African Orphan Crops Consortium (AOCC): A public-private partnership for enablement of African plant scientists through development of open source genomics resources for promoting food and nutritional security in Africa through orphan crops

1. African Orphan Crops Consortium (AOCC):
A public-private partnership for
enablement of African plant scientists
through development of open source
genomics resources for promoting food and
nutritional security in Africa through
orphan crops
Prasad S. Hendre (ICRAF, Kenya), Alice Muchugi (ICRAF, Kenya);Song Bo (BGI,
China), Xun Xu (BGI, China), Shifeng Cheng (BGI, China), Xin Liu (BGI, China);
Jonathan Featherston (ARC, SA), Featherston (ARC, SA), Charles Hefer (ARC,
SA), Jasper Rees (ARC, SA); Allen Van Deynze (UCD, USA); Ramni Jamnadass
(ICRAF, Kenya)
1

2. 2
AOCC: Summary
DNA-marker Based
Production of
“Quality SEED”
Good Crop: High
yield, climate
resilience,
biotic/abiotic
stress tolerance
Good Harvest: Good nutrition
New value chains
New products
New markets
Good remuneration
Good Market

3. 3
Genomics Lab African Plant Breeding Academy
Activity Flow Marker Assisted Selection
• Trains 120
African plant
breeders by
2019 to use
genomics tools
• Already trained
~50 plant
breeders in two
batches
• Encourages to
write joint
projects
• Important
especially for
tree crops
where a
breeding cycle
can run for a
decade or
more
AOCC: Translational Agri-genomics

4. 4
Species Selection: Trees, Herbs, Shrubs, Vines, Annuals
Scientific name Common name Scientific name Common name Scientific name Common
name
1 Adansonia digitata Baobab 21 Elaeis guineensis Oil Palm 41 Saba comorensis Rubber vines
2 Adansonia kilima Baobab 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 50 Vitellaria paradoxaShea Butter
11 Canarium
madagascariense
Canarium 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 cainito 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

5. Activity Flow Chart: AOCC
5
Phenotyping
data
SNP Assays Genotyping
data
Field trialLab Resource Generation
Phenotype and Genotype Association
NARS, CG etc.
LGC
CyVerse
Google
BGI, Univ. Gent
Illumina
Illumina &
Thermo Fisher
Scientific

6. Our Process
Genome sequencing, RNA
sequencing and annotation
of 101 genomes
2
Re-sequencing of 100
accessions of each species
3
Breeding programs use this
information
4
ICRAF
CG
centers
National
institutes
Regional
partnerships
1
Germplasm
acquisition
Yield
Resistance
to diseases
and pests
Climate
resilience
Nutrition
Unrestricted IP access to all
4

7. AOCC-ICRAF: Domestication, Diversity
and Delivery of improved tree germplasm
AOCC
Genomics,
sequencing,
diversity
BSO
High Yielding
varieties
Phenotyping in breeding
seed orchards for:
✓ Food/Nutrition
✓ Timber
✓ Fodder
✓ Bio-mass
Markers
MAS
Conventional
breeding
(OSO)
Improved
varieties
Yield
Resistance
to diseases
and pests
Climate
resilience
Nutrition

8. 8
Activities: Summary till Nov 2017
1. AOCC has touched upon 31 tree
species till date
2. Genome sequencing going on
for 24 species @ BGI, China.
3. 6 tree genomes to be released
in 2017-18
4. 8 species ready for re-seq @
AOCC genomics lab
4. Re-seq completed for ~50
accessions across 2 species @
AOCC and Dow genomics lab
5. Transcriptome seq begins for 16
species @ ARC, South Africa
and ready for another 9 species
6. AOCC genomics lab coordinates
sample collection, RNA/DNA
extraction, and logistics
Species name Common name Whole genome
sequencng (WGS)
Re-sequencing Transcriptome
sequencing
1 Annona senegalensis Wild Custard Apple Final assembly Yet to begin 14 RNAs sent
2 Artocarpus heterophyllus Jack Tree, Fenesi Final assembly Yet to begin 11 RNAs sent
3 Faidherbia albida Acacia (Apple-ring) Final assembly 29 by Dow 11 RNAs sent
4 Sclerocarya birrea Marula, Mng’ongo Final assembly 100 received 14 RNAs sent
5 Moringa oleifera Moringa, Drumstick tree Final assembly 40 by Dow 10 RNAs sent
6 Artocarpus altilis Breadfruit, Mshelisheli Final assembly Yet to begin 6 RNAs sent
7 Adansonia digitata Baobab, Mbuyu ON 5 received Tissue collected
8 Adansonia kilima Baobab, Mbuyu ON Yet to begin Tissue collected
9 Anacardium occidentale Cashew, Korosho ON Yet to begin 9 RNAs sent
10 Dovyalis caffra Kei Apple, Kei-appel ON Yet to begin 11 RNAs sent
11 Parinari curatellifolia Mobola plum, Mbura ON 5 received Yet to begin
12 Parkia biglobosa Nere, African Locust ON Yet to begin 8 RNAs sent
13 Saba senegalensis Gumvines, Mbungu ON Yet to begin Yet to begin
14 Uapaca kirkiana Wild apple, Wild loquat ON 100 received 2 RNAs sent
15 Casimiroa edulis White sapote ON Yet to begin 15 RNAs sent
16 Dacryodes edulis African Plum, Safoutier ON Yet to begin 8 RNAs sent
17 Vitellaria paradoxa Shea Butter ON Yet to begin Yet to begin
18 Ziziphus mauritiana Jujube, Mkunazi ON Yet to begin 9 RNAs sent
19 Tamarindus indica Tamarind ON Yet to begin Tissue collected
20 Syzygium guineense Water berry, Mzuari ON Yet to begin Tissue collected
21 Irvingia gabonensis Sweet bush mango, Dika DNA Yet to begin Yet to begin
22 Ricinodendron heudelotii Ground Nut Tree, Muawa DNA Yet to begin Tissue collected
23 Detarium microcarpum Sweet detar ON Yet to begin Yet to begin
24 Garcinia livingstonii African Mangosteen ON Yet to begin Yet to begin
25 Vitex doniana Chocolate berries, Mfudu Yet to begin Yet to begin Tissue collected
26 Allanblackia stulhmanii Allanblackia Yet to begin Yet to begin Tissue collected
27 Strychnos cocculoides Kaffir Orange Yet to begin 100 received 11 RNAs sent
28 Strychnos spinosa Kaffir Orange Yet to begin Yet to begin Tissue collected
29 Annona reticulata Custard apple Yet to begin Yet to begin Tissue collected
30 Vangueria madagascariensis African medlers Yet to begin Yet to begin 14 RNAs sent
31 Passiflora edulis Passion fruit Yet to begin Yet to begin 14 RNAs sent
32 Elaeis guineensis Oil Palm, Mchikichi By collaborator Yet to begin By collaborator
33 Mangifera indica Mango, Maembe By collaborator Yet to begin By collaborator
34 Macadamia ternifolia Macadamia By collaborator Yet to begin By collaborator
35 Persea americana Avocado, Ikloviu By collaborator Yet to begin By collaborator
36 Psidium guajava Guava, Mpera Other group Yet to begin Other group
37 Mangifera indica Mango, Maembe Other group Yet to begin Other group
38 Morus alba Mulberry Other group Yet to begin Other group

9. 9
Organism
Estimated
Genome size
Ploidy
Heter/
Homozygous
Genome
survey
Lablab purpureus 0.43 Gb 2X Homo Normal
Vigna subterranee 0.51 Gb 2X Homo Normal
Tamarindus indica 1.67 Gb 2X Homo Normal
Detarium microcarpum 0.53 Gb 4X Heter HH
Faidherbia albida 0.66 Gb 2X Heter HH
Parkia biglobosa NA NA NA NA
Artocarpus altilis 0.80 Gb 2X Homo RR&HH
Artocarpus heterophyllus 1.01 Gb 2X Homo RR&HH
Ziziphus mauritiana NA NA NA unkown
Dovyalis caffra 0.44 Gb 2X Homo Normal
Parinari curatefolia NA NA NA unkown
Garcinia livingstonei NA NA NA unkown
Uapaca kirkiana NA NA NA unkown
Casmiroa dulis 1.21 Gb 4X Homo RR
Sclerocarya birrea 0.37 Gb 2X Heter HH
Dacryodes edulis 0.74 Gb 4X Homo HH
Adansonia digitate 2.9 Gb 4X Heter --
Adansonia kilima 2.9 Gb 4X Heter --
Moringa oleifera 0.28 Gb 2X Heter RR&HH
Syzygium guineense NA NA NA unkown
Solanum nigrum NA NA NA unkown
Solanum aethicopicum 1.17 Gb 2X Homo RR
Saba senegalensis NA NA NA unkown
Vitellaria paradoxa NA NA NA --
Celosia argentea 2.1 Gb 2X Homo Normal
Elusine coracana 1.29 Gb 4X Homo RR
Elusine indica 1.23 Gb 2X Homo RR
Digitaria exilis 0.71 Gb 2X Homo RR
Annona senegalensis 0.74 Gb 2X Homo RR
Notes：
HH：Highly heterozygous
RR：Repeat-rich
Pentapetalae
Fabids
Asterids
Lamiids
Malvids
Mesangiospermae
Fabaceae
Poaceae
Salicaceae
Clusiaceae
Chrysobalanaceae
Malvaceae
Myrtaceae
Moringaceae
Burseraceae
Solanaceae
Apocynaceae
Sapotaceae
Amaranthaceae
Annonaceae
Rhamnaceae
Moraceae
Phyllanthaceae
Rosales
Malpighiales
Sapindales
Fabales
Rutaceae
Rosids
29 genomes are ongoing in BGI

10. 10
Solanaceae
Poaceae
Annonaceae
Annona senegalensis
(Wild Custard Apple)
Vigna subterranee
(Bambara groundnut)
Fabaceae
Solanum aethiopicum
(African Eggplant)
Sclerocarya birrea
(Marula)
Lablab purpureus
(Lab lab Bean)
Faidherbia albida
(Apple-ring)
Elusine coracana
(Finger Millet)
Artocarpus heterophyllus
(Jack Fruit)
Artocarpus altilis
(Breadfruit)
Anacardiaceae
Moraceae
Moringaceae Moringa oleifera
(Drumstick Tree)
Sequencing Assembly Assembly Evaluation Annotation
Data (Gb）
Assembled
size (Mb）
Scaffold
N50(Mb)
Contig
N50(Kb)
BUSCO
Repeat
content
# of Genes
82G 395 0.62 32.22 93.10% 31.19% 27,449
86G 535 0.64 19.15 92.10% 38.34% 31,921
166Gb 654 0.69 42.03 93.20% 57.39% 34,797
129Gb 833 1.54 16.9 95.20% 52.04% 33,514
153Gb 982 0.55 26.68 95% 51.04% 59,519
144Gb 331 0.34 21.35 96.10% 37.21% 18,230
121Gb 217 0.98 45.27 90.10% (Ugent) (UGent)
128Gb 1,026 0.52 39.71 95% 54.07% 44,431
186Gb 1,257 2.29 30.42 97.30% 55.83% 89,926
88Gb 688 0.98 40 94% 46.95% 37,550
10 genomes along with 6 trees are assembled at BGI

11. 11
African Plant Breeding Academy (AfPBA)
• Dec 2013: Opened at ICRAF
• Target to train 120 professional African plant breeders to use
genomics tools in their breeding programs in a span of five years
• Managed by University of California, Davis
• Administrated and hosted by ICRAF
✓ Dec 2014: 1st cohort of 23 students graduated; 9 countries
✓ Dec 2016: 2nd cohort of 25 students graduated; 16 countries
✓ May 2017: 3rd cohort of 35 students being trained; 19 countries
✓ Majority of them with Ph.D.
✓ Uncompromising selection process streamlined to maintain
gender and regional balance
Cohort 1
Cohort 2
Cohort 3

12. 12
Dedication and Launch of Illumina Hiseq4000 Sequencer
Dr. Howard Yana-Shapiro (Mars Inc.), Founder AOCC during
the launch on 23rd May 2017
Newly inaugurated HiSeq4000
Dr. Howard Yana-Shapiro, Dr. Tony Simons (ICRAF), Dr. Cindy
Lawley (Illumina), Dr. Ryan Rapp (Illumina)

13. AOCC Website: http://africanorphancrops.org/
13

14. AOCC network (open)
14
• African Bean
consortium
• Bionnovate
• Bioversity
• CIAT
• Cleome consortium
• Crop Breeding
Institute, Zimbabwe
• Crops for the Future
Research Centre
• Dioscorea consortium
• Ethiopian Orphan
Crops Centre
• Fababean consortium
• Hohenheim University
• ICARDA
• ICRISAT
• IITA
• Illumina Inc.
• Lentil Sequencing
consortium
• MoBreed
• National Research
Council – Canada
• NWO Food & Business
Applied Research Fund
• Pan African Bean
Alliance
• Shea Consortium
• Sweet Potato
Consortium
• University of Georgia
• USDA-ARS Subtropical
Horticultural Research
Station
• USDA-ARS, Wisconsin
• World Vegetable Centre
Illumina Greater Good Initiative 2015

15. 15
Uncommon Collaborators