REDUCING THE ENVIRONMENTAL IMPACT OF OYSTER CULTURE BY SELECTING FOR SPAT THAT MOST EFFICIENTLY USES NATURAL RESOURCES by Stephanie Anne Hall Submitted in partial fulfilment of the requirements for the degree of Master of Science at Dalhousie University Halifax, Nova Scotia March 2017 © Copyright by Stephanie Anne Hall, 2017 Dedicated to my parents, Stephen and Eileen Whom have been my biggest supporters and source of inspiration ii Table of Contents LIST OF TABLES ........................................................................................................... ix LIST OF FIGURES ...........................................................................................................x ABSTRACT ...................................................................................................................... xi LIST OF ABBREVIATIONS AND SYMBOLS USED .............................................. xii ACKNOWLEDGEMENTS .......................................................................................... xiv CHAPTER 1: INTRODUCTION .....................................................................................1 1.1. Introduction .........................................................................................................1 1.2. Oyster Industry ...................................................................................................1 1.2.1. History of the oyster industry in North America ..................................................... 1 1.2.2. Oyster aquaculture in Canada .................................................................................. 2 1.3. The Eastern oyster (Crassostrea virginica) ........................................................3 1.3.1. Natural distribution range ........................................................................................ 3 1.3.2. Production in North America ................................................................................... 4 1.4. Features and anatomy of the Eastern oyster (Crassostrea virginica) .............4 1.4.1. General anatomy ...................................................................................................... 4 1.4.2. Digestive system ...................................................................................................... 6 1.4.3. Reproduction ............................................................................................................ 7 1.4.3.1. Larval lifecycle ......................................................................................................... 8 1.4.4. Environmental tolerances and growth ...................................................................... 8 1.5. The Eastern oyster aquaculture production ...................................................10 1.5.1. Oyster culture in the Maritime Provinces .............................................................. 10 1.5.1.1. Wild spat collection ................................................................................................ 10 1.5.1.2. Grow-out methods .................................................................................................. 10 1.5.2. Hatchery production methods ................................................................................ 11 iii 1.5.2.1. Feed production ..................................................................................................... 11 1.5.2.2. Broodstock conditioning ........................................................................................ 11 1.5.2.3. Larval rearing ........................................................................................................ 14 1.5.2.4. Spat rearing ........................................................................................................... 15 1.6. Production issues with oyster aquaculture industry ......................................16 1.6.1. Environmental impacts of oyster aquaculture ........................................................ 16 1.6.1.1. Exceeding carrying capacity of an ecosystem ....................................................... 16 1.6.1.2. Biodeposits: Implications for benthic environment ............................................... 16 1.6.2. Spat collection variability ...................................................................................... 17 1.7. Review of genomic information known on the Eastern oysters ....................18 1.7.1. General genetic information known ....................................................................... 18 1.7.2. Genetic markers ..................................................................................................... 19 1.7.2.1. Disease markers ..................................................................................................... 19 1.7.2.2. Growth markers ..................................................................................................... 19 1.7.2.3. Population genomics .............................................................................................. 20 1.8. Development of a hatchery-based selective breeding program ....................21 1.8.1. Existing selective breeding programs .................................................................... 21 1.8.2. Marker-assisted selective breeding programs ........................................................ 23 1.8.2.1. RAD-seq analysis: a tool for marker discovery in non-model species .................. 23 1.8.3. Importance of development of a hatchery industry in Atlantic Canada ................. 24 1.8.4. Important traits for a breeding program ................................................................. 25 1.8.4.1. Stress and disease resiliency .................................................................................. 25 1.8.4.2. Feed efficiency ratio and growth ........................................................................... 25 1.8.5. Implications of introducing hatchery reared spat into ecosystem .......................... 27 1.9. Project Rationale ...............................................................................................29 1.10. Objectives ...........................................................................................................30 1.11. References ..........................................................................................................30 iv CHAPTER 2: COMPARISON OF ABSORPTION EFFICIENCIES BETWEEN WILD AND CULTURED OYSTERS, (CRASSOSTREA VIRGINICA) FROM BOUCTOUCHE, NEW BRUNSWICK DURING A THERMAL CHALLENGE ....44 2.1. Introduction .......................................................................................................44 2.2. Objectives ...........................................................................................................49 2.3. Hypothesis ..........................................................................................................49 2.4. Materials and Methods .....................................................................................50 2.4.1. Oyster collection and acclimation .......................................................................... 50 2.4.2. Thermal stress challenge ........................................................................................ 51 2.4.3. Absorption efficiency ............................................................................................. 51 2.4.4. Condition index ...................................................................................................... 52 2.4.5. Statistical analysis .................................................................................................. 52 2.5. Results ................................................................................................................52 2.5.1. Absorption efficiency ............................................................................................. 52 2.5.2. Condition index ...................................................................................................... 54 2.5. Discussion ...........................................................................................................54 2.5.1. Absorption efficiency ............................................................................................. 54 2.5.1.1. Source of oysters .................................................................................................... 54 2.5.1.2. Temperature ........................................................................................................... 56 2.5.1.3. Other potential factors effecting absorption efficiency results .............................. 57 2.5.2. Condition index ...................................................................................................... 59 2.6. Conclusions ........................................................................................................60 2.7. References ..........................................................................................................61 CHAPTER 3: SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) IN THE EASTERN OYSTER (CRASSOSTREA VIRGINICA) CORRELATED TO ABSORPTION EFFICIENCY USING RAD-SEQUENCING AND DE NOVO ANALYSIS .......................................................................................................................68 v 3.1. Introduction .......................................................................................................68 3.1. Objectives and Hypothesis................................................................................72