Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis

BMC Genomics

Melony J. Sellars¹  Nga T. T. Vu²  Kyall R. Zenger²  Jarrod L. Guppy²  Dean R. Jerry³  Catarina N. S. Silva⁴  Shannon R. Kjeldsen⁴ 

[1] Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, 4811, Townsville, QLD, Australia;CSIRO Agriculture & Food, Integrated Sustainable Aquaculture Production Program, Queensland Bioscience Precinct, 4067, St Lucia, Australia;Present address: Genics Pty Ltd, Level 5, Gehrmann Building. 60 Research Road, 4067, St Lucia, QLD, Australia;Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, 4811, Townsville, QLD, Australia;Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, 4811, Townsville, QLD, Australia;Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, 4811, Townsville, QLD, Australia;Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, 4811, Townsville, QLD, Australia;Tropical Futures Institute, James Cook University, Singapore, Singapore;Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, 4811, Townsville, QLD, Australia;

关键词: Aquaculture;    Population genetics;    Prawn;     Functional annotation;    Genotype–environment interaction;   

DOI  :  10.1186/s12864-020-07084-x

来源: Springer

【 摘 要 】

BackgroundRestrictions to gene flow, genetic drift, and divergent selection associated with different environments are significant drivers of genetic differentiation. The black tiger shrimp (Penaeus monodon), is widely distributed throughout the Indian and Pacific Oceans including along the western, northern and eastern coastline of Australia, where it is an important aquaculture and fishery species. Understanding the genetic structure and the influence of environmental factors leading to adaptive differences among populations of this species is important for farm genetic improvement programs and sustainable fisheries management.ResultsBased on 278 individuals obtained from seven geographically disparate Australian locations, 10,624 high-quality SNP loci were used to characterize genetic diversity, population structure, genetic connectivity, and adaptive divergence. Significant population structure and differentiation were revealed among wild populations (average FST = 0.001–0.107; p <  0.05). Eighty-nine putatively outlier SNPs were identified to be potentially associated with environmental variables by using both population differentiation (BayeScan and PCAdapt) and environmental association (redundancy analysis and latent factor mixed model) analysis methods. Clear population structure with similar spatial patterns were observed in both neutral and outlier markers with three genetically distinct groups identified (north Queensland, Northern Territory, and Western Australia). Redundancy, partial redundancy, and multiple regression on distance matrices analyses revealed that both geographical distance and environmental factors interact to generate the structure observed across Australian P. monodon populations.ConclusionThis study provides new insights on genetic population structure of Australian P. monodon in the face of environmental changes, which can be used to advance sustainable fisheries management and aquaculture breeding programs.

【 授权许可】

CC BY