School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.
Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
Mar Biotechnol (NY). 2024 Feb;26(1):60-73. doi: 10.1007/s10126-023-10277-6. Epub 2023 Dec 26.
Understanding the genetic composition and regional adaptation of marine species under environmental heterogeneity and fishing pressure is crucial for responsible management. In order to understand the genetic diversity and adaptability of yellowfin seabream (Acanthopagrus latus) along southern China coast, this study was conducted a seascape genome analysis on yellowfin seabream from the ecologically diverse coast, spanning over 1600 km. A total of 92 yellowfin seabream individuals from 15 sites were performed whole-genome resequencing, and 4,383,564 high-quality single nucleotide polymorphisms (SNPs) were called. By conducting a genotype-environment association analysis, 29,951 adaptive and 4,328,299 neutral SNPs were identified. The yellowfin seabream exhibited two distinct population structures, despite high gene flow between sites. The seascape genome analysis revealed that genetic structure was influenced by a variety of factors including salinity gradients, habitat distance, and ocean currents. The frequency of allelic variation at the candidate loci changed with the salinity gradient. Annotation of these loci revealed that most of the genes are associated with osmoregulation, such as kcnab2a, kcnk5a, and slc47a1. These genes are significantly enriched in pathways associated with ion transport including G protein-coupled receptor activity, transmembrane signaling receptor activity, and transporter activity. Overall, our findings provide insights into how seascape heterogeneity affects adaptive evolution, while providing important information for regional management in yellowfin seabream populations.
了解海洋物种在环境异质性和捕捞压力下的遗传组成和区域适应性对于负责任的管理至关重要。为了了解中国南方沿海黄鳍鲷的遗传多样性和适应性，本研究对生态多样性沿海地区的黄鳍鲷进行了景观基因组分析，跨度超过 1600 公里。对来自 15 个地点的 92 个黄鳍鲷个体进行了全基因组重测序，共获得了 4383564 个高质量的单核苷酸多态性（SNP）。通过进行基因型-环境关联分析，鉴定出了 29951 个适应性 SNP 和 4328299 个中性 SNP。尽管各地点之间存在高度基因流动，但黄鳍鲷表现出两种截然不同的种群结构。景观基因组分析表明，遗传结构受到多种因素的影响，包括盐度梯度、生境距离和海流。候选基因座等位基因变异的频率随盐度梯度而变化。这些基因座的注释表明，大多数基因与渗透压调节有关，如 kcnab2a、kcnk5a 和 slc47a1。这些基因在与离子转运相关的途径中显著富集，包括 G 蛋白偶联受体活性、跨膜信号转导受体活性和转运体活性。总的来说，我们的研究结果提供了关于景观异质性如何影响适应性进化的见解，同时为黄鳍鲷种群的区域管理提供了重要信息。
