title: The genetic map of goldfish (Carassius auratus) provided insights to the divergent genome evolutions in the Cyprinidae family.
abstract: A high-density linkage map of goldfish (Carassius auratus) was constructed using RNA-sequencing. This map consists of 50 linkage groups with 8,521 SNP markers and an average resolution of 0.62 cM. Approximately 84% of markers are in protein-coding genes orthologous to zebrafish proteins. We performed comparative genome analysis between zebrafish and medaka, common carp, grass carp, and goldfish to study the genome evolution events in the Cyprinidae family. The comparison revealed large synteny blocks among Cyprinidae fish and we hypothesized that the Cyprinidae ancestor undergone many inter-chromosome rearrangements after speciation from teleost ancestor. The study also showed that goldfish genome had one more round of whole genome duplication (WGD) than zebrafish. Our results illustrated that most goldfish markers were orthologous to genes in common carp, which had four rounds of WGD. Growth-related regions and genes were identified by QTL analysis and association study. Function annotations of the associated genes suggested that they might regulate development and growth in goldfish. This first genetic map enables us to study the goldfish genome evolution and provides an important resource for selective breeding of goldfish.
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China.
authors.forename: You-Yi
authors.initials: YY
authors.lastname: Kuang
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China.
authors.forename: Xian-Hu
authors.initials: XH
authors.lastname: Zheng
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 10014, China.|Tianjin Fisheries Research Institute, Tianjin, 300221, China.
authors.forename: Chun-Yan
authors.initials: CY
authors.lastname: Li
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 10014, China.
authors.forename: Xiao-Min
authors.initials: XM
authors.lastname: Li
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China.
authors.forename: Ding-Chen
authors.initials: DC
authors.lastname: Cao
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China.
authors.forename: Guang-Xiang
authors.initials: GX
authors.lastname: Tong
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China.
authors.forename: Wei-Hua
authors.initials: WH
authors.lastname: Lv
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Xu
authors.affiliation: Stem Cell Program of Boston Children's Hospital, Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China.
authors.forename: Xiao-Feng
authors.initials: XF
authors.lastname: Zhang
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China.
authors.forename: Zhi-Peng
authors.initials: ZP
authors.lastname: Sun
authors.affiliation: Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
authors.forename: Shahid
authors.initials: S
authors.lastname: Mahboob
authors.affiliation: Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
authors.forename: Khalid A
authors.initials: KA
authors.lastname: Al-Ghanim
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 10014, China.
authors.forename: Jiong-Tang
authors.initials: JT
authors.lastname: Li
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China.
authors.forename: Xiao-Wen
authors.initials: XW
authors.lastname: Sun
mesh_terms: D000818:Animals; D005075:Biological Evolution; D002874:Chromosome Mapping; D003530:Cyprinidae / Q000235:genetics / Q000502:physiology; D016678:Genome; D006054:Goldfish / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D009990:Oryzias / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D026801:Synteny