BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, 518083, China.
Sci China Life Sci. 2018 Aug;61(8):934-946. doi: 10.1007/s11427-017-9161-4. Epub 2018 Mar 12.
The orange-spotted grouper, Epinephelus coioides, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study (GWAS) on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restrictionsite associated DNA sequencing. In this research, 261,366 single nucleotide polymorphisms (SNPs) were developed, in which 110 SNPs were identified to be correlated with growth and 20 SNPs were further confirmed to be associated with both body weight and total length. From these identified SNPs, we annotated a total of 34 genes, including adgrb2, csnkza1, cers5, col22a1, creb5, dnd1, dzank1, dnai1, npy2r, fat3, lrrk2, lrp5, map3k9, and so on. Among these candidate genes, npy2r (neuropeptide Y receptor Y2) was reported to play a critical role in growth of the orange-spotted grouper. In addition, population structure, principal component analysis, kinship matrix and linkage disequilibrium were examined to verify the accuracy and reliability of our GWAS results. Our data will also provide a valuable genetic resource for further marker-assisted selection program to improve growth quality in groupers.
黄斑石斑鱼，Epinephelus coioides，由于其重要的经济价值，是中国和东南亚国家最受欢迎的鱼类之一。然而，黄斑石斑鱼生长的分子机制尚未完全了解。在此，我们对 198 个自然种群进行了全基因组关联研究（GWAS），旨在通过限制酶相关 DNA 测序筛选黄斑石斑鱼全基因组中的生长相关基因座。在这项研究中，开发了 261366 个单核苷酸多态性（SNP），其中 110 个 SNP 与生长相关，20 个 SNP 进一步证实与体重和全长相关。从这些鉴定的 SNP 中，我们总共注释了 34 个基因，包括 adgrb2、csnkza1、cers5、col22a1、creb5、dnd1、dzank1、dnai1、npy2r、fat3、lrrk2、lrp5、map3k9 等。在这些候选基因中，npy2r（神经肽 Y 受体 Y2）被报道在黄斑石斑鱼的生长中起着关键作用。此外，还检查了种群结构、主成分分析、亲缘关系矩阵和连锁不平衡，以验证我们 GWAS 结果的准确性和可靠性。我们的数据也将为进一步的标记辅助选择计划提供有价值的遗传资源，以提高石斑鱼的生长质量。
