1. Alice Muchugi Genetic Resources Unit World Agroforestry Centre (ICRAF)
Genome sequencing to unlock the potential of African indigenous fruit tree species
Alice Muchugi
Genetic Resources Unit
World Agroforestry Centre (ICRAF)

2. Global challenges
World population current estimated at 7.5 billion up from 6.6 billion in 2006 (
Most SSA countries within the top 50 countries with high growth rates
more people
more food needed

3. Global challenges
Climate change

4. SSA…….. Most economies rely on agriculture
High competition for arable land (farming, human settlement and other developments)
Under-utilization of arable land-yield per Ha
Add climate change impact:
Lowers agricultural productivity
Increased poverty (49% of the population falling below the $1.25 per day threshold)

5. Hidden hunger
Vitamins
Micro-nutrients

6. Solutions?? SDGs etc CGIAR-SRF
Goal 1. End poverty in all its forms everywhere
Goal 2: End hunger, achieve food security and improved nutrition, and promote sustainable agriculture
etc
CGIAR-SRF
Reduced Poverty
Improved Food and Nutritional Security
Improved NRM and Ecosystem Services

7. What is to be done differently?
Increase production -better performing varieties?
Increase diversity on farms -new crops?
Fruit port folio

8. New tree crops State of World Forest Genetic Resources (FAO, 2014)
‘Although a range of to is the most
widely used estimate for the number of tree species country reports mention only species of trees, shrubs, palms and bamboo; of these, genetic-level information is available for only 500 to 600 species’

9. The concern Continued loss of forest biodiversity
Deforestation for farming lands-
Deforestation for settlement and Devt-
Natural calamities-fires/floods
Effect of climate change on species ecology
By end of last millennium, around 10% of the world’s 60,000 to 100,000 tree species were threatened with extinction
IUCN Red List of Threatened Species-approx. 1,200 trees and shrubs as “critically endangered”, 1,700 as “endangered” and another 3,700 as “vulnerable”

10. Highly valued trees
Wild harvesting continue even where there are ready markets
Limited or no planting on farms
No intra- and inter- species diversity conservation efforts

11. The ICRAF Genebank
5200 accessions representing 190 tree species in LTS
Over 500 accessions representing 120 agroforestry tree species deposited at Svalbard Global Seed Vault, Norway seeds in LTS
Over 10,000 accessions of 44 species established either from seeds or clonally located in
37 sites in 14 countries in
Africa, Latin America South
Asia and South East Asia
Irvingia wombolu (Cameroon)
Strychnos cocculoides (Zambia)

12. Challenges in conserving tree genetic resources
Large number of genera;
What tree to prioritize in conservation?
Tree functions (product/services)
Inter –species diversity
Intra-species diversity
Regional preferences
Most fruit trees species have recalcitrant seeds have to conserved as live plants
Long generation intervals (some spp 1st flower in years)
Large growth forms (require large space)
Generally outbreeding reproductive systems
Some species exhibit dioecy
Threat from environmental factors (diseases/pest/flood) and human interference
20,000 wheat accessions can be regenerated in 4 months in 3ha of land, some tree species may take about 0.25ha for one accession that may require an isolation distance of 400m

13. Takes a long time to develop better cultivars
ICRAF tree improvement program
Takes a long time to develop better cultivars

14. Allanblackia spp-untapped potential
High quality oil, solid at room temperatures
8 year old tree in fruit (Ghana)
Product launch in Sweden in 2015

15. AOCC: a special Private Public Partnership
Vision
To provide localized solutions to address stunting, hunger and chronic malnutrition of African children and population through improvement in the African agro-forestry ecosystem by
enhancing the quality of food through nutrition
increasing access to food through high yields and disposable income
building sustainable national level breeding programs using smarter, faster and economic technologies
Objectives
To develop next generation genomics resources (whole genome sequence, transcriptome sequence, SNP marker arrays/panels) for 101 African Orphan crops/trees
Infrastructure development: AOCC Genomics Lab at ICRAF

16. AOCC species: 52 annuals Scientific name Common name 1
Abelmoschus caillei
Okra 21
Dioscorea alata
Yams 41
Sphenostylis stenocarpa
Yambean 2
Allium cepa
Onion 22
Dioscorea dume torum
Bitter yam 42
Talinum fruticosum
Ceylon spinach 3
Amaranthus blitum
Amaranth 23
Dioscorea rotundata 43
Telfairia occidentalis
Fluted gourd 4
Amaranthus cruentus
Grain amaranth 24
Eleusine coracana
Finger Millet 44
Tylosema esculentum
Marama bean 5
Amaranthus tricolor
Vegetable amaranth, 25
Ensete ventricosum
Enset 45
Vangueria madagascariensis
African Medlars 6
Basella alba
Vine spinach 26
Gnetum africanum
African Gnetum 46
Vangueria infausta 7
Brassica carinata
Ethiopia Mustard 27
Ipomoea batatas
Sweet Potato Leaves 47
Vicia faba
Favabean 8
Cassia obtusifolia
Sickle Senna 28
Lablab purpureus
Lab lab Bean 48
Vigna radiata
Mungbean 9
Celosia argentea
Celosia 29
Lens culinaris
Lentils 49
Vigna subterranea
Bambara groundnut 10
Citrullus lanatus
Watermelon 30
Macrotyloma geocarpum
Geocarpa groundnut 50
Vitellaria paradoxa
Shea Butter 11
Cleome gynandra
Spiderplant 31
Momordica charantia
Bittergourd 51
Xanthosoma sagittifolium
Elephant ears 12
Colocasia esculenta
Taro 32
Musa acuminata AAA Group
Bananas 52
Xanthosoma spp
Cocoyams, Arrowroots 13
Corchorus olitorius
Jute mallow 33
Musa balbisiana 14
Crassocephalum rubens
Yoruban bologi 34
Musa x paradisica AAB Group
Plantains 15
Crotalaria juncea
Sunn hemp 35
Passiflora edulis
Passion Fruit 16
Crotalaria ochroleuc a
Rattlebox 36
Phaseolus vulgaris
Green Bean 17
Cucumis metuliferus
Horned Melon 37
Plectranthus esculentus
African Potato 18
Cucurbita maxima
Pumpkin 38
Plectranthus rotundifolius 19
Cyphomandra betacea
Cape tomato 39
Solanum aethiopicum
African Eggplant 20
Digitaria exilis
Fonio 40
Solanum nigrum
African Nightshade

17. AOCC species: 49 trees/shrubs
Scientific name
Common name 1
Adansonia digitata
Baobab 21
Elaeis guineensis
Oil Palm 41
Saba comorensis
Rubber vines 2
Adansonia kilima 22
Faidherbia albida
Acacia (Apple-ring) 42
Sclerocarya birrea
Marula 3
Allanblackia floribunda
veg tallow tree 23
Garcinia livingstonei
African Mangosteen 43
Strychnos spinosa
African Orange 4
Anacardium occidentale
Cashew 24
Garcinia mangostana
Mangosteen 44
Syzygium guineense
Water berry 5
Annona senegalensis.
Wild Custard Apple 25
Hibiscus sabdariffa
Roselle 45
Tamarindus indica
Tamarind 6
Annona reticulata
Custard Apple 26
Icacina oliviformis
False yam 46
Uapaca kirkiana
Wild loquat 7
Artocarpus heterophyllus
Jack Tree 27
Irvingia gabonensis
Sweet bush mango 47
Vitex doniana
Chocolate berries 8
Artocarpus altilis
Breadfruit 28
Landolphia spp
Gumvines 48
Ximenia caffra
Sour plum 9
Balanites aegyptiaca
Balanites 29
Lannea microcarpa
Tree grapes 49
Ziziphus
Jujube 10
Boscia senagalensis
Aizen, Nabedega 30
Macadamia ternifolia
Macadamia 11
Canarium madagascariense
Canarium nut, Ramy nut 31
Mangifera indica
Mango 12
Carica papaya
Papaya 32
Moringa oleifera
Drumstick tree, 13
Carissa spinarum
Carissa 33
Morus alba
Mulberry 14
Casimiroa edulis
White sapote 34
Opuntia monacantha
Prickly pear 15
Chrysophyllum
Star apple 35
Parinari curatellifolia
Mobola plum 16
Cocos nucifera
Coconut 36
Parkia biglobosa
African Locust 17
Dacryodes edulis
African Plum 37
Persea americana
Avocado 18
Detarium senegalense
Sweet detar 38
Pistacia vera
Pistachio 19
Diospyros mespiliformis
African persimmon 39
Psidium guajava
Guava 20
Dovyalis caffra
Kei Apple 40
Ricinodendron heudelotii
Ground Nut Tree

18. Fruits trees Shea butter Allanblackia Baobab African plum Bush mango
Amarula

19. Important nutrients in some AOCC species
Nutritional content
and health benefit
Shea tree
Fruits: high in fats (stearic and oleic), antioxidants, medicinal and industrial use
Moringa
Leaves and fruits: vit A, vit C, Ca, K, proteins, oleic acid, Fe, Cu, Mn
Uapaca kirkiana
Fruit: Sugar (high energy), low in fat, potassium, vit C, fiber
Ziziphus
Immune booster, anti oxidant, Mg, K, Cu, niacin, Ca, Mn, P, Fe
Vitex doniana (black plum)
Fruit: fiber, protein, vitamins, micronutrients but contains anti nutritional factors
Carica papaya
Fruit: low in nutrition, vit C, folate, vit A
Casimiroa edulis
Medicinal value, high sugar, vit C, vit A, anti oxidant, anti cancerous
African eggplant
Fruit, leaves: fiber, K, Mn, Fe, Mg, Ca, P, vit B6, C, E, K
Passiflora edulis
Fruit: Fiber, anti oxidant, vit C, vit A, Fe, Cu, Mg, P
Species
Nutritional content
and health benefit
Bambara groundnut
Seed: CHO, oil, high quality protein, iron, calcium, potassium
African nightshade
Bud, flower, fruit: high protein, micronutrient, medicinal, Fe, I, Zn, vit A
Finger millet
Seeds: CHO, Ca, methionine aa, vit A, B1, B2
Pigeon pea
Seeds: proteins (essential aa)
Spider plant
Leaves, shoot: beta carotene, vit C, Ca, Fe, anti oxidant, anti inflammatory
Amaranthus
Leaves: CHO, protein, vit K, Fe, riboflavin, vit A, B6, Mn, Fe, Cu, Ca, Mg, K, P, fiber,
Seeds: gluten-free, high quality protein (eaa, lysine), low fat, Ca, Fe, Mg,
Baobab
Leaves: vit C, carotene, anti oxidant, K, Ca, medicinal value
Fruits: high soluble fiber, multi-vitamin, Fe, Mg, K, Vit C, antioxidant, anti inflammatory, immune booster
Allanblackia
Seed oil: cooking, food and soap industry,
Desert date
Famine food, high fiber, K, Fe, Mn, Zn, Cu

20. Application of Genomics for Trait Enhancement
From known candidate genes
Intrinsic yield genes (IYG)- Eg. ANT, ARF, GRF, EBP, EXP etc.
Genes involved in nutrient storage proteins- Eg. Ferritin
Genes involved in nutrient transport/translocation in plant body- Eg. NAS, IRT, YSL, VIT
Genes involved in nutrient uptake/translocation- Eg. Mugineic acid phytosiderophores, IRO
Climate adaptation: drought/salinity- DREB, ABA receptors etc.
Shelf life- Polygalacturonase, ACC synthase
From unknown (discovery/exploration of causative genes)
Genomics- GWAS studies (phenotype, eQTL, metabolic profiling etc.)
Transcriptomics- Differentially expressed genes
Epigenetics- Change in methylation/acetylation patterns in DNA/proteins
Systems biology- GO/Pathway/Regulatory network mapping and candidate gene discovery
Other OMICS

21. Current activities: Progress made: Reference genome sequencing
Resequencing
Transcriptome sequencing
Progress made:
Elusine coracana (WGS completed)
Annona senegalensis (WGS completed)
Solanum aethiopicum (WGS completed)
Moringa oleifera (WGS near completion)
Screlocarya birrea (WGS near completion)
Adansonia digitata (WGS near completion)
Faidherbia albida (WGS near completion)

22. Africa Plant breeding Academy
To train 250 practicing African plant breeders in the most advanced theory and technologies for plant breeding in support of critical decisions for crop improvement such as the use of genomic information
23 breeders graduated in 2015; 29 more to graduate in Dec 2016

23. Partners
MORE PARTNERS WELCOME!!
Visit

24.
ASANTE