Presented by Jasper Rees, Agricultural Research Council, South Africa, at the Workshop on Animal Genetic Research for Africa (Biosciences for Farming in Africa), Nairobi, 10-11 September 2015

1. Livestock genomics—Experiences from South Africa
Jasper Rees
Agricultural Research Council, South Africa
ReesJ@arc.agric.za
Animal Genetic Research for Africa (Biosciences for Farming
in Africa), Nairobi, 10-11 September 2015

2. Livestock Genomics
• Population diversity studies - SNPs
– Cattle, goats, chickens
• Diversity studies – genome sequencing
– Nguni Cattle, buffalo
• Genetic studies
– Swakara sheep; pig disease
• Genomic Selection
– Livestock Genomics Consortium

3. Sequence based Genomics Applications
Sequencing applications
• Genomes,
• De novo and re-sequencing
• SNPs and CNV calling
• Transcriptomes,
• De novo and re-sequencing
• SNPs and splicing variation
• Expression profiling
• Small RNA
• discovery and expression
analysis
SNP applications
• GWAS
• Association Genetics
• Cultivar, Breed and Parental ID
• Genomic Selection
• SNP validation
• Candidate Genes
• Diversity studies
• Methylation
SSR applications
• Cultivar, Breed and Parental ID
• Population Genetics

4. Commercial
meat type breeds
B: Savanna
C: Kalahari Red
D: Boer
Developed breeds
E-G: Village ecotypes phenotypic representations
Kwazulu-Natal (Zulu)
North West (Tswana)
Limpopo (Venda)
Eastern Cape (Xhosa)
Local language
and does not
represent breeds
Naming system
H: Feral goat population
Tankwa
Genetics of SA indigenous goat populations
Nguni ecotype
• SA Veld goats
• Indigenous
ecotypes
• Kept by breeders
in Kwazulu-Natal

5. PC1 vs PC2
Boer
Savanna
Kalahari Red
Zulu
Venda
Tswana
Xhosa
Tankwa
Commercial
Village ecotypes
Nguni
PC
A
Population
PC1 Commercial vs
Indigenous
PC2 Tankwa
PC3 Zulu/Venda vs
Tswana/Xhosa
PC4 Tswana vs Xhosa
PC5 Outliers of Savanna
and KR
PCA shows genetic identity of SA Goats

6. Individual #
0.00.20.40.60.81.0
Individual #
0.00.20.40.60.81.0
Individual #
0.00.20.40.60.81.0
Individual #
0.00.20.40.60.81.0
Individual #
0.00.20.40.60.81.0
Individual #
Ancestry
0.00.20.40.60.81.0
Boer KR Nguni Savanna Tankwa Tswana Venda Xhosa Zulu
K = 7
K = 6
K = 5
K = 4
K = 3
K = 2
Population structure using Admixture

7. Genetic value of SA Indigenous Goats
• Populations clustered according to their production systems
• Genetic differences between commercial, village and feral goat
populations
• Weak between commercial populations differences
• The feral goat population stands out as a unique genetic resource
separated from both the commercial and village ecotypes
 Diverse gene pool with indications of unique set of alleles prevailing in
different production systems
 With accurate descriptors of the production environment we might be able
to determine alleles and genotypes conferring genetic adaptation

8. Copy Number Variations in the genomes of SA
indigenous
• CNVs
 Structural variation randomly distributed in the genome.
 Could be associated with production, disease resistance as well as
genetic defects traits
• Investigating CNVs in SA cattle using Bovine SNP50K data
• Infer on associations of CNVs to economic & adaptation traits

9. Structural variations in genomes

10. Pathways enriched by genes covered by
CNVR|regions in Nguni cattle

11. Signatures of selection in indigenous cattle

12. Genomic regions under selection in the
SA cattle and their associated QTLs.
Breeds1 BTA UMD3.1
coordinate (bp)
SNPS Size (kb) Smoothed
FST
Candidate genes QTL
AFR vs HOL,
NGU vs HOL
3 35,255,950-
35,785,053
5 529.10 0.28 KCNA2, CYM PROK1,
PROK1, LAMTOR,
SLC16A4, UBL4B
Milk fat percentage, milk
protein percentage, body
weight, height, somatic cell
count
AFR vs HOL,
NGU vs HOL
5 4,472,786-
4,598,476
4 125.69 0.42 - Tenderness score, teat
placement, shear force
AFR vs HOL,
NGU vs HOL
5 114,085,555-
114,594,935
3 509.38 0.48 ERC1, FBXL14,
WNT5B, ADIPOR2
Hip height, rump length,
calving ease, height,
ovulation, type, rump angle
NGU vs HOL 7 71,038,040-
71,240,079
4 202.04 0.25 EBF1 Somatic cell count, milking
speed, tick resistance, heel
depth, social separation--
vocalisation

13. “I gave blood…. Did you?”

14. Wildlife genetics – conservation or
commercialisation?

15. Finding the gene for Big Horns…

16. Engineering the gene for No Horns
• Polled gene has been mapped
• Start of genome engineering

17. Stress resistance genes
• Senepol cattle are a heat resistant temperate
zone breed
• Genetic analysis shows a mutation truncating
the PRLR (prolactin receptor) protein which
results in resistance to heat stress - short hair,
sweating
• If engineered into other breeds will it result in
heat tolerance?

18. Livestock Pathogens and vaccines
• Foot and mouth disease
• Avian flu and Newcastle disease virus
• Bluetongue
• Rabies
• Rift Valley Fever
• Anthrax and related Bacilli
• Bovine Tuberculosis
• Salmomella, E.coli
• Tetse flies
• Ticks (many!)
• Molecular modeling on FMD vaccine program

19. Insect Research
• Vectors for Plant, animal and human
pathogens
• Parasitoid wasps and other predators
• Plants – SIT, fungal, viral, nematodes
• Animals – tick vaccines
• Pests and Malaria – GM male sterile
technology - Oxitec

20. Livestock at Risk
35% of 15 m. Cattle
55% of 6.5 m. Sheep
20% of 25 m. Goats
Tick distribution in South Africa
Not found in the Karoo

21. Sterile Insect Technique
• SIT was pioneered in the 1950s by Bushland and
Knipling
• Awarded the 1992 World Food Prize.
• Used in 1954 on the island of Curacao to control
the New World screwworm
• The US officially eradicated the screwworm using
SIT in 1982
• Central America declared screwworm free in
2001.

22. Navigation ²
English
Sterile insect technique for fruit fly control
9/9/2015 FruitFly Africa | Plan, Co-ordinate and Manage Area-wide Fruit Fly Control Programmes
Navigation
Welcome to FruitFly Africa
South Africa is host to two species of fruit flies of economic importance, the Mediterranean fruit fly
(Ceratitis capitata) and the Natal fruit fly (C. rosa). Both species are international quarantine pests.
Fruit Fly Africa is an industry owned service body created to plan, co-ordinate and execute area-wide fruit fly
control programmes. This is done in collaboration with producers and local government in various production
regions in partnership with the National Department of Agriculture, Forestry and Fisheries (DAFF).
The programmes are based on international best practice as contained in the Technical Manual drafted in line
with the requirements and conditions set by the International Atomic Energy Association (IAEA) and the
English
Navigation ²
Welcome to FruitFly Africa
South Africa is host to two species of fruit flies of economic importance, the Mediterranean fruit fly
(Ceratitis capitata) and the Natal fruit fly (C. rosa). Both species are international quarantine pests.
Fruit Fly Africa is an industry owned service body created to plan, co-ordinate and execute area-wide fruit fly
control programmes. This is done in collaboration with producers and local government in various production
regions in partnership with the National Department of Agriculture, Forestry and Fisheries (DAFF).
The programmes are based on international best practice as contained in the Technical Manual drafted in line
with the requirements and conditions set by the International Atomic Energy Association (IAEA) and the
Agricultural Research Council (ARC). Area based programmes are tailor-made for specific production regions.
The Sterile Insect Technique (SIT) forms part of the integrated approach.
Responsibilities of Fruitfly Africa
English
Navigation ²
Welcome to FruitFly Africa
South Africa is host to two species of fruit flies of economic importance, the Mediterranea
(Ceratitis capitata) and the Natal fruit fly (C. rosa). Both species are international quarantin
Fruit Fly Africa is an industry owned service body created to plan, co-ordinate and execute area-
control programmes. This is done in collaboration with producers and local government in variou
regions in partnership with the National Department of Agriculture, Forestry and Fisheries (DAFF
The programmes are based on international best practice as contained in the Technical Manual
with the requirements and conditions set by the International Atomic Energy Association (IAEA) a
Agricultural Research Council (ARC). Area based programmes are tailor-made for specific produ
The Sterile Insect Technique (SIT) forms part of the integrated approach.
Responsibilities of Fruitfly Africa
Establishment of operations and communications centres responsible for effective liaison o
management activities in all relevant areas.
Engli
9/9/2015 FruitFly Africa | Plan, Co-ordinate and Manage Area-wide Fruit Fly Control Programmes
Navigation ²
English

23. Self-Limiting Gene function in
transgenic insects9/9/2015 How the Self-Limiting Gene Works | Oxitec
http://www.oxitec.com/ridl-science/understanding-ridl-science/molecular-biology/
http://www.oxitec.com/ridl-science/understanding-ridl-science/mole
How the Self-Limiting Gene Works | Oxitec
9/9/2015 How the Self-Limiting Gene Works | Oxitec
http://www.oxitec.com/ridl-science/understanding-ridl-science/molecular-biology/

24. Production of self-limiting insects
• Insects produced
with tetracycline
• Adults released to
mate with wild
populations
• Progeny die
without Tet
• GM insects have
fluorescent
markers for
tracking

25. 1. Identification of problem pest/s [could be due to resistance (efficacy), residues
(reduced MRL's), withdrawal of chemical active from market due to health and/or
environmental issues, chemical costs (importation, etc.), and/or organic market
requirements]
2. Survey/collection of pathogens (directly: diseased insects and/or indirectly from
soil using the insect-trap method)
3. Isolation of pathogens with potential for development as bioinsecticide/s (verify
pathogenicity – Koch’s Postulates)
4. Bioassays (LC50 and LT50) to select most virulent isolate/s
5. Mass production and formulation (quality control in terms of germination, purity
and shelf-life)
6. Field trials to generate data for registration (the package would include
efficacy, shelf-life, quality and possibly toxicological data)
7. Marketing/distribution
DEVELOPMENT OF BIO-INSECTICIDES: 7 KEY STEPS

26. October 2010
www.irac-online.org
Current status of insect resistance against chemical insecticides

27. INSECT PATHOGENS AND THEIR USE IN PEST CONTROL
5 ENTITIES:
1. Bacteria*
2. Viruses
3. Protozoa
4. Nematodes
5. Fungi*
Live cells applied (e.g., Serratia entomophila – grubs in Nieu Zeeland)
Toxin applied (e.g., Bacillus thuringiensis produces Cry toxins)
(Bt var. kurstaki, aizawai, israelensis)
Transgenic plants (e.g., Bt toxin expression within the host plant)
Virions applied (e.g., Baculoviridae: NPV / GV – against Lepidoptera)
Spores applied (e.g., Nosema locustae – grasshoppers and crickets)
Infective juveniles (IJ’s) applied (e.g., Heterorhabditis bacteriophora – white grubs
Steinernema carpocapsae – root weevils)
Spores applied (e.g., Metarhizium anisopliae – white grubs, spittlebugs, locusts
Beauveria bassiana – white grubs, aphids, whiteflies)
* Including endophytic associations with host plant

28. TYPICAL SIGNS OF INFECTION WITH BEAUVERIA
Larval stage infected with B. bassina (left). Photo: JL Hatting Fungal growth mainly confined to cadaver. Photo: T Goble
Adult beetle infected with B. bassiana. Photo: JL Hatting
Also look for other infected Coleoptera !
JL Hatting JL Hatting

29. TYPICAL SIGNS OF INFECTION WITH METARHIZIUM
Larval and adult stage infected with Metarhizium
Dry spore columns (‘sporocarps’) on insect cuticle
Photo: Bekker Underwood® Photo: T. Goble
As a general rule, if the fungus is white, purplish or yellow/green to
orange in colour, and mainly confined to the insect body, collect it !

30. Survey/collection of pathogens
Direct collection of diseased/dead insects
…BACTERIA…
Milky disease caused by Bacillus popilliae. Photo: T. Jackson
Grubs infected with S. marcescens.
Photo: T. Jackson
In vitro culture of S. marcescens (Photo: JL Hatting)
Bacillus popilliae, B. thuringiensis, Serratia entomophila, S. marcescens and S. proteamaculans

31. Survey/collection of pathogens
Direct collection of diseased/dead insects
…NEMATODES…
Heterorhabditis bacteriophora, H. zealandica
Steinernema carpocapsae, S. glaseri and S. scarabaei
Carry symbiotic bacteria
Two important genera:
Heterorhabditis and Steinernema
Cadaver with light brown, yellow to cream colour
Steinernema sp. Heterorhabditis sp.
Dark brown to brick red colour

32. Field trial with fungus against bollworm, Helicoverpa armigera
Field trials being conducted by ARC-SGI and PHP (Pty) Ltd.
Fungus: Nomuraea rileyi

33. ENTOMOPATHOGENIC FUNGUS AGAINST BOLLWORM, Helicoverpa armigera
0
20
40
60
80
100
120
1 2 3 4 5 6 7 8 9 10 11 12 13 14
A
B
C
D
E
F
G
Control
Mortality
1
3
5
7
9
11
13
0
2
4
6
8
10
12
14
16
18
20
A
B
C
D
E
F
G
Control
Food intake
Time
Time
Fungus: Nomuraea rileyi

34. The cactus mealybug, Hypogeococcus pungens has been released as a biological
control agent against queen of the night cactus infestations in South Africa. The agent
has established well at all release sites, and has proved to be extremely damaging. How-
ever, since only the male mealybugs can fly, the agents’ dispersal is limited, and manual
intervention is required in areas where they are not present.
DESCRIPTION
Mealybugs are covered in a mass of white, waxy threads, and live in colonies clustered
on the stem tips or along the ridges (i). Females are pinkish, the size of a pinhead, and
never emerge from beneath the threads. Immature females are mobile only briefly, while
males remain mobile, complete their life cycle on a more exposed part of the plant, and
grow wings when they mature.
LIFE CYCLE
Females lay single eggs that hatch within minutes. The nymphs are called crawlers (ii)
because they have functional legs which they use to crawl to the tips of plants. From
here, they may be dispersed by wind to nearby plants where they congregate into new
colonies. Females become sessile, continue producing wax, have 3 nymphal stages, and
mature as adults after about a month. After their second moult, males pupate in a white,
ical
gent
ow-
nual
red
N PLANTS
ICA
i
ngens has been released as a biological
tus infestations in South Africa. The agent
as proved to be extremely damaging. How-
he agents’ dispersal is limited, and manual
e not present.
waxy threads, and live in colonies clustered
ales are pinkish, the size of a pinhead, and
ature females are mobile only briefly, while
e on a more exposed part of the plant, and
nutes. The nymphs are called crawlers (ii)
y use to crawl to the tips of plants. From
by plants where they congregate into new
roducing wax, have 3 nymphal stages, and
eir second moult, males pupate in a white,
se in search of females.
ii
i
mealybug, Hypogeococcus pungens has been released as a biological
against queen of the night cactus infestations in South Africa. The agent
ed well at all release sites, and has proved to be extremely damaging. How-
nly the male mealybugs can fly, the agents’ dispersal is limited, and manual
s required in areas where they are not present.
ON
re covered in a mass of white, waxy threads, and live in colonies clustered
tips or along the ridges (i). Females are pinkish, the size of a pinhead, and
e from beneath the threads. Immature females are mobile only briefly, while
n mobile, complete their life cycle on a more exposed part of the plant, and
when they mature.
single eggs that hatch within minutes. The nymphs are called crawlers (ii)
y have functional legs which they use to crawl to the tips of plants. From
ay be dispersed by wind to nearby plants where they congregate into new
males become sessile, continue producing wax, have 3 nymphal stages, and
ults after about a month. After their second moult, males pupate in a white,
n, emerge with wings, and disperse in search of females.
AMAGE
s and all nymphs have long, thready mouthparts that are used to suck sap
ts. They tend to feed on the growth tips, causing deformities, and eventually
wth (iii). They also frequently congregate on each areole (the clusters of
stem ridges), giving a snowy appearance (i). Females feed throughout their
s males only feed as nymphs. Adult males only live for a few days.
QUEEN OF THE NIGHT
g is extremely damaging. Although a large, infested cactus takes time to die,
ii
iii
i
en released as a biological
in South Africa. The agent
e extremely damaging. How-
persal is limited, and manual
nd live in colonies clustered
, the size of a pinhead, and
are mobile only briefly, while
posed part of the plant, and
mphs are called crawlers (ii)
to the tips of plants. From
re they congregate into new
have 3 nymphal stages, and
ult, males pupate in a white,
females.
s that are used to suck sap
g deformities, and eventually
each areole (the clusters of
emales feed throughout their
ive for a few days.
sted cactus takes time to die,
ii
iii
i
ath the threads. Immature females are mobile only briefly, while
mplete their life cycle on a more exposed part of the plant, and
ature.
that hatch within minutes. The nymphs are called crawlers (ii)
tional legs which they use to crawl to the tips of plants. From
rsed by wind to nearby plants where they congregate into new
me sessile, continue producing wax, have 3 nymphal stages, and
out a month. After their second moult, males pupate in a white,
ith wings, and disperse in search of females.
mphs have long, thready mouthparts that are used to suck sap
d to feed on the growth tips, causing deformities, and eventually
ey also frequently congregate on each areole (the clusters of
s), giving a snowy appearance (i). Females feed throughout their
y feed as nymphs. Adult males only live for a few days.
THE NIGHT
ly damaging. Although a large, infested cactus takes time to die,
s and fruit which limits its reproduction. Surrounding seedling
When the cactus infestation becomes sparse, the insects may not
and will have to be transferred manually to prevent them from
s should be done in spring and summer, but not after rain be-
ave been dislodged. The other biological control agent released
rn beetle, Nealcidion cereicola, is not as widespread. At sites
esent, the cactus is considered to be under complete biological
control methods are necessary. Both insects are also effective
(Harrisia martinii), and can be harvested from these plants.
ii
iv
iii

35. ARC Quarantine Glasshouse 2015

36. Regulatory Considerations
• Genetic selection of indigenous wildlife for
commercial purposes
• Genetic modification of animals for improved
resistance to stress
• Introduction of exotic species for biocontrol
• Genetic engineering of insects for control of pests
and disease vectors
• Are vaccines regulated as GM? Depends if are
living organisms – so viral vaccines are excempt
from regulation.

37. Acknowledgements
• Farai Muchadeyi, Magretha Wang, Khanyi
Mdladla, Khukhani Khanyile; ARC-BTP
• Norman Maiwashe ARC-API
• Justin Hatting ARC-SGI
• Roger Price and Lin Sztab ARC PPRI

38. ARC Biotechnology Platform
BTP-Core@arc.agric.za
Jasper Rees
ReesJ@arc.agric.za