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 o...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 restriction-site 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, csnkzal, cers5, co122al, creb5, dndl, dzankl, dnail, 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.展开更多
本研究通过简化基因组测序(2b-RAD)技术,对浙江省三门湾海域定居性优势无脊椎动物(哈氏仿对虾、口虾蛄、脊尾白虾、三疣梭子蟹、曼氏无针乌贼、棒锥螺和牡蛎)进行遗传结构和遗传多样性分析,以评估三门湾海域水生无脊椎动物资源现状,并...本研究通过简化基因组测序(2b-RAD)技术,对浙江省三门湾海域定居性优势无脊椎动物(哈氏仿对虾、口虾蛄、脊尾白虾、三疣梭子蟹、曼氏无针乌贼、棒锥螺和牡蛎)进行遗传结构和遗传多样性分析,以评估三门湾海域水生无脊椎动物资源现状,并为渔业可持续发展提供物种遗传资源监测依据。7个物种共获得12336~108139个SNP位点,变异位点比例为0.168%~1.571%。遗传分析结果显示,7个物种的平均核苷酸多样性(Pi)为0.147~0.306,平均观测杂合度(Ho)为0.142~0.289,多态信息含量(Polymorphism Information Content,PIC)为0.124~0.234,个体间平均遗传距离为0.118~0.246。本研究表明,三门湾水域7种代表性无脊椎动物中,生物群体变异位点比例较低,遗传多样性水平较低,且相同种群个体间的遗传分化较小,结合本次对三门湾海域渔业资源调查分析,这可能与人工增殖放流等因素有关。展开更多
基金supported by National Natural Science Foundation of China (31370047)Shenzhen Scientific R&D Grant (GJHS20160331150703934)Shenzhen Dapeng Special Program for Industrial Development (KY20160102, KY20170205)
文摘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 restriction-site 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, csnkzal, cers5, co122al, creb5, dndl, dzankl, dnail, 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.
文摘本研究通过简化基因组测序(2b-RAD)技术,对浙江省三门湾海域定居性优势无脊椎动物(哈氏仿对虾、口虾蛄、脊尾白虾、三疣梭子蟹、曼氏无针乌贼、棒锥螺和牡蛎)进行遗传结构和遗传多样性分析,以评估三门湾海域水生无脊椎动物资源现状,并为渔业可持续发展提供物种遗传资源监测依据。7个物种共获得12336~108139个SNP位点,变异位点比例为0.168%~1.571%。遗传分析结果显示,7个物种的平均核苷酸多样性(Pi)为0.147~0.306,平均观测杂合度(Ho)为0.142~0.289,多态信息含量(Polymorphism Information Content,PIC)为0.124~0.234,个体间平均遗传距离为0.118~0.246。本研究表明,三门湾水域7种代表性无脊椎动物中,生物群体变异位点比例较低,遗传多样性水平较低,且相同种群个体间的遗传分化较小,结合本次对三门湾海域渔业资源调查分析,这可能与人工增殖放流等因素有关。
