An Integrated Physical and Genetic Map of the Rice Genome

Chen, Mingsheng; Presting, Gernot G.; Barbazuk, W. Brad; Goicoechea, José Luis; Blackmon, Barbara; Fang, Guang-Chen; Kim, Hye‐Ran; Frisch, David; Yu, Yeisoo; Sun, Shouhong; Higingbottom, Stephanie; Phimphilai, John; Phimphilai, Dao; Thurmond, S.; Gaudette, Brian T.; Li, Ping; Liu, Jingdong; Hatfield, Jamie; Main, Dorrie; Farrar, Kasey; Henderson, Caroline; Barnett, Laura; Costa, R.; Williams, Brian J.; Walser, Suzanne; Atkins, Michael B.; Hall, Caroline R.; Budiman, Muhammad A.; Tomkins, J. P.; Luo, Meizhong; Bancroft, Ian; Salse, Jérôme; Regad, Farid; Mohapatra, Trilochan; Singh, Nagendra; Tyagi, Akhilesh K.; Soderlund, Carol; Dean, Ralph A.; Wing, Rod A.

doi:10.1105/tpc.010485

Cited by 402 publications

(278 citation statements)

References 25 publications

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“…By adding the predicted physical lengths of all gaps derived from the FISH experiment and YAC or genetic maps, we predict a total length of 198.7 Mbp for the six rice chromosomes studied, excluding the nuclear organizing region (NOR) on chromosome 9 (Table 1). The predicted total sizes of the entire chromosomes 1, 6, 8, and 9 are comparable with the results of a ®ngerprint experiment (Chen et al, 2002). However, the entire sizes predicted for chromosomes 2 and 7 are shorter in our study.…”

Section: Discussionsupporting

confidence: 89%

“…Early studies based on DNA content estimated the rice genome to be about 430 Mbp (Arumuganathan and Earle, 1991). Construction of a BAC ®ngerprint-based physical map of the japonica rice variety Nipponbare led to a size prediction of about 400 Mbp for its euchromatic region (Chen et al, 2002). Analysis of a draft sequence derived by whole-genome shotgun sequencing furthermore indicated the genome size of an indica rice variety to be 466 Mbp (Yu et al, 2002).…”

Section: Discussionmentioning

confidence: 99%

“…Previous studies have demonstrated signi®cant differences in recombination frequency along the length of each rice chromosome (Chen et al, 2002;Wu et al, 2002; Zhao et al, 2002). As these differences were detected by using whole YAC or BAC contigs rather than the interval region between each neighboring marker, this information on recombination frequency is of limited value for studies on gene isolation by map-based cloning.…”

Section: Recombination Frequency On Each Chromosomementioning

confidence: 97%

“…These clones were sequenced with 10-fold redundancy to ensure a sequence quality of 99.99% accuracy. By merging the above sequenced physical map with the CUGI (Clemson University Genomics Institute, USA) BAC contig map with the help of end sequences (Chen et al, 2002;Mao et al, 2000), 349 CUGI BAC clones were added to the maps for gap closure and contig extension. As of April 2003, the physical maps of chromosomes 1, 2, and 6±9 comprised 1814 PAC and BAC clones with only 20 physical gaps ( Figure 1; Table 1).…”

Section: Construction Of Physical Mapsmentioning

confidence: 99%

“…All PAC and BAC libraries were derived from DNA of a single rice variety, Nipponbare (Oryza sativa L., japonica), and were constructed by two academic centers (RGP and CUGI) and one private company (Monsanto, St Louis, USA; Baba et al, 2000;Barry, 2001;Chen et al, 2002 …”

Section: Clone Resourcesmentioning

confidence: 99%

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Physical maps and recombination frequency of six rice chromosomes

Wu¹,

Mizuno²,

et al. 2003

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These authors contributed equally to this work. SummaryWe constructed physical maps of rice chromosomes 1, 2, and 6±9 with P1-derived arti®cial chromosome (PAC) and bacterial arti®cial chromosome (BAC) clones. These maps, with only 20 gaps, cover more than 97% of the predicted length of the six chromosomes. We submitted a total of 193 Mbp of non-overlapping sequences to public databases. We analyzed the DNA sequences of 1316 genetic markers and six centromere-speci®c repeats to facilitate characterization of chromosomal recombination frequency and of the genomic composition and structure of the centromeric regions. We found marked changes in the relative recombination rate along the length of each chromosome. Chromosomal recombination at the centromere core and surrounding regions on the six chromosomes was completely suppressed. These regions have a total physical length of about 23 Mbp, corresponding to 11.4% of the entire size of the six chromosomes. Chromosome 6 has the longest quiescent region, with about 5.6 Mbp, followed by chromosome 8, with quiescent region about half this size. Repetitive sequences accounted for at least 40% of the total genomic sequence on the partly sequenced centromeric region of chromosome 1. Rice CentO satellite DNA is arrayed in clusters and is closely associated with the presence of Centromeric Retrotransposon of Rice (CRR )-and RIce RetroElement 7 (RIRE7 )-like retroelement sequences. We also detected relatively small coldspot regions outside the centromeric region; their repetitive content and gene density were similar to those of regions with normal recombination rates. Sequence analysis of these regions suggests that either the amount or the organization patterns of repetitive sequences may play a role in the inactivation of recombination.

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Section: Discussionsupporting

confidence: 89%

Section: Discussionmentioning

confidence: 99%

Section: Recombination Frequency On Each Chromosomementioning

confidence: 97%

Section: Construction Of Physical Mapsmentioning

confidence: 99%

Section: Clone Resourcesmentioning

confidence: 99%

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Physical maps and recombination frequency of six rice chromosomes

Wu¹,

Mizuno²,

et al. 2003

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Contig mapping and analysis

Siddiqui

Jones

2005

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

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Physical mapping and the creation of contig maps remains a valuable tool for genomics research. This section describes the methods and techniques used to create contig maps from restriction fragment fingerprint information. It mentions some of the bioinformatics challenges associated with building a high‐quality map and points to ongoing research that is attempting to address this problem. This section also illustrates how tiling path clones are chosen from a redundant set of clones.

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Construction and Application of Genomic DNA Libraries

Kim¹,

Yang²,

Kudrna³

et al. 2004

Handbook of Plant Biotechnology

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Crop failures, pathogenic outbreaks and famine are serious problems facing society. Understanding an organism's genome will help provide the genetic tools needed to solve these complex problems in a shorter time and with less effort. To efficiently study an organism's genome, it can be partitioned into a permanent and stable collection of DNA fragments, called a library. Such libraries provide convenient access to a genome for both laboratory and breeding applications. Genomic libraries can be used as substrates to physically map and sequence entire genomes, clone agriculturally important genes and to investigate gene expression patterns. Further, genomic libraries also provide powerful tools and resources for evaluating germplasm conservation stocks and biological diversity. The ongoing explosion of genetic data and molecular clone resources has opened new scientific possibilities to researchers venturing across all avenues of applied science. In this chapter we will present the details for small and large insert library construction and their applications.

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An Integrated Physical and Genetic Map of the Rice Genome

Cited by 402 publications

References 25 publications

Physical maps and recombination frequency of six rice chromosomes

Physical maps and recombination frequency of six rice chromosomes

Contig mapping and analysis

Construction and Application of Genomic DNA Libraries

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