title: A plant-transformation-competent BIBAC/BAC-based map of rice for functional analysis and genetic engineering of its genomic sequence.
abstract: 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.
authors.affiliation: Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843-2474, USA.
authors.forename: Yaning
authors.initials: Y
authors.lastname: Li
authors.forename: Taesik
authors.initials: T
authors.lastname: Uhm
authors.forename: Chengwei
authors.initials: C
authors.lastname: Ren
authors.forename: Chengcang
authors.initials: C
authors.lastname: Wu
authors.forename: Teofila S
authors.initials: TS
authors.lastname: Santos
authors.forename: Mi-Kyung
authors.initials: MK
authors.lastname: Lee
authors.forename: Bo
authors.initials: B
authors.lastname: Yan
authors.forename: Felipe
authors.initials: F
authors.lastname: Santos
authors.forename: Aimin
authors.initials: A
authors.lastname: Zhang
authors.forename: Chantel
authors.initials: C
authors.lastname: Scheuring
authors.forename: Alma
authors.initials: A
authors.lastname: Sanchez
authors.forename: Anna C
authors.initials: AC
authors.lastname: Millena
authors.forename: Henry T
authors.initials: HT
authors.lastname: Nguyen
authors.forename: Hongda
authors.initials: H
authors.lastname: Kou
authors.forename: Daqun
authors.initials: D
authors.lastname: Liu
authors.forename: Hong-Bin
authors.initials: HB
authors.lastname: Zhang
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D020451:Contig Mapping; D016172:DNA Fingerprinting; D018744:DNA, Plant / Q000235:genetics; D015723:Gene Library; D005818:Genetic Engineering; D018745:Genome, Plant; D012275:Oryza / Q000235:genetics*; D020161:Physical Chromosome Mapping; D014170:Transformation, Genetic
chemical_list: D018744:DNA, Plant