title: Construction of high-resolution recombination maps in Asian seabass.
abstract: A high-density genetic map is essential for de novo genome assembly, fine mapping QTL for important complex traits, comparative genomic studies and understanding the mechanisms of genome evolution. Although a number of genomic resources are available in Asian seabass (Lates calcarifer), a high-density linkage map is still lacking. To facilitate QTL mapping for marker-assisted selection and genome assembly, and to understand the genome-wide recombination rates, we constructed high density linkage maps using three families and genotyping by sequencing.
  
  
  
  A high-density consensus linkage map consisting of 8, 274 markers was constructed based on sex-averaged genetic maps. The genetic maps were then aligned and integrated with the current genome assembly of Asian seabass. More than 90% of the genome contig sequences were anchored onto the consensus genetic map. Evidence of assembly errors in the current genome assembly was identified. A fragment of up to 2.5 Mb belonging to LG14 was assembled into Chr15. The length of family-specific sex-averaged maps ranged from 1348.96 to 1624.65 cM. Female maps were slightly longer than male maps using common markers. Female-to-male ratios were highly variable both across chromosomes within each family and throughout three families for each chromosome. However, the distribution patterns of recombination along chromosomes were similar between sexes across the whole genome. The overall recombination rates were significantly correlated with genome-wide GC content and the correlations were revealed to be stronger in females than in males.
  
  
  
  These high-density genetic maps provide not only essential tools for facilitating de novo genome assembly and comparative genomic studies in teleosts, but also critical resources for fine mapping QTL and genome-wide association mapping for economically important traits in Asian seabass.
authors.affiliation: Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
authors.forename: Le
authors.initials: L
authors.lastname: Wang
authors.affiliation: Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
authors.forename: Bin
authors.initials: B
authors.lastname: Bai
authors.affiliation: Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.|Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
authors.forename: Peng
authors.initials: P
authors.lastname: Liu
authors.affiliation: Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
authors.forename: Shu Qing
authors.initials: SQ
authors.lastname: Huang
authors.affiliation: Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.|School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
authors.forename: Zi Yi
authors.initials: ZY
authors.lastname: Wan
authors.affiliation: Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
authors.forename: Elaine
authors.initials: E
authors.lastname: Chua
authors.affiliation: Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
authors.forename: Baoqing
authors.initials: B
authors.lastname: Ye
authors.affiliation: Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore. genhua@tll.org.sg.|Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore. genhua@tll.org.sg.|School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. genhua@tll.org.sg.
authors.forename: Gen Hua
authors.initials: GH
authors.lastname: Yue
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D005260:Female; D023281:Genomics; D060005:Genotyping Techniques; D008297:Male; D010473:Perciformes / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics; D011995:Recombination, Genetic; D012727:Sex Characteristics
keywords: GC content; Genome assembly; Linkage map; Recombination rates; Selective breeding