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Livestock genomics—Experiences from South Africa
Jasper Rees
Agricultural Research Council, South Africa
ReesJ@arc.agric.z...
Livestock Genomics
• Population diversity studies - SNPs
– Cattle, goats, chickens
• Diversity studies – genome sequencing...
Sequence based Genomics Applications
Sequencing applications
• Genomes,
• De novo and re-sequencing
• SNPs and CNV calling...
Commercial
meat type breeds
B: Savanna
C: Kalahari Red
D: Boer
Developed breeds
E-G: Village ecotypes phenotypic represent...
PC1 vs PC2
Boer
Savanna
Kalahari Red
Zulu
Venda
Tswana
Xhosa
Tankwa
Commercial
Village ecotypes
Nguni
PC
A
Population
PC1 ...
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...
Genetic value of SA Indigenous Goats
• Populations clustered according to their production systems
• Genetic differences b...
Copy Number Variations in the genomes of SA
indigenous
• CNVs
 Structural variation randomly distributed in the genome.
...
Structural variations in genomes
Pathways enriched by genes covered by
CNVR|regions in Nguni cattle
Signatures of selection in indigenous cattle
Genomic regions under selection in the
SA cattle and their associated QTLs.
Breeds1 BTA UMD3.1
coordinate (bp)
SNPS Size (...
“I gave blood…. Did you?”
Wildlife genetics – conservation or
commercialisation?
Finding the gene for Big Horns…
Engineering the gene for No Horns
• Polled gene has been mapped
• Start of genome engineering
Stress resistance genes
• Senepol cattle are a heat resistant temperate
zone breed
• Genetic analysis shows a mutation tru...
Livestock Pathogens and vaccines
• Foot and mouth disease
• Avian flu and Newcastle disease virus
• Bluetongue
• Rabies
• ...
Insect Research
• Vectors for Plant, animal and human
pathogens
• Parasitoid wasps and other predators
• Plants – SIT, fun...
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 i...
Sterile Insect Technique
• SIT was pioneered in the 1950s by Bushland and
Knipling
• Awarded the 1992 World Food Prize.
• ...
Navigation ²
  English
Sterile insect technique for fruit fly control
9/9/2015 FruitFly Africa | Plan, Co-ordinate and Man...
Self-Limiting Gene function in
transgenic insects9/9/2015 How the Self-Limiting Gene Works | Oxitec
http://www.oxitec.com/...
Production of self-limiting insects
• Insects produced
with tetracycline
• Adults released to
mate with wild
populations
•...
1. Identification of problem pest/s [could be due to resistance (efficacy), residues
(reduced MRL's), withdrawal of chemic...
October 2010
www.irac-online.org
Current status of insect resistance against chemical insecticides
INSECT PATHOGENS AND THEIR USE IN PEST CONTROL
5 ENTITIES:
1. Bacteria*
2. Viruses
3. Protozoa
4. Nematodes
5. Fungi*
Live...
TYPICAL SIGNS OF INFECTION WITH BEAUVERIA
Larval stage infected with B. bassina (left). Photo: JL Hatting Fungal growth ma...
TYPICAL SIGNS OF INFECTION WITH METARHIZIUM
Larval and adult stage infected with Metarhizium
Dry spore columns (‘sporocarp...
Survey/collection of pathogens
Direct collection of diseased/dead insects
…BACTERIA…
Milky disease caused by Bacillus popi...
Survey/collection of pathogens
Direct collection of diseased/dead insects
…NEMATODES…
Heterorhabditis bacteriophora, H. ze...
Field trial with fungus against bollworm, Helicoverpa armigera
Field trials being conducted by ARC-SGI and PHP (Pty) Ltd.
...
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
...
The cactus mealybug, Hypogeococcus pungens has been released as a biological
control agent against queen of the night cact...
ARC Quarantine Glasshouse 2015
Regulatory Considerations
• Genetic selection of indigenous wildlife for
commercial purposes
• Genetic modification of ani...
Acknowledgements
• Farai Muchadeyi, Magretha Wang, Khanyi
Mdladla, Khukhani Khanyile; ARC-BTP
• Norman Maiwashe ARC-API
• ...
ARC Biotechnology Platform
BTP-Core@arc.agric.za
Jasper Rees
ReesJ@arc.agric.za
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Livestock genomics—Experiences from South Africa

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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

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Livestock genomics—Experiences from South Africa

  1. 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. 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. 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. 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. 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. 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. 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. 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. 9. Structural variations in genomes
  10. 10. Pathways enriched by genes covered by CNVR|regions in Nguni cattle
  11. 11. Signatures of selection in indigenous cattle
  12. 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. 13. “I gave blood…. Did you?”
  14. 14. Wildlife genetics – conservation or commercialisation?
  15. 15. Finding the gene for Big Horns…
  16. 16. Engineering the gene for No Horns • Polled gene has been mapped • Start of genome engineering
  17. 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. 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. 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. 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. 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. 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. 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. 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. 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. 26. October 2010 www.irac-online.org Current status of insect resistance against chemical insecticides
  27. 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. 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. 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. 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. 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. 32. Field trial with fungus against bollworm, Helicoverpa armigera Field trials being conducted by ARC-SGI and PHP (Pty) Ltd. Fungus: Nomuraea rileyi
  33. 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. 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. 35. ARC Quarantine Glasshouse 2015
  36. 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. 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. 38. ARC Biotechnology Platform BTP-Core@arc.agric.za Jasper Rees ReesJ@arc.agric.za

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