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Prof E van Marle-Köster (PhD Pr. Anim. Sci.)
Genomic technology for
sustainable livestock production
2 November 2017 SA Stud Book Association
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Contents
▪ Introduction
▪ Biotechnologies
▪ Post Genomics
▪ Adoption: producer & consumer
▪ Conclusions
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World population of 9 Billion
people
2050
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Sustainable
production…Sustainable production…
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Introduction
Livestock numbers (2016 DAFF)
Beef cattle: 13.8 million
Dairy cattle:1.million
Sheep: 24,5 million
Goat: 11 million
Angora goats:700 000
Pigs: 1.57 million
Per capita consumption
Beef: 20.93 kg/year
Milk: 37.7 kg/year
Cheese:
Mutton: 3.5 kg/year
Pork: 4.8 kg/year
Broiler meat: 38.58kg
Eggs: 7.89 kg – 134 eggs
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Introduction
▪ Sustainable production:
▪ Beef
▪ Dairy
▪ Sheep & goats
▪ Pigs
▪ Poultry
▪ Challenges/Burning issues?
▪ Fertility
▪ Feed efficiency
▪ Resistance to internal &
intestinal parasites
▪ Product quality
▪ Animal health
▪ Genetics/management & nutrition
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What do we have available
to answer to the challenges?
Biotechnology…..
Reproductive biotechnology
Feed biotechnology
Genetic Biotechnology
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Biotechnology in future
Will have to address challenges such as:
• Climate change
• Adaptive breeds
• Feeding a growing population with less natural resources
• Increased efficiency
• Diseases
• Improved diagnostic testing /resistance
• Product quality & safety
• Consumer concerns & traceability
• Animal welfare
• Polled animals
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Reproduction biotechnology
▪ Regularly available:
▪ AI
▪ MOET
▪ Sexed semen
▪ Application depending on species
▪ SCNT
▪ Limited application
▪ Success rate low
▪ Relative expensive technology
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Reproduction biotechnology
▪ Stem cell technology - self renewing cells
▪ Use of somatic stem cells of genetically superior bulls
▪ Transplant into testis of less superior bulls
▪ Cells established in the seminiferous tubules
▪ Less superior bulls producing superior offspring
▪ Holds potential for sub-tropical regions/tropical adapted
▪ Developing countries
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Feed biotechnology
▪ Technology developments:
▪ Climate change - CH4 emissions in ruminants
▪ Need select cattle RFI mitigation strategy
▪ > 70 % of variation in daily CH4 explained by DMI
▪ Improve feed efficiency to reduce CH4
▪ Efficient animals eat less – growth similar
▪ Challenge lies in accurate measurements
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Feed biotechnology
▪ RC: respiration chambers
▪ Closed system
▪ More stress & DMI disrupted
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Green Emission Monitoring system
▪ Advantages:
▪ Animal can move freely
▪ Emission only when head
in chamber
▪ RFID tag recording
▪ No stress
▪ No disruption of feed intake
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Potential for collection of hard to measure
phenotypes..
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Grow Safe systems.. Collect useful phenotypes
more accurate selection of growth
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Feed biotechnology
▪ > 70% feed costs in poultry & pig production
▪ AGP’s used for enhancing production
▪ Focus on microbial populations
▪ Concept of micro gut - Ilya Metchnikov, a Russian scientist,
▪ a century ago related general human health to
▪ microbial GIT communities
▪ claimed that illness and aging caused by toxic
substances
▪ bacterial organisms found in the large intestine (Van de
Guchte et al., 2006).
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Feed biotechnology
▪ Studies of microbiome /micro gut
▪ Limited many years: culture-dependent microbiology
▪ difficult to determine the microbial species
▪ most gut microbes are dominantly anaerobic.
▪ Apply genomic technology to study the micro biome
▪ Sequencing of DNA of bacteria from gut ▪ Establish Bacterial diversity & abundance
▪ For improvement of gut health
▪ Important role in removal of AGP in mono gastric diets
▪ Use pro-biotics
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Improving the host nutrition- digestibility &
availability of feedMetabolic function
Improving intestinal morphology:
development of the microvilli & epithelial
cells
Improving immunity
▪ Protective: reducing intestinal pathogens
Functions of microbiome
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Genomic technology
▪ Commercialized & available to breeders
▪ Microsatellite marker testing
▪ 12-18 markers
▪ Limitations inbred populations
▪ SNP-based parentage testing
▪ Effective & more accurate
▪ Added value if GS is used
▪ UP Study: design appropriate panel SA beef
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Genomic technology
▪ Major genes & causative mutations
▪ Genetic variants - beneficial
▪ Genetic defects
▪ Diagnostic testing ( CVM, BLAD, DUMPS….)
▪ Genomic selection
▪ High density SNP arrays & high through put genotyping
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Genomic selectionDairy cattle
▪ Official dairy GEBV released, 2009
Holstein & Jersey
▪ Large reference populations
▪ 15 000 genotypes
▪ Holstein & Jersey
▪ Doubled genetic gain for traits of
economic importance
▪ Increased accuracy of selection at a
young age
▪ Reduce Ig
Beef cattle
▪ USA: Angus & Hereford large reference
populations > 2000 bulls
▪ Routine typing low density chips
Hereford Young Sire Testing Program
(NRSP)
• Access to 2,500 cows and heifers
Sustained Cow Fertility – (SCF)
▪ Dry Matter Intake
▪ Ireland: ICBF
▪ Routine GEBV
▪ Customized chips
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Genomic selection
▪ Technology well established
▪ Expect customized SNP chips
▪ Low and high density
▪ More affordable chips for routine genomic selection
▪ Australia/ Ireland/ USA breeds “own” chips
▪ SNP discovery with added sequencing of animals in all species
▪ Will add breed specific markers
▪ Discovery of specific QTL for LOF alleles/ traits
▪ Markers for traceability
▪ Disease resistance
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Post Genomics – functional genomics
▪ Study Differential expressed genes (DEG’s)
▪ Expression in same tissues/different breeds
▪ Different effects of diet
▪ Nutritional interactions
▪ Heat stress & other E stressors
▪ Holds potential to study adaptive mechanisms
▪ Epigenetic effects during production
▪ Expression is changes due to external factor
▪ DNA code does not change
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Precision genetics – “new kid on the
block”
▪ Design & breed with precision…
▪ Offers the chance to:
▪ “add ” a novel alleles/genes
▪ Remove unwanted trait
▪ Alter the specific trait
▪ Novel/specific modification will not alter the current
performance achieved to date
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Gene-editing
▪ Involves gene-editing (GE’s) using site specific nucleases
▪ Molecular scissors that cut DNA –high efficiency
▪ 3 types DNA endonucleases:
▪ Cas9 from bacterial CRISPR/Cas system
▪ TALEN (transcriptor-activated–like-endonuclease)
▪ ZFN’s Zinc finger nucleases
▪ Double break at target site
▪ Triggers either a non-homologous repair(NHEJ) or
conservative homology direct repair(HDR)
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Gene-editing
• First success story:
• Angus polled – polled Celtic allele
• Transfer of PC – “editing the horn allele” (US Holstein)
• Done at California Davis university
• Resulted in bull calves: Spotigy & Buri
• Important to note:
• DNA sequence used to replace the horn allele
• Originates from the same location as the polled
• Not foreign DNA
• Editing done in bovine embryo fibroblast
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Optimism with caution…..
▪ GE holds promise
▪ Easier as SCNT – use fibroblast
▪ More precise than homologous recombination(HR)
▪ Safer…
▪ GE: change in existing DNA
▪ - knock in /knock-out effect
▪ VS
▪ GMO: moving genes between species
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Optimism with caution…..
▪ BUT
▪ Expensive technology
▪ Consumer push back
▪ GE products regulated by FDA in USA
▪ First product approved & on the dinner table
▪ Atlantic Salmon( Salmo Salar)
▪ GE for fast growth
▪ Adult size in 16-28 months
▪ Eat 25%less
▪ 20 % more feed efficient
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Future…. in livestock
▪ Technology development √
▪ Genetic improvement & related research √
▪ Challenges…
▪ Consumers?
▪ Regulations?
▪ Adoption and cost benefits?
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SA Adoption & of biotechnology…
Technology Low - med high remarks
Reproduction √ √ Species depended
Feed related √
Parentage √ √ Species depended
Diagnostics √ √ Species depended
GS √
Functional genomics
X
Gene- editing X
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Biotechnology have presented animal producers andgeneticists with new insight for geneticimprovement & enhancing production
Biotechnology provides avenues for addressingchallenges not solved by conventional selection
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https://www.youtube.com/watch?v=6B-CH-NCdiY
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Thank you/ Dankie/
Ke a leboga