Selective Breeding. Maren Wellenreuther, Senior Scientist MWC Teacher professional Development 2017

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1 Selective Breeding Maren Wellenreuther, Senior Scientist MWC Teacher professional Development 2017

2 What is selective breeding? The selection of desirable traits and choosing which individuals breed in order to increase these traits in the offspring

3 It s an old concept 1) Traditional animal breeding Phenotypic selection Been around for 1000s of years Breeders select observable phenotypic traits such as size, colour and shape 7000 BC

4 Quantitative Genetics Addition of quantitative genetics 100 years ago Allows the calculation of individual breeding values for genetic improvement Ronald Fisher, 1918 The Correlation between Relatives on the Supposition of Mendelian Inheritance

5 Breeding in the genomics era Revolution in genomics applications caused a paradigm shift in animal breeding 2) Genomics assisted breeding schemes Marker assisted selection (MAS)/Genomic selection (GS) Few decades/10 years MAS concentrates on a few markers GS uses a dense set of genome-wide markers Tracks all genetic variance

6 Advantages of genomics informed breeding 1. Selection on polygenic traits Many quantitative traits (growth rates, disease resistance ) are made up of many genes with small effect. Difficult to select on with phenotypic selection. 2. Improved time-efficiency Traits can be selected on before they are expressed. 3. Lower costs Breeding gains can be expected faster compared to traditional methods. Knowledge of relatedness matrices means that animals can be held together.

7 Biological implications of breeding: cons Loss of variety Can change evolutionary trajectories Detrimental if individuals carry a fault Animal discomfort NZ Livestock Improvement Cooperation Spontaneous hairy genetic mutation -lactation failure, -excessively hairy pelage and -thermoregulatory dysfunction

8 Belgian Blue: The super cow

9 Biological implications of breeding: pros Requires no company patent Higher profit Can enhance disease/stress tolerance Can create new varieties Exotic varieties of maize are collected to add genetic diversity when selectively breeding new domestic strains

10 Outline of talk A genomics assisted breeding programme on the native NZ fish snapper 1. Background a) The PFR seafood group b) Aquaculture in New Zealand and early breeding efforts at PF 2. Selective breeding of snapper Phenotyping software Genomic resources 3. Future goals Handbook for other species

11 Seafood Portfolio

12 Nelson Seafood Research Facility Seafood Research Facility

13 Nelson Seafood Research Facility

14 Aquaculture in New Zealand Aquaculture is fastest growing animal production sector Three species together contribute to more than 90% of production: Greenshell mussels, Pacific oysters and King salmon Urgent need for alternatives to reduce reliance on the big three Opportunity: develop new species to diversify market

15 Snapper is an ideal candidate Valuable species Domesticated for 10+ years Spawns readily Variable growth Same age

16 Challenges when breeding fish Essentially wild: Broodstock only a few generations removed from wild ancestors Snapper No obvious individual differences: use of expensive tags Hard to sex based on phenotype or genotype, i.e. lack sexual dimorphism Spawning biology: group spawning

17 Rapid phenotyping ID individuals based on morphology Ontogenetic time series Phenotypic traits Morphometrics (e.g. length) Colour Deformities Life history events (e.g. disease) Automatically extracts traits and send to database

18 Colour Morphology

19 Genomic approaches & resources Snapper genome Genome status Scaffolds: 5,998 Scaffold length : 738 Mb CEGMA - genes complete: 82% CEGMA - genes partial: 95% Optical mapping N50 before: N50 after: 1.5 Mb 4.4 Mb

20 Genotyping: DNA extraction» High quality DNA:» >20kb DNA bands» Low fragmentation» Major improvements:» Tail fins» Heat treatment» 80 o C» 5 min» Pre-storage Heat treated Untreat ed

21 Genotyping by Sequencing (GBS) (From Elshire et al., 2011 PLOS One)

22 Data output» HiSeq 2500» Single end» 8 lanes» >180M reads per lane Lane Single Reads Data Output (Gb) 1 194,831, ,497, ,367, ,657, ,398, ,163, ,408, ,600, Total 1,628,925,

23 Data output Total Reads: 1,628,925,469 F0: Grandparents n=25 F1: Parents n=70 F2: Offspring n=577 Filtered Reads: 1,524,492, ,468 20,311 10,968 SNPs with > 7x coverage SNPs present in 75% of population and with MAF > 0.05 SNPs placed on linkage map

24 F0 - Grandparents F1 Parents Male F2 - Offspring Female Unknown

25 100mm Female Male 100mm

26 Linkage map construction Software: LepMap2 Informative individuals: 297 LOD limit: 14 Mapped loci: 10,968 Total length: 1,363 cm Average marker spacing : cm

27 Weight (1 year old) Software: GridQTL, Analysis: Half-sib (n = 224)

28 Next steps

29 Summary» Breeding programme build on solid knowledge of phenotype and genotype» Resources will be available for many years» Can be modified for use on other species Hatchery reared fish are also useful for» Supplementation of wild populations

30 2014 snapper release Ceremony at the Seafood Research Facility to release 7000 karati/snapper fingerlings into the Nelson Haven In recognition of the late Te Rangi o Kiwa John Morgan of Ngati Rarua and his many decades of contribution to fisheries in Te Tau Ihu

31 Event was co-hosted by MPI and was part of a two week release programme of more than 35,000 fish

32 Thank you