Transcript Presentation - IAC 2016, New Delhi

Genome sequencing to unlock
the potential of African
indigenous fruit tree species
Alice Muchugi
Genetic Resources Unit
World Agroforestry Centre (ICRAF)
Global challenges
• World population current estimated at
7.5 billion up from 6.6 billion in 2006 (
http://www.worldometers.info/worldpopulation/)
• Most SSA countries within the top 50
countries with high growth rates
more people
more food needed
Global challenges
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)
• Vitamins
• Micro-nutrients
Solutions??
SDGs
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
What is to be done differently?
• Increase production -better performing
varieties?
• Increase diversity on farms -new crops?
New tree crops
• State of World Forest Genetic Resources (FAO,
2014)
‘Although a range of 80 000 to 100 000 is the most
widely used estimate for the number of tree species
country reports mention only 8 000 species of trees,
shrubs, palms and bamboo; of these, genetic-level
information is available for only 500 to 600 species’
The concern
• Continued loss of forest biodiversity
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Deforestation for farming landsDeforestation for settlement and DevtNatural 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”
Highly valued trees
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Wild harvesting continue even where there are ready markets
Limited or no planting on farms
No intra- and inter- species diversity conservation efforts
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)
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
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Long generation intervals (some spp 1st flower in 15-20 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
ICRAF tree improvement program
Takes a long time to develop better cultivars
Allanblackia spp-untapped potential
• High quality oil, solid at room temperatures
8 year old tree in fruit (Ghana)
Product launch in Sweden in 2015
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
a. enhancing the quality of food through nutrition
b. increasing access to food through high yields and disposable income
c. 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
http://africanorphancrops.org/
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AOCC species: 52 annuals
Scientific name
Common name
Abelmoschus caillei Okra
Allium cepa
Onion
Amaranthus blitum Amaranth
Amaranthus
Grain amaranth
cruentus
5 Amaranthus tricolor Vegetable amaranth,
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2
3
4
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23
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Scientific name
Common name
Dioscorea alata
Yams
Dioscorea dume torum Bitter yam
Dioscorea rotundata
Yams
Eleusine coracana
Finger Millet
25 Ensete ventricosum
Enset
6 Basella alba
7 Brassica carinata
Vine spinach
Ethiopia Mustard
26 Gnetum africanum
27 Ipomoea batatas
8 Cassia obtusifolia
9 Celosia argentea
Sickle Senna
Celosia
28 Lablab purpureus
29 Lens culinaris
African Gnetum
Sweet Potato
Leaves
Lab lab Bean
Lentils
10 Citrullus lanatus
Watermelon
11 Cleome gynandra
Spiderplant
30 Macrotyloma
geocarpum
31 Momordica charantia
Geocarpa
groundnut
Bittergourd
12 Colocasia esculenta
Taro
Bananas
13 Corchorus olitorius
14 Crassocephalum
rubens
15 Crotalaria juncea
16 Crotalaria ochroleuc
a
17 Cucumis metuliferus
18 Cucurbita maxima
Jute mallow
Yoruban bologi
32 Musa acuminata AAA
Group
33 Musa balbisiana
34 Musa x paradisica AAB
Group
35 Passiflora edulis
36 Phaseolus vulgaris
19 Cyphomandra
betacea
20 Digitaria exilis
Cape tomato
37 Plectranthus esculentus African Potato
38 Plectranthus
African Potato
rotundifolius
39 Solanum aethiopicum
African Eggplant
Fonio
40 Solanum nigrum
Sunn hemp
Rattlebox
Horned Melon
Pumpkin
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42
43
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Scientific name
Common name
Sphenostylis stenocarpa Yambean
Talinum fruticosum
Ceylon spinach
Telfairia occidentalis
Fluted gourd
Tylosema esculentum
Marama bean
45 Vangueria
madagascariensis
46 Vangueria infausta
47 Vicia faba
African Medlars
48 Vigna radiata
49 Vigna subterranea
Mungbean
Bambara
groundnut
Shea Butter
50 Vitellaria paradoxa
51 Xanthosoma
sagittifolium
52 Xanthosoma spp
African Medlars
Favabean
Elephant ears
Cocoyams,
Arrowroots
Bananas
Plantains
Passion Fruit
Green Bean
African
Nightshade
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AOCC species: 49 trees/shrubs
Scientific name
Common name
1 Adansonia digitata Baobab
2 Adansonia kilima
Baobab
3 Allanblackia
floribunda
4 Anacardium
occidentale
5 Annona
senegalensis.
6 Annona reticulata
7 Artocarpus
heterophyllus
8 Artocarpus altilis
9 Balanites
aegyptiaca
10 Boscia senagalensis
11 Canarium
madagascariense
12 Carica papaya
13 Carissa spinarum
14 Casimiroa edulis
15 Chrysophyllum
16 Cocos nucifera
17 Dacryodes edulis
18 Detarium
senegalense
19 Diospyros
mespiliformis
20 Dovyalis caffra
Scientific name
21 Elaeis guineensis
22 Faidherbia albida
veg tallow tree
23 Garcinia livingstonei
Cashew
24 Garcinia mangostana
Wild Custard Apple
25 Hibiscus sabdariffa
Custard Apple
Jack Tree
26 Icacina oliviformis
27 Irvingia gabonensis
Breadfruit
Balanites
Common name
Oil Palm
Acacia (Applering)
African
Mangosteen
Mangosteen
Scientific name
41 Saba comorensis
42 Sclerocarya birrea
Common name
Rubber vines
Marula
43 Strychnos spinosa
African Orange
44 Syzygium guineense
Water berry
Roselle
45 Tamarindus indica
Tamarind
46 Uapaca kirkiana
47 Vitex doniana
28 Landolphia spp
29 Lannea microcarpa
False yam
Sweet bush
mango
Gumvines
Tree grapes
Wild loquat
Chocolate
berries
Sour plum
Jujube
Aizen, Nabedega
Canarium nut, Ramy
nut
Papaya
Carissa
White sapote
Star apple
Coconut
African Plum
Sweet detar
30 Macadamia ternifolia
31 Mangifera indica
Macadamia
Mango
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Drumstick tree,
Mulberry
Prickly pear
Mobola plum
African Locust
Avocado
Pistachio
African persimmon
39 Psidium guajava
Guava
Kei Apple
40 Ricinodendron
heudelotii
Ground Nut Tree
Moringa oleifera
Morus alba
Opuntia monacantha
Parinari curatellifolia
Parkia biglobosa
Persea americana
Pistacia vera
48 Ximenia caffra
49 Ziziphus
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Fruits trees
Shea butter
Allanblackia
Baobab
Bush mango
African plum
Amarula
Important nutrients in some AOCC species
Species
Nutritional content
and health benefit
Species
Nutritional content
and health benefit
Shea tree
Fruits: high in fats (stearic and
oleic), antioxidants, medicinal and
industrial use
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)
Moringa
Uapaca kirkiana
Leaves and fruits: vit A, vit C, Ca, K,
proteins, oleic acid, Fe, Cu, Mn
Fruit: Sugar (high energy), low in fat,
potassium, vit C, fiber
Ziziphus
Immune booster, anti oxidant, Mg,
K, Cu, niacin, Ca, Mn, P, Fe
Spider plant
Vitex doniana
(black plum)
Fruit: fiber, protein, vitamins,
micronutrients but contains anti
nutritional factors
Leaves, shoot: beta carotene, vit C, Ca,
Fe, anti oxidant, anti inflammatory
Amaranthus
Carica papaya
Fruit: low in nutrition, vit C, folate,
vit A
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,
Casimiroa edulis
Medicinal value, high sugar, vit C, vit
A, anti oxidant, anti cancerous
Baobab
African eggplant
Fruit, leaves: fiber, K, Mn, Fe, Mg,
Ca, P, vit B6, C, E, K
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
Passiflora edulis
Fruit: Fiber, anti oxidant, vit C, vit A,
Fe, Cu, Mg, P
Allanblackia
Seed oil: cooking, food and soap industry,
Desert date
Famine food, high fiber, K, Fe, Mn, Zn, Cu
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 biologyGO/Pathway/Regulatory network
mapping and candidate gene
discovery
Other OMICS
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Current activities:
• Reference genome sequencing
• Resequencing
• Transcriptome sequencing
Progress made:
1.
2.
3.
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6.
7.
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)
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
Partners
MORE PARTNERS WELCOME!!
 Visit
http://africanorphancrops.org/
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http://www.worldagroforestry.org/tree-diversity
ASANTE