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

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