Lal Monal M, Southgate Paul C, Jerry Dean R, Zenger Kyall R
Centre for Sustainable Tropical Fisheries and Aquaculture (CSTFA), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia; College of Marine and Environmental Sciences (CMES), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia.
Mar Genomics. 2016 Feb;25:57-68. doi: 10.1016/j.margen.2015.10.010. Epub 2015 Nov 3.
Population genomic investigations on highly dispersive marine organisms typically require thousands of genome-wide SNP loci to resolve fine-scale population structure and detect signatures of selection. This information is important for species conservation efforts and stock management in both wild and captive populations, as well as genome mapping and genome wide association studies. Double digest Restriction site-Associated DNA Sequencing (ddRADseq) is a recent tool for delivering genome wide SNPs for non-model organisms. However, its application to marine invertebrate taxa has been limited, particularly given the complex and highly repetitive nature of many of these organisms' genomes. This study develops and evaluates an optimised ddRADseq technique together with associated analyses for generating genome-wide SNP data, and performs population genomic analyses to inform aquaculture and fishery management of a marine bivalve, the black-lip pearl oyster Pinctada margaritifera. A total of 5243 high-quality genome-wide SNP markers were detected, and used to assess population structure, genome diversity, detect Fst outliers and perform association testing in 156 individuals belonging to three wild and one hatchery produced populations from the Fiji Islands. Shallow but significant population structure was revealed among all wild populations (average pairwise Fst=0.046) when visualised with DAPC and an individual network analysis (NetView P), with clear evidence of a genetic bottleneck in the hatchery population (NeLD=6.1), compared to wild populations (NeLD>192.5). Fst outlier detection revealed 42-62 highly differentiated SNPs (p<0.02), while case-control association discovered up to 152 SNPs (p<0.001). Both analyses were able to successfully differentiate individuals between the orange and black tissue colour morphotypes characteristic of this species. BLAST searches revealed that five of these SNPs were associated with a melanin biosynthesis pathway, demonstrating their biological relevance. This study has produced highly informative SNP and population genomic data in P. margaritifera, and using the same approach promises to be of substantial value to a range of other non-model, broadcast-spawning or marine invertebrate taxa.
对高度分散的海洋生物进行群体基因组研究通常需要数千个全基因组SNP位点，以解析精细尺度的群体结构并检测选择特征。这些信息对于野生和圈养种群的物种保护及种群管理，以及基因组图谱绘制和全基因组关联研究都很重要。双酶切限制性位点关联DNA测序（ddRADseq）是一种为非模式生物提供全基因组SNP的最新工具。然而，其在海洋无脊椎动物类群中的应用一直有限，尤其是考虑到许多此类生物基因组的复杂性和高度重复性。本研究开发并评估了一种优化的ddRADseq技术以及相关分析，用于生成全基因组SNP数据，并进行群体基因组分析，以为一种海洋双壳贝类——黑唇珍珠牡蛎珠母贝的水产养殖和渔业管理提供信息。共检测到5243个高质量的全基因组SNP标记，并用于评估156个个体的群体结构、基因组多样性、检测Fst离群值以及进行关联测试，这些个体来自斐济群岛的三个野生种群和一个孵化场培育的种群。当用DAPC和个体网络分析（NetView P）进行可视化时，在所有野生种群中揭示出了微弱但显著的群体结构（平均成对Fst = 0.046），与野生种群（NeLD>192.5）相比，孵化场种群中存在明显的遗传瓶颈证据（NeLD = 6.1）。Fst离群值检测揭示了42 - 62个高度分化的SNP（p<0.02），而病例对照关联发现了多达152个SNP（p<0.001）。两项分析都能够成功区分该物种特有的橙色和黑色组织颜色形态型之间的个体。BLAST搜索显示，其中五个SNP与黑色素生物合成途径相关，证明了它们的生物学相关性。本研究在珠母贝中产生了信息量丰富的SNP和群体基因组数据，使用相同方法有望对一系列其他非模式、散播产卵或海洋无脊椎动物类群具有重要价值。
