Genome-Wide Association Study of Body Shape-Related Traits in Large Yellow Croaker ( Larimichthys crocea )
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ORIGINAL ARTICLE
Genome-Wide Association Study of Body Shape-Related Traits in Large Yellow Croaker (Larimichthys crocea) Shengnan Kong 1,2 & Zhixiong Zhou 2 & Tao Zhou 2 & Ji Zhao 1,2 & Lin Chen 2 & Huanling Lin 2 & Fei Pu 1 & Qiaozhen Ke 1,2 & Huaqiang Bai 2 & Peng Xu 1,2 Received: 8 May 2020 / Accepted: 5 July 2020 # Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract Large yellow croaker (Larimichthys crocea) is one of the most important cultured marine fish on the southeast coast of China. Its body shape is important for the aquaculture industry since it affects the behavior such as swimming, ingesting, and evading, as well as customer preference. Due to the greater consumer demand of small head, slender body large yellow croaker, selecting and breeding of slender individuals with the assistance of genetic markers will benefit the industry quickly. In this study, several traits were employed to represent body shape, including body depth/body length (BD/BL), body thickness/body length (BT/BL), caudal peduncle depth/caudal peduncle length (CPDLR), tail length/body length (TL/BL), and body area/head area (BA/HA). Genome-wide association study was conducted with a panmictic population of 280 individuals to identify SNP and genes potentially associated with body shape. A set of 20 SNPs on 12 chromosomes were identified to be significantly associated with body shape-related traits. Besides, 5 SNPs were identified to be suggestive associated with CPDLR and BT/BL. Surrounding these SNPs, we found some body shape-related candidate genes, including fabp1, acrv1, bcor, mstn, bambi, and neo1, which involved in lipid metabolism, TGF-β signaling, and BMP pathway and other important regulatory pathways. These results will be useful for the understanding of the genetic basis of body shape formation and helpful for body shape controlling of large yellow croaker by using marker-assisted selection. Keywords Large yellow croaker . Body shape . ddRAD . GWAS . Genetic improvement
Introduction Body shape, as a complex phenotypic trait, is closely linked to the interactions between genetic background and enviroment (Rogers et al. 2012; Rogers and Jamniczky 2014). In teleost, shape differentiation can influence the ability to swim, forage, and evade predators (Walker 2010; Reid and Peichel 2010). Shengnan Kong and Zhixiong Zhou contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10126-020-09983-2) contains supplementary material, which is available to authorized users. * Peng Xu [email protected] 1
State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde 352103, China
2
Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
Hence, dissecting the genomic basis may contribute to the evolution research of body shape in teleost. For example, an elongated body shape could reduce drag and enhance swim
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