title: A high-resolution comparative map of porcine chromosome 4 (SSC4).
abstract: We used the IMNpRH2(12,000-rad) RH and IMpRH(7,000-rad) panels to integrate 2019 transcriptome (RNA-seq)-generated contigs with markers from the porcine genetic and radiation hybrid (RH) maps and bacterial artificial chromosome finger-printed contigs, into 1) parallel framework maps (LOD ≥ 10) on both panels for swine chromosome (SSC) 4, and 2) a high-resolution comparative map of SSC4, thus and human chromosomes (HSA) 1 and 8. A total of 573 loci were anchored and ordered on SSC4 closing gaps identified in the porcine sequence assembly Sscrofa9. Alignment of the SSC4 RH with the genetic map identified five microsatellites incorrectly mapped around the centromeric region in the genetic map. Further alignment of the RH and comparative maps with the genome sequence identified four additional regions of discrepancy that are also suggestive of errors in assembly, three of which were resolved through conserved synteny with blocks on HSA1 and HSA8.
authors.affiliation: Department of Biological Science and Engineering, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, China.
authors.forename: J-G
authors.initials: JG
authors.lastname: Ma
authors.forename: T-C
authors.initials: TC
authors.lastname: Chang
authors.forename: H
authors.initials: H
authors.lastname: Yasue
authors.forename: A D
authors.initials: AD
authors.lastname: Farmer
authors.forename: J A
authors.initials: JA
authors.lastname: Crow
authors.forename: K
authors.initials: K
authors.lastname: Eyer
authors.forename: H
authors.initials: H
authors.lastname: Hiraiwa
authors.forename: T
authors.initials: T
authors.lastname: Shimogiri
authors.forename: S N
authors.initials: SN
authors.lastname: Meyers
authors.forename: J E
authors.initials: JE
authors.lastname: Beever
authors.forename: L B
authors.initials: LB
authors.lastname: Schook
authors.forename: E F
authors.initials: EF
authors.lastname: Retzel
authors.forename: C W
authors.initials: CW
authors.lastname: Beattie
authors.forename: W-S
authors.initials: WS
authors.lastname: Liu
mesh_terms: D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D022202:Chromosomes, Artificial, Bacterial; D033481:Chromosomes, Mammalian / Q000235:genetics*; D051417:Focal Adhesion Kinase 1 / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D016013:Likelihood Functions; D018895:Microsatellite Repeats / Q000235:genetics; D021101:Radiation Hybrid Mapping; D013045:Species Specificity; D013552:Swine / Q000235:genetics*; D026801:Synteny / Q000235:genetics
chemical_list: D051417:Focal Adhesion Kinase 1; C496050:PTK2 protein, human