title: Gene map of large yellow croaker (Larimichthys crocea) provides insights into teleost genome evolution and conserved regions associated with growth.
abstract: The genetic map of a species is essential for its whole genome assembly and can be applied to the mapping of important traits. In this study, we performed RNA-seq for a family of large yellow croakers (Larimichthys crocea) and constructed a high-density genetic map. In this map, 24 linkage groups comprised 3,448 polymorphic SNP markers. Approximately 72.4% (2,495) of the markers were located in protein-coding regions. Comparison of the croaker genome with those of five model fish species revealed that the croaker genome structure was closer to that of the medaka than to the remaining four genomes. Because the medaka genome preserves the teleost ancestral karyotype, this result indicated that the croaker genome might also maintain the teleost ancestral genome structure. The analysis also revealed different genome rearrangements across teleosts. QTL mapping and association analysis consistently identified growth-related QTL regions and associated genes. Orthologs of the associated genes in other species were demonstrated to regulate development, indicating that these genes might regulate development and growth in croaker. This gene map will enable us to construct the croaker genome for comparative studies and to provide an important resource for selective breeding of croaker.
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Yindou Road, Xiamen, P.R. China.
authors.forename: Shijun
authors.initials: S
authors.lastname: Xiao
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Yindou Road, Xiamen, P.R. China.
authors.forename: Panpan
authors.initials: P
authors.lastname: Wang
authors.affiliation: CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, P.R. China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Yindou Road, Xiamen, P.R. China.
authors.forename: Lujing
authors.initials: L
authors.lastname: Fang
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Yindou Road, Xiamen, P.R. China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, P.R. China.
authors.forename: Jiong-Tang
authors.initials: JT
authors.lastname: Li
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Yindou Road, Xiamen, P.R. China.
authors.forename: Zhi-Yong
authors.initials: ZY
authors.lastname: Wang
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D002875:Chromosomes / Q000235:genetics; D017124:Conserved Sequence; D019143:Evolution, Molecular; D015321:Gene Rearrangement / Q000235:genetics; D008040:Genetic Linkage; D016678:Genome; D023281:Genomics; D009990:Oryzias / Q000235:genetics; D010473:Perciformes / Q000235:genetics* / Q000254:growth & development*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D023701:Smegmamorpha / Q000235:genetics; D026801:Synteny / Q000235:genetics; D015027:Zebrafish / Q000235:genetics