valuable resources for functional genomics in rice, such as complete genome sequencing, high-density genetic maps, a full length cDNA database, genome-wide transcriptome data, and a large number of mutants. Of these, rice mutant lines are very important to definitively determine functions of genes associated with valuable agronomic traits. In this revi...
2 Citations Source Cite
Published on Jan 1, 2010in BMC Genomics 3.73
Juana Marcela Córdoba3
Estimated H-index: 3
(International Center for Tropical Agriculture),
Carolina Chavarro13
Estimated H-index: 13
(International Center for Tropical Agriculture)
+ 2 AuthorsM.W. Blair49
Estimated H-index: 49
(International Center for Tropical Agriculture)
Background Common bean (Phaseolus vulgaris L.) is the most important legume for direct human consumption and the goal of this study was to integrate a recently constructed physical map for the species with a microsatellite based genetic map using a BAC library from the genotype G19833 and the recombinant inbred line population DOR364 × G19833.
51 Citations Source Cite