Construction of high-resolution recombination maps in Asian seabass

BMC Genomics

Research Article

Bin Bai¹  Shu Qing Huang¹  Le Wang¹  Baoqing Ye¹  Elaine Chua¹  Peng Liu²  Gen Hua Yue³  Zi Yi Wan⁴ 

[1] Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore, Singapore;Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore, Singapore;Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore, Singapore;Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore, Singapore;Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore, Singapore;School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore, Singapore;Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore, Singapore;School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore, Singapore;

关键词: Linkage map;    Genome assembly;    Recombination rates;    GC content;    Selective breeding;   

DOI  :  10.1186/s12864-016-3462-z

 received in 2016-10-03, accepted in 2016-12-22,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundA 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.ResultsA 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.ConclusionsThese 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.

【 授权许可】

CC BY   
© The Author(s). 2017