plant-transformation-competent BIBAC/BAC-based map of rice for functional analysis and genetic engineering of its genomic sequence
Sequencing of the rice genome has provided a platform for functional genomics research of rice and other cereal species. However, multiple approaches are needed to determine the functions of its genes and sequences and to use the genome sequencing results for genetic improvement of cereal crops. Her...
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| Veröffentlicht in: | Genome 2007-03, Vol.50 (3), p.278-288 |
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| creator | Li, Y Uhm, T Ren, C Wu, C Santos, T.S Lee, M.K Yan, B Santos, F Zhang, A Scheuring, C |
| description | Sequencing of the rice genome has provided a platform for functional genomics research of rice and other cereal species. However, multiple approaches are needed to determine the functions of its genes and sequences and to use the genome sequencing results for genetic improvement of cereal crops. Here, we report a plant-transformation-competent, binary bacterial artificial chromosome (BIBAC) and bacterial artificial chromosome (BAC) based map of rice to facilitate these studies. The map was constructed from 20 835 BIBAC and BAC clones, and consisted of 579 overlapping BIBAC/BAC contigs. To facilitate functional analysis of chromosome 8 genomic sequence and cloning of the genes and QTLs mapped to the chromosome, we anchored the chromosomal contigs to the existing rice genetic maps. The chromosomal map consists of 11 contigs, 59 genetic markers, and 36 sequence tagged sites, spanning a total of ca. 38 Mb in physical length. Comparative analysis between the genetic and physical maps of chromosome 8 showed that there are 3 “hot” and 2 “cold” spots of genetic recombination along the chromosomal arms in addition to the “cold spot” in the centromeric region, suggesting that the sequence component contents of a chromosome may affect its local genetic recombination frequencies. Because of its plant transformability, the BIBAC/BAC map could provide a platform for functional analysis of the rice genome sequence and effective use of the sequencing results for gene and QTL cloning and molecular breeding. |
| doi_str_mv | 10.1139/G07-006 |
| format | Article |
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However, multiple approaches are needed to determine the functions of its genes and sequences and to use the genome sequencing results for genetic improvement of cereal crops. Here, we report a plant-transformation-competent, binary bacterial artificial chromosome (BIBAC) and bacterial artificial chromosome (BAC) based map of rice to facilitate these studies. The map was constructed from 20 835 BIBAC and BAC clones, and consisted of 579 overlapping BIBAC/BAC contigs. To facilitate functional analysis of chromosome 8 genomic sequence and cloning of the genes and QTLs mapped to the chromosome, we anchored the chromosomal contigs to the existing rice genetic maps. The chromosomal map consists of 11 contigs, 59 genetic markers, and 36 sequence tagged sites, spanning a total of ca. 38 Mb in physical length. Comparative analysis between the genetic and physical maps of chromosome 8 showed that there are 3 “hot” and 2 “cold” spots of genetic recombination along the chromosomal arms in addition to the “cold spot” in the centromeric region, suggesting that the sequence component contents of a chromosome may affect its local genetic recombination frequencies. Because of its plant transformability, the BIBAC/BAC map could provide a platform for functional analysis of the rice genome sequence and effective use of the sequencing results for gene and QTL cloning and molecular breeding.</description><identifier>ISSN: 0831-2796</identifier><identifier>EISSN: 1480-3321</identifier><identifier>DOI: 10.1139/G07-006</identifier><identifier>PMID: 17502901</identifier><identifier>CODEN: GENOE3</identifier><language>eng</language><publisher>Canada: NRC Research Press</publisher><subject>Bacteria ; bacterial artificial chromosomes ; Base Sequence ; BIBAC ; binary bacterial artificial chromosomes ; cartographie physique ; Chromosome Mapping - methods ; Chromosomes ; Chromosomes, Artificial, Bacterial - genetics ; Chromosomes, Plant - genetics ; clonage positionnel ; clones ; Contig Mapping ; Crops ; DNA Fingerprinting ; DNA libraries ; DNA, Plant - genetics ; functional genomics ; Gene Library ; Genes ; Genetic aspects ; Genetic Engineering ; genetic markers ; Genetic transformation ; Genome, Plant ; Genomics ; génie génétique ; génomique fonctionnelle ; Molecular biology ; molecular cloning ; Oryza - genetics ; Oryza sativa ; Physical Chromosome Mapping ; physical mapping ; positional cloning ; Rice ; sequence tagged sites ; transformation génétique ; Transformation, Genetic</subject><ispartof>Genome, 2007-03, Vol.50 (3), p.278-288</ispartof><rights>COPYRIGHT 2007 NRC Research Press</rights><rights>Copyright National Research Council of Canada Mar 2007</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c599t-6c0ddd4a6894fc63573b8617cd375b758006bb98921d05783f375401a42e11af3</citedby><cites>FETCH-LOGICAL-c599t-6c0ddd4a6894fc63573b8617cd375b758006bb98921d05783f375401a42e11af3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://cdnsciencepub.com/doi/pdf/10.1139/G07-006$$EPDF$$P50$$Gnrcresearch$$H</linktopdf><linktohtml>$$Uhttps://cdnsciencepub.com/doi/full/10.1139/G07-006$$EHTML$$P50$$Gnrcresearch$$H</linktohtml><link.rule.ids>314,776,780,2919,27901,27902,64401,64979</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17502901$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Belzile, F.</contributor><creatorcontrib>Li, Y</creatorcontrib><creatorcontrib>Uhm, T</creatorcontrib><creatorcontrib>Ren, C</creatorcontrib><creatorcontrib>Wu, C</creatorcontrib><creatorcontrib>Santos, T.S</creatorcontrib><creatorcontrib>Lee, M.K</creatorcontrib><creatorcontrib>Yan, B</creatorcontrib><creatorcontrib>Santos, F</creatorcontrib><creatorcontrib>Zhang, A</creatorcontrib><creatorcontrib>Scheuring, C</creatorcontrib><title>plant-transformation-competent BIBAC/BAC-based map of rice for functional analysis and genetic engineering of its genomic sequence</title><title>Genome</title><addtitle>Génome</addtitle><description>Sequencing of the rice genome has provided a platform for functional genomics research of rice and other cereal species. However, multiple approaches are needed to determine the functions of its genes and sequences and to use the genome sequencing results for genetic improvement of cereal crops. Here, we report a plant-transformation-competent, binary bacterial artificial chromosome (BIBAC) and bacterial artificial chromosome (BAC) based map of rice to facilitate these studies. The map was constructed from 20 835 BIBAC and BAC clones, and consisted of 579 overlapping BIBAC/BAC contigs. To facilitate functional analysis of chromosome 8 genomic sequence and cloning of the genes and QTLs mapped to the chromosome, we anchored the chromosomal contigs to the existing rice genetic maps. The chromosomal map consists of 11 contigs, 59 genetic markers, and 36 sequence tagged sites, spanning a total of ca. 38 Mb in physical length. Comparative analysis between the genetic and physical maps of chromosome 8 showed that there are 3 “hot” and 2 “cold” spots of genetic recombination along the chromosomal arms in addition to the “cold spot” in the centromeric region, suggesting that the sequence component contents of a chromosome may affect its local genetic recombination frequencies. Because of its plant transformability, the BIBAC/BAC map could provide a platform for functional analysis of the rice genome sequence and effective use of the sequencing results for gene and QTL cloning and molecular breeding.</description><subject>Bacteria</subject><subject>bacterial artificial chromosomes</subject><subject>Base Sequence</subject><subject>BIBAC</subject><subject>binary bacterial artificial chromosomes</subject><subject>cartographie physique</subject><subject>Chromosome Mapping - methods</subject><subject>Chromosomes</subject><subject>Chromosomes, Artificial, Bacterial - genetics</subject><subject>Chromosomes, Plant - genetics</subject><subject>clonage positionnel</subject><subject>clones</subject><subject>Contig Mapping</subject><subject>Crops</subject><subject>DNA Fingerprinting</subject><subject>DNA libraries</subject><subject>DNA, Plant - genetics</subject><subject>functional genomics</subject><subject>Gene Library</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic Engineering</subject><subject>genetic markers</subject><subject>Genetic transformation</subject><subject>Genome, Plant</subject><subject>Genomics</subject><subject>génie génétique</subject><subject>génomique fonctionnelle</subject><subject>Molecular biology</subject><subject>molecular cloning</subject><subject>Oryza - genetics</subject><subject>Oryza sativa</subject><subject>Physical Chromosome Mapping</subject><subject>physical mapping</subject><subject>positional cloning</subject><subject>Rice</subject><subject>sequence tagged sites</subject><subject>transformation génétique</subject><subject>Transformation, 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BIBAC/BAC-based map of rice for functional analysis and genetic engineering of its genomic sequence</title><author>Li, Y ; Uhm, T ; Ren, C ; Wu, C ; Santos, T.S ; Lee, M.K ; Yan, B ; Santos, F ; Zhang, A ; Scheuring, C</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c599t-6c0ddd4a6894fc63573b8617cd375b758006bb98921d05783f375401a42e11af3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Bacteria</topic><topic>bacterial artificial chromosomes</topic><topic>Base Sequence</topic><topic>BIBAC</topic><topic>binary bacterial artificial chromosomes</topic><topic>cartographie physique</topic><topic>Chromosome Mapping - methods</topic><topic>Chromosomes</topic><topic>Chromosomes, Artificial, Bacterial - genetics</topic><topic>Chromosomes, Plant - genetics</topic><topic>clonage positionnel</topic><topic>clones</topic><topic>Contig Mapping</topic><topic>Crops</topic><topic>DNA 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However, multiple approaches are needed to determine the functions of its genes and sequences and to use the genome sequencing results for genetic improvement of cereal crops. Here, we report a plant-transformation-competent, binary bacterial artificial chromosome (BIBAC) and bacterial artificial chromosome (BAC) based map of rice to facilitate these studies. The map was constructed from 20 835 BIBAC and BAC clones, and consisted of 579 overlapping BIBAC/BAC contigs. To facilitate functional analysis of chromosome 8 genomic sequence and cloning of the genes and QTLs mapped to the chromosome, we anchored the chromosomal contigs to the existing rice genetic maps. The chromosomal map consists of 11 contigs, 59 genetic markers, and 36 sequence tagged sites, spanning a total of ca. 38 Mb in physical length. Comparative analysis between the genetic and physical maps of chromosome 8 showed that there are 3 “hot” and 2 “cold” spots of genetic recombination along the chromosomal arms in addition to the “cold spot” in the centromeric region, suggesting that the sequence component contents of a chromosome may affect its local genetic recombination frequencies. Because of its plant transformability, the BIBAC/BAC map could provide a platform for functional analysis of the rice genome sequence and effective use of the sequencing results for gene and QTL cloning and molecular breeding.</abstract><cop>Canada</cop><pub>NRC Research Press</pub><pmid>17502901</pmid><doi>10.1139/G07-006</doi><tpages>11</tpages></addata></record> |
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| source | NRC Research Press; MEDLINE |
| subjects | Bacteria bacterial artificial chromosomes Base Sequence BIBAC binary bacterial artificial chromosomes cartographie physique Chromosome Mapping - methods Chromosomes Chromosomes, Artificial, Bacterial - genetics Chromosomes, Plant - genetics clonage positionnel clones Contig Mapping Crops DNA Fingerprinting DNA libraries DNA, Plant - genetics functional genomics Gene Library Genes Genetic aspects Genetic Engineering genetic markers Genetic transformation Genome, Plant Genomics génie génétique génomique fonctionnelle Molecular biology molecular cloning Oryza - genetics Oryza sativa Physical Chromosome Mapping physical mapping positional cloning Rice sequence tagged sites transformation génétique Transformation, Genetic |
| title | plant-transformation-competent BIBAC/BAC-based map of rice for functional analysis and genetic engineering of its genomic sequence |
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