Iita yam breeding 2005-2015

A member of CGIAR consortium www.iita.org
Workshop on Implementation of IITA’s Genetic Improvement Strategy
Antonio Lopez-Montes, R. Bhattacharjee and team
Ibadan 8th to 10th of 2013
Yam Breeding at IITA
2005-2015

STRATEGIC PILLARS
Diversity and Variability
Farmers agro-ecological knowledge
and farmers decision-making
Participatory Value Chain Strategy

 Diverse yam species
D. alata
D. dumetorum
D. bulbifera
D. rotundata
 Diverse varieties
within species
D. alata
Heterogeneous varieties
Food security Resilience Sustainability Income generation Interspp. hybrids
Diversity and Variability
STRATEGIC PILLARS
D. esculenta
D. trifida
D. dumetorum

KNOWLEDGE INTEGRATION: FARMERS AGRO-ECOLOGICAL KNOWLEDGE
AND FARMERS DECISION-MAKING MODELS
Breeding feedback
Accelerate selection
Traits and climate change
Accelarate adoption
Planning
Capacity broadening
Understanding diversity
STRATEGIC PILLARS

Participatory Value Chain Strategy
STRATEGIC PILLARS

Breeding Objectives and Target Areas
With primary focus on D. rotundata and D. alata,
the principal objectives for genetic
improvement include:
1. High and stable tuber yield
2. Tuber characteristics that facilitate harvesting
and are valued by consumers (e.g. shape, size,
storability, dry matter content and food quality)
3. Resistance to biotic stresses (e.g. viruses,
anthracnose, nematodes)
4. Tolerance to abiotic stresses (e.g. low soil
nutrients, drought)
5. Suitability to major cropping systems (e.g. plant
architecture, and maturity period).
6. Nutritional value and metabolites
Impact zones and major cropping systems four agro ecological zones
across Sub-Saharan Africa. Source: Sanginga (2012).
OBJECTIVES

Redefinition of environments: Geographic Domain-Yam
production systems
Current Suitability: CRP-Climate Change

Prioritized Markets Positioning, Ghana
2013 – 2020
Market Fresh YAM
Processed Yam
Food
Processed Yam
Industry ingredients
EXPORT High (1) Medium (3) Medium High (2)
DOMESTIC High (1) High (1) High (1)
NICHE, HIGH VALUE High (1) Medium High (2) Medium (3)
MARKETS END USERS

GEOGRAPHIC DOMAIN AND AGROECOLOGICAL ZONES
YAM PRODUCTION SYSTEMS
(Human being, Environment and Yam)
Participatory Priority setting and Value chain strategy
Reduction of time to recommend screening protocols
PRE- BREEDING BREEDING
VARIETY DEVELOPMENT AND DELIVERING
Parents selection
Progenies selection
Traits Inheritance
Inbreeding
Phenotyping and
Genotyping Spp.
Core collection and
Core Diversity set
Inter-specific
Hybridization
Aneuploidy
Re-definition
OfEnviroments
Speedingup
theselection
Knowledgeand
useofdiversity
STRUCTURE OF THE PROGRAM
Accelerate
adoption

Redefinition of environments: Yam production systems
Characterization
Livelih ood
• Food Security
• Income Level
• Income Flows
• Employment
• Poverty-capability
• Well-being
• Gender Effects
Resilien ce
• Production Risk
• Market Risk
• Response to Shocks
Na tu ra l Resou rces
Ba se
• Water Resources
• Soil Resources
• Forest Resources
•
Im p a ct
Livelih ood Stra teg ies
 Agricultural
Intensification
 Agricultural
Extensification
 Agricultural
Diversification
 Agricultural
Specialization
 Non-agricultural
P rocess of
Ch a n g e
Differen tia ted Socia l
Actors
Livelih ood
Resou rces
P rod u ction System
• Weather (Rainfall and Temperature)
• Soil Units scale less than 1:300.000
• Land use with yam species
• Length Growing season
Econ om ic Fin a n cia l
• Savings and Loans
• Productive Assets
• Land
• Labor
• Markets
Hu m a n
• Formal Education
• Capabilities
• Agency
• Gender
• Leadership
• Values
• Origin and Ethnicity
• Family Characteristics
Socia l:
• Participation and Role in
Organizational Processes
• Personal Contacts
• Influential People
• Knowledge Sharing
Opportunities
• Service Providers
• Collective Action
• Community Characteristics
Endowmentsand
Entitlements
Su p p ort
In stitu tion s a n d
Extern a l
In terven tion
Develop m en t
Sta te
Livelih ood
Activities
Basic or
Livelihood
Innovations
Process
Innovations
Gottret and White (2001), Livelihood means
Soil map Yam production map
Poverty Level map
Rainfall map
Biophysical zones Production systems

FARMERS’ CHARACTERISATION: TYPES….
TYPE 1.TYPE 2.TYPE 3.
TYPE 4.
34 12

0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
TYPE 1 TYPE 2 TYPE 3 TYPE 4
Women
Men
GENDER
FARMERS’ CHARACTERISATION: TYPES….

GENDER CATEGORIES
Women: Young
Old
Men: Young
Old
FARMERS’ CHARACTERISATION: TYPES…

2 - 4
months
8-10 months
10-20 seed for PT
Speeding up the selection: Reduction of time to develop
From 9 to 4 yrs

Speeding up the selection: Screening protocols
NEMATODES
N.U.EANTHRACNOSE
EARLY- LATE MAT
DROUGHT TOLER

INOCULATION METHODS
0 50 100
12 15 74
R
T
S
Pathogen survey Pathogen Diversity analysis More Virulent strains
TDa F1 selection 2011-2012
ANTRACHNOSE SCREENING PROTOCOL USING VINE CUTTING

D.alataandD.rotundata
Improving
meristem culture
Vine
propagation
Minituber
propagation
Propagation

Years Phenotypic Selection at IITA
5-year cycle, 9 years to release*
1 1000 crosses among (sexed diallel and general crossing blocks)
2 1500 seedlings;
Two to Three month after sowing: F1C1 screened at screen house for:
Anthracnose: 5 vines in vertical sacks
Viruses: 5 vines in vertical sacks
Nematodes: 5 vines in vertical sacks
Seed tuber production: 25-30 vines in vertical sacks
3 400 clones single 10 plants row, preliminary trial at IITA
4 100 clones in Family Replicated Trials (FRT), 10 m single row, three reps (staked
and no staked system), three environments
5 30 clones, Advanced Trial (AT), four reps, 6 x 6 plants per plot; three
environments.
Selection of clones for inclusion in crosses
6 10 to 15 Nomination and Multiplication
7 10-15 Multilocational trials 10 localities
8 10-15 Multilocational trials 10 localities
9 3-5 Outstanding exceptional varieties Registration, multiplication and release

rotundata 67%
alata 25%
bulbifera 2%
cayenensis 2%
dumetorum 1.6%
esculenta 0.7%
preusii 0.3%
manganotiana 0.25%
3200 accessions – 1500 in vitro
Knowledge and use of diversity: Pre-breeding
METHODS USED (CONVENTIONAL AND
MOLECULAR/GENOMICS-ASSISTED BREEDING )

Latin America &
Caribbeanaccessions
3,200 accessions
Source: Asiedu, 2010
Africa: 90-95% accessions
Asia:
…..accessions
Pacific
…..accessions
METHODS USED (CONVENTIONAL AND
MOLECULAR/GENOMICS-ASSISTED BREEDING )

Inter-specific Hybridization
Refinement of embryo rescue
techniques to improve efficiency
of interspecific hybridization in
IITA’s yam breeding scheme
Ovule culture obtained from
crosses between species
D. alata D.
rotundata
D.
cayenensis
Breeding
Objective
High susc.
YAD,
inferior
tuber
YAD resist.
and good
texture
Objective 2
Objective 3
Bulbils
production
x Objective 4
Objective 3
x Long leaf
area duration
Objective 1
x Higher tuber
carotenoids
content
Objective 1
Objective 6
Early
maturity
Longer tuber
dormancy
x Objective 2
Objective 5

Inbreeding
Monoecious Haploids
Diallel crosses
Back crosses4120 Progenies
Anther culture
Characterization of plant material
Flower size, anther size, anther color etc.
 Investigation of suitable medium
and culture condition
Growth regulator, yam powder,
temperature
Anther, pollen
and pollen
tube growth
%

Selection of Parents I
A core collection of 391 accessions from six species was defined on
the basis of morphological characteristics.
Characterized using SSR markers separated into ploidy groups
using flow cytometry.
Additional germplasm contributed by research partners in West
Africa and materials identified from IITA’s field trials were also used
as parental materials for crossing.
The characterization and evaluation of germplasm from these
various sources for morphological and agronomic attributes, tuber
quality, ploidy status, and flowering ability, etc. leaded to the
selection as parents of accessions with traits relevant to the
objectives of the program.

• Screening for resistance to Meloidogyne species
and Scutellonema bradys was also carried out.
• Evaluation of potential parental accessions for
anthracnose resistance was based on symptom
expression following inoculation with specific
strains of Colletotrichum gloeosporioides.
• Similarly germplasm was challenged with specific
yam viruses through mechanical or vector
transmission, followed by observations of
symptoms as well as ELISA and PCR tests.

1. Metabolite profiling
1.1. (Dioscin): D. alata (15 accessions), D. dumetorum (14 accessions), and D.
bulbifera (6 accessions). However D. rotundata (12 accessions), D.
mangenotiana (1 accession), D. praehensilis (2 accessions), D. cayenensis
(5 accessions) : NO FOUND.
1.2. Secondary metabolite profile of 53 accessions of D. dumetorum , saponin,
alkaloids, cardiac glycosides, terpenoids and steroids.
Generation of improved populations based o the diversity of the
accessions
Phenotyping and Genotyping Spp.

2. Host Plant Resistance
2.1. Host plant resistance to yam nematodes (D. dumetorum) and viruses (in D.
alata and D. rotundata) were identified.
2.2. The genetic basis of the resistance to a Nigerian isolate of yam mosaic
virus (YMV), genus Potyvirus.
2.3. Different sources of resistance to anthracnose have also been identified in
previous studies at IITA and the genetic basis for the resistance to a major
moderately virulent strain in Nigeria has been reported.
2.4. Botanical seed free of viruses
2.5. Breeding for viruses resistance

3. Response to soil nutrients and efficiency of nutrient use
4. Tuber food quality
4.1. Pasting characteristics of fresh yams as indicators of textural quality in a major food
product
4.2. Sensory evaluation of ‘amala’ from Dioscorea alata
4.3. Physicochemical and pasting characterisation of Dioscorea alata
100 Elite materials characterization
5. Tuber micronutrient density
5.1. Screening germplasm for tuber iron and zinc contents
5.2. Tuber total carotenoids in Dioscorea cayenensis and Dioscorea dumetorum
(New populations generated with selected parents from this screening)
5.3. Influence of environment and genotype x environment interactions
5.4. Tuber tannin content
5.5. Tuber phytate content
5.6. Tuber ascorbic acid (Vitamin C) content
5.7. Variation in nutrient retention during processing of yam into food products

Aneuploidy
1. DETERMINATION AND MANIPULATION OF PLOIDY LEVELS IN
DOMESTICATED Dioscorea SPP (32 accessions of D. alata, 23
accessions of D. dumentorum and 32 accessions of D. rotundata)..
Colchicine treatment and interploid hybridization were employed in
inducing new ploidy materials.
Generated populations under evaluation
2. Potential assessment of somatic polyploidization as a breeding tool
to improve economical traits of guinea yams Dioscorea cayenensis
and D. rotundata
To investigate optimum concentration of Colchicine: to start

NEMATODES
N.U.EANTHRACNOSE
EARLY- LATE MAT
DROUGHT TOLER
Selection of Parents II :

Parents and progenies selection
FAMILYIES REPLICATED TRIALS SEXED DIALLEL CROSSES
Full and half sib families (30-40)
Each family / 3 groups – 3 block
Data recorded each clone
Selection within each block
Reps allow for a Statistical
phenotypic selection (Gardner (1961)
Replicated information for each family
Selection Index (SI)
Information use to derive the relative values
of the parents that generated the families
General Combining Ability
GCA
Specific Combining Ability
SCA
Additive
Dominance
Determination of breeding values of parental
lines through the analysis of GCA = additive
and SCA= heterotic, using a combination of
monoecious and sexed diallel crosses
Selection of Parents II :

• In this case superior clones male and female
representing multiple traits are crossed using
open pollination blocks. Multiple traits
populations are generated to be screened
using the through output protocols tested in
different environments and also delivered to
the national programmes. A new breeding
cycle will be generated with the selected
clones per population and intercrosses for a
new cycle.
Half Sibs Modified Recurrent
Selection (HSMRS)

M
M M
M M
M
F
1 2 3 4 5 6 7 8 9 10 11 12 13 14
1 28 8 23 18 26 7 21 25 17 9 22 4 18 26
2 25 27 11 12 10 6 20 1 15 5 24 13 9 14
3 22 14 15 9 16 4 13 14 23 12 2 27 11 25
4 20 3 24 19 5 2 18 3 6 7 8 19 10 16
5 17 2 7 1 6 8 10 9 13 4 3 20 6 21
6 21 18 16 4 3 7 13 21 17 11 15 1 5 23
7 12 13 6 10 11 5 14 1 3 9 24 7 2 10
8 1 14 23 19 9 22 15 25 16 6 10 8 22 3
9 24 8 20 1 17 27 3 12 20 14 19 12 18 11
10 10 15 26 7 11 2 21 10 5 7 28 9 17 25
11 17 12 13 10 19 8 4 8 1 13 3 12 4 16
12 21 4 18 5 22 15 26 5 18 15 7 23 1 4
13 8 23 6 20 14 9 17 11 19 21 16 6 14 26
14 3 5 11 2 24 7 13 12 20 8 24 11 27 2
15 7 1 9 16 8 10 5 1 9 4 6 2 5 18
16 10 17 3 2 1 14 6 13 17 1 22 15 3 12
17 22 12 19 4 15 12 4 19 14 25 10 7 13 19
18 25 14 6 21 28 18 7 8 5 18 11 23 16 8
19 24 11 20 13 9 10 2 3 13 12 4 14 20 17
20 2 26 8 23 16 5 27 11 15 21 24 6 9 2
(HSMRS)
M
M M
M M
M
F
M
M M
M M
MF

Full Sibs Modified Recurrent
Selection (FSMRS)
• Paired crosses made between individuals in the
population by season, best families and clones within
families will be identified. The best clones after
evaluations in different environments and the best
families will be recombined for a new breeding cycle.
• Selected parents male and female crossed to generate
by parental populations for target traits. Best families
and clones within families are identified. The best
clones after evaluations in different environments and
the best families are recombined for a new breeding
cycle.

Recurrent selection among selfed
families (monoecious clones)
• Evaluation based on self-pollinated progeny, formed by one
generation of selfing among several TDr monoecious clones.
• Season 1. So plants from the population are selfed and inter-
crosses to produce So:1 full sib lines
• Season 2. So:1lines (clones) propagated using vine cutting
• Season 3. So:1 Evaluated, best lines selected from a family
replicated trial (FRT); full sib lines will go for FSMRS and best
selected from FRT.
• Season 4. Selected lines to be inter-crossed and selfed,
producing the Cycle 1 population with new full sib lines.
• Season 5. Self new So plants as in Season 1….

GCA
SCA
Additive
Dominance

A member of CGIAR consortium www.iita.orgA member of CGIAR consortium www.iita.org
Yam: USAID-Linkage project
Focus: Screening for anthracnose disease; development of additional markers; construction of
linkage map; QTL mapping for anthracnose disease; de novo sequencing of parental lines; GBS
of parents and progenies (Dioscorea alata)
Yam anthracnose symptom variation
Training: Christian Nwadili (PhD student, Nigeria); 1 IT student
Partnership: NRCRI, Nigeria; USDA-ARS, Stoneville, USA; Clemson University, Clemson, USA

SSRs from EST-sequences
More than 40,000 EST sequences: about 1152 SSRs developed
Three cDNA libraries
sequenced on Roche 454
and assembled using CAP3
SSRFinder software for
SSR discovery
BLASTx was used to screen SSR
containing ESTs against non-
redundant DNA database
BLASTx data screened for presence of
ribosomal, retro-element, GAG protein,
chloroplast, and mitochondrial SSRs
Identification of 1152 EST-SSRs and tested for
polymorphism on two parents:
- 523 markers were considered good (445 with
single locus; 70 with
two loci, maybe duplicated genes; 8 multi-
allelic, indicating polyploidy)
- 92 failed to work (10% failure)
- 537 monomorphic
- 388 out of 445 showed polymorphism (33.7%)
when tested on both parents
Genotyping of parents and 94 mapping population progenies with 388 EST-
SSRs

Linkage mapping
NHsB9_c14199_2_a0.0
Oc_93_a3.3
Oc_2671_a3.6
Oc_280_a5.6
Wc_946_a7.7
Oc_917_a8.1
Oc_6126_a11.2
Os87_lrc4432_a11.8
Wc_1531_a13.1
NHsA8_c4355_5_a13.2
Wc_422_a13.7
Oc_5893_a15.6
Oc_3971_a17.2
Oc_3766_b18.9
Oc_5267_a36.0
Oc_2822_b39.0
Oc_6102_a39.2
Oc_1655_a39.6
Oc_1780_a39.9
Oc_2567_a40.3
Oc_1923_a40.4
Os87_c878_a40.8
Oc_3766_a40.9
Oc_4872_aNHs87_lrc10426_a41.2
Wc_983_a41.4
Oc_2822_a41.5
NHc_7064_aOs87_c8656_a41.6
Ws87_c7372_a41.8
Wc_5349_a42.0
Oc_6095_a42.1
Os87_c10305_a42.3
Oc_827_a42.4
Wc_5951_aOc_3442_a42.5
Oc_5145_aWc_3253_b
Oc_170_bOc_509_a42.6
Wc_1217_a42.8
Oc_5632_a42.9
Wc_962_a43.0
Wc_2471_b43.1
Oc_5610_a43.3
Oc_715_aOc_5427_a43.4
NHsA8_c11845_2_a43.6
NHsA8_c10400_3_a43.7
NHc_4243_a43.8
Oc_6940_a43.9
Oc_5040_bOc_6673_a44.1
NHsA8_c12061_3_aNHc_3698_a
Oc_1852_a44.3
NHsB9_c15621_2_aWs87_lrc3111_a44.5
Oc_5847_a44.6
NHsA8_c10860_2_a44.7
OsA8_c9342_3_aOc_5183_b44.8
Oc_1889_a44.9
Oc_119_aOc_3771_a45.1
Wc_775_aOc_3705c45.2
OsA8_c8444_5_a45.4
Oc_2415_aWc_1977_a45.6
NHc_3405_a45.7
NHc_1324_aOc_4996_b45.8
Wc_3915_a46.0
Oc_5440_aOc_238_a46.1
NHc_116_a46.3
Oc_582_a46.6
Oc_108_bWc_4336_a46.9
NHsB9_c13279_2_a47.0
NHs87_c4761_aWc_777_a47.5
Oc_5164_aWc_2185c48.0
NHc_5720_a48.8
Oc_304_a49.4
lrc7566cOsA8_c14521_2_a49.7
Oc_2743_a50.6
Oc_2999_a60.5
OsA8_c12359_2_a62.5
NHc_4781_a74.7
NHc_7134_a75.8
NHsA8_c4909_5_a77.5
Oc_246_b80.6
NHsA8_c12200_2_a82.3
LG 1 Oc_5890_a0.0
NHsA8_c8784_3_a18.9
Oc_525_a58.6
Oc_907_a66.2
NHsA8_c13798_2_a66.3
Oc_5076_a68.5
Oc_3321_a71.6
NHsA8_c9294_2_a73.1
Oc_913_a75.4
Oc_3101_a77.3
NHsA8_c12478_2_a78.1
NHsA8_c6498_3_a82.1
NHsB9_c12106_2_a85.3
Oc_3462_b106.4
Oc_2340_a139.5
Oc_6191_a157.1
Wc_3404_a188.6
LG 2 Oc_823_a0.0
Oc_4253_a7.5
Os87_lrc4228_b13.4
Oc_5302_a29.8
Oc_3618_b45.2
NHc_4075_a49.8
Wc_1200_a68.7
Oc_809_a69.6
Oc_3895_a71.1
Oc_2852_a87.0
Os87_c8742_a92.1
NHc_4998c96.5
Oc_3758c98.7
Oc_5925_a110.4
Oc_1099_a119.4
Oc_425_a122.6
Oc_4418_a134.0
Wc_4410_a164.7
NHsA8_c4553_8_a166.1
LG 3 Oc_4494_a0.0
Wc_1746_a36.2
NHc_1817_a38.3
OsA8_c2962_23_a43.3
Oc_2051_a55.5
Oc_6893_a63.8
Oc_2985_a74.8
Oc_232_a83.1
Oc_2491_a92.8
Oc_2231_a110.6
Oc_5238_a133.7
OsA8_c5428_4_a148.4
Oc_3654_b159.0
Ws87_c12398_a167.2
Oc_446_a200.6
LG 4 OsA8_c14040_2_a0.0
Oc_2390_a16.0
Oc_345_a33.6
Oc_6956_a39.5
Wc_3230_a104.5
Oc_4895c108.0
NHsA8_c2056_3_a124.1
Os87_c4651_a142.3
OsB9_c15460_2_a162.7
NHc_451_b201.3
Oc_441_a230.4
LG 5 Oc_3261_a0.0
NHsB9_c5688_4_a20.8
Oc_1444_a46.4
Os87_lrc7943_a46.8
Oc_1547_a75.8
Wc_215_a91.9
Oc_3189_a99.7
Os87_lrc10167_a116.4
OsA8_c5283_4_a131.1
Os87_c937_a149.8
Os87_lrc4003_a157.3
NHc_3428c159.1
Os87_lrc2126_a166.5
Oc_44_a172.2
NHc_7097_a183.9
Oc_897_a192.7
LG 6 Oc_4996_a0.0
Oc_469_a1.5
Wc_349_a11.5
WsA8_c2862_10_a17.6
NHs87_lrc10359_a19.7
NHc_4375_a24.2
Oc_5784_a31.1
Oc_2093_a32.7
Oc_7219_a37.8
Wc_2749_a41.9
Oc_3461_a61.8
Oc_2019_a86.6
NHc_3467_a94.1
Oc_3981_a94.7
Oc_6374_a150.1
Oc_6374_b151.1
NHsA8_c10943_3_a157.1
OsA8_c11757_2_a159.3
Oc_5573_a162.5
NHc_4316_a167.9
Oc_4478_a176.6
Oc_2445_a177.1
NHsA8_c6591_5_a177.2
Oc_2244_a216.6
Oc_2506_b222.6
Oc_3284_b239.0
LG 7 Wc_5986_a0.0
Oc_798_a1.3
Oc_5988_a4.5
Oc_1893_a24.6
Oc_1520_a28.7
NHs87_c8985_a49.2
Oc_315_a56.7
Ws87_c5038_a61.0
Oc_3418_a62.6
Wc_3717_a68.4
Oc_587_a94.5
Oc_1854_a115.1
NHs87_c10016_a119.2
Oc_6143_a127.2
Oc_3139_a133.2
Oc_2947_b138.6
Oc_6057_a143.1
NHsA8_c14662_2_a144.9
Oc_4953_a147.4
OsB9_c10038_2_a156.9
LG 8
Oc_649_b0.0
Wc_3659_a1.7
Os87_lrc4485_a6.2
Oc_5781_a7.5
Oc_1259_a9.2
Oc_1191_a12.7
Oc_6996_a14.0
Oc_1786_a24.3
Wc_2084_a38.7
NHsB9_c12604_2_a51.2
NHsB9_c9853_3_a63.2
Oc_2473_a87.8
Oc_214_a89.3
Os87_lrc6408_a90.6
Oc_3348_a91.9
Oc_5843_a93.8
Oc_6461_a95.2
Oc_4677_b102.0
Oc_2676_b110.2
WC_4163_a133.9
Ws87_c5895_a134.3
NHsB9_c9943_3_a166.6
Oc_2436c185.9
LG 9 Oc_2918_a0.0
NHc_5174_a6.0
OsA8_c8687_3_a24.5
Oc_4913_a27.8
Oc_5458_a36.9
Oc_393_b48.6
Wc_1967_a59.1
Oc_5561_b67.6
Wc_5485_a76.5
Oc_6343_a79.5
Oc_2912_a109.5
Oc_4870_b120.1
Oc_437_a133.4
Oc_1712_a182.4
Wc_531_a201.5
LG 10 Wc_1972_a0.0
NHc_6686_a1.3
Oc_3982_a1.9
Wc_6827_a31.2
OsA8_c6740_3_a32.1
NHc_2230_a54.7
Oc_5813_a56.1
NHsA8_c10398_2_a74.0
Oc_4539_a92.4
Oc_5164_b95.7
Oc_4740_a96.5
Oc_1949_a97.2
Os87_c4229_a98.6
Oc_4278_a101.1
Oc_6227_a102.7
Oc_808_a105.1
Oc_2845_a125.9
NHsB9_c8296_4_a142.7
LG 11 NHsA8_c6820_3_a0.0
NHs87_c7757_a5.9
Oc_4934_a8.4
Wc_1831_b12.4
Wc_5531_a42.6
Oc_4153_a46.5
Oc_5825_a52.1
NHsB9_c12502_2_a63.6
Os87_c1577_a85.7
Oc_4851_b95.0
Oc_3279_a110.1
Wc_5474_a125.0
Oc_3885_b148.9
OsA8_c3957_8_a152.1
Oc_586_a158.3
NHc_2801_a162.6
Os87_c2260_a189.7
Oc_5183_a198.1
Oc_4843_a208.2
LG 12 Oc_2590_a0.0
Wc_5598_a34.4
Oc_7063_b35.2
Oc_2034_a36.3
Oc_5879_a47.1
Oc_6261_b51.3
NHsB9_c11476_3_a88.8
NHc_4784_a97.7
Wc_3780_a104.5
Oc_30_d106.7
Oc_3780_b114.6
Oc_1632_a119.1
Oc_346_a126.4
Oc_3374_a143.0
LG 13 Oc_7240_b0.0
Oc_1113_a2.9
Os87_c10557_a51.4
Oc_2173c60.2
Oc_5905_a71.2
NHc_6655_a84.7
Wc_1981_a97.0
Oc_4536_b99.8
Oc_2863_b104.3
Oc_1176_a117.6
Oc_6254_a121.0
Oc_4606_a121.8
Oc_81_a124.9
NHsA8_c12375_2_a125.3
Os87_lrc5487_a127.0
Oc_5228_a129.5
Oc_1666_a155.5
NHsA8_c6374_5_a181.3
Oc_360_a199.8
Oc_5975_a218.5
LG 14
Oc_6746_a0.0
Oc_539_a25.9
OsA8_c11048_2_a75.9
Os87_c10801_a80.3
Os87_c4483_a81.2
OsA8_c3639_17_a86.8
NHsA8_c14455_2_a110.7
NHc_941_a113.4
Os87_c12339_a115.0
NHsB9_c10590_2_a144.6
LG 15 NHsB9_c11075_2_a0.0
Oc_2627_a34.3
Oc_4881_a48.7
OsA8_c1060_15_a56.1
Oc_6491_a59.3
Wc_5539_a77.1
Oc_183c97.8
Wc_5003_a100.6
Oc_320_b112.5
NHsB9_c12667_2_a114.9
Oc_594_b127.7
OsB9_c9685_3_a155.7
Oc_3186_a169.9
Oc_205_a173.6
Oc_2065_a195.0
LG 16 Oc_5095_b0.0
Oc_5771_a25.7
Oc_2141_a58.1
Oc_5707_a64.5
Oc_763_a108.0
Wc_7052_a135.2
Oc_4329_a138.1
LG 17 NHsB9_c13489_2_a0.0
NHsA8_c11104_2_a12.3
Ws87_lrc7506_a16.6
NHsA8_c13522_2_a*60.5
Wc_2196_b91.3
Oc_2744_a93.2
LG 18 Oc_2589_a0.0
Oc_1165_ab6.0
Oc_5127_a7.6
Oc_1165_a9.2
Oc_1165_ac10.3
NHs87_lrc8239_a25.0
Oc_2547_a54.6
LG 19 Oc_4991_a0.0
Oc_2132_a28.2
Oc_664_a37.9
Oc_5740_a42.6
Oc_4055_a47.8
LG 20
-Total length: 3229.548 cM with 97 markers
mapped on LG 1 and 6 markers in LG 20

QTL analysis
Bhattacharjee et al (2015). SSR-based genetic linkage map and identification of QTL (s) for
anthracnose disease in Dioscorea alata (under review)
Year Linkage group Marker interval Position interval LOD %var Pvalue(F)
Significan
ce level
Average
3oc_5302_a - Wc_1200_a 29.837 - 68.747 2.51 7.598 0.006075**
11Wc_1972_a - Oc_2845_a 0 - 125.949 3.605 11.217 0.000656***
12Wc_1831_b - Oc_4843_a 12.393 - 208.223 2.883 8.807 0.00285**
14Os87_c10557_a - Oc_1666_a 51.393 - 155.473 4.964 15.985 4.14E-05***
16NHsB9_c11075_2_a - Oc_2065_a 0 - 194.979 2.395 7.229 0.007675**
2013
LOD %var Pvalue(F)
1Oc_917_a - NHc_4781_a 8.076 - 74.710 4.038 9.303 0.000404***
3oc_5302_a - Wc_1200_a 29.837 - 68.747 3.952 9.086 0.000477***
10NHc_5174_a - Wc_531_a 5.95 - 201.506 4.889 11.512 7.78E-05***
11Wc_1972_a - Oc_2845_a 0 - 125.949 2.029 4.446 0.0197*
12Wc_1831_b - Oc_4843_a 12.393 - 208.223 3.214 7.252 0.001991**
14Os87_c10557_a - Oc_1666_a 51.393 - 155.473 5.716 13.747 1.57E-05***
16NHsB9_c11075_2_a - Oc_2065_a 0 - 194.979 2.453 5.431 0.008679**
2012
LOD %var Pvalue(F)
1Oc_917_a - NHc_4781_a 8.076 - 74.710 2.569 7.952 0.006934**
2Oc_3101_a - Wc_3404_a 77.318 - 188.567 2.257 6.932 0.012682*
4Oc_232_a - Oc_2231_a 83.095 - 110.612 1.731 5.249 0.035067*
7Oc_469_a - OsA8_c11757_2_a 1.544 - 159.330 2.086 6.38 0.017659*
11Wc_1972_a - Oc_2845_a 0 - 125.949 2.436 7.515 0.008971**
14Os87_c10557_a - Oc_1666_a 51.393 - 155.473 4.14 13.333 0.000332***
16NHsB9_c11075_2_a - Oc_2065_a 0 - 194.979 3.575 11.349 0.00099***
2011
LOD %var Pvalue(F)
3oc_5302_a - Wc_1200_a 29.837 - 68.747 2.578 8.852 0.00467**
12Wc_1831_b - Oc_4843_a 12.393 - 208.223 2.572 8.832 0.00472**
14Os87_c10557_a - Oc_1666_a 51.393 - 155.473 1.775 5.975 0.02482*
17Oc_5095_b - Oc_763_a 0 - 108.034 1.489 4.976 0.04506*

Development of SSR markers in D. alata
Parent 1 vs Parent 2
2041 SSRs matched but monomorphic
572 SSRS matched
503 SSRs did not match to the other
parent
Parent 2 vs Parent 1
2027 SSRs matched but monomorphic
573 SSRS matched
515 SSRs did not match to the other
parent
Test results of 572 genomic-SSRs
primers on Parent 1 and Parent 2
92 monomorphic
468 polymorphic (82%)
12 failed (2.1%)
Saski et al (2015). Development of genomic
and molecular resources for water yam.
Published in PLOS One journal

GBS analysis
P2
P1
convert
hapmap to
joinmap
Tolerance
threshold
filter
chi-sq test
Final output
pass
tolerance, %
missing, and
Chi-sq
distribution
• Neighbor-Joining tree (no obvious
clustering of resistance and
susceptibility)
• Allelic diversity observed for the SNPs
based on which individuals can be
grouped
New computational pipeline developed

Yam: CRPRTB complementary
projectFocus: Genotyping by sequencing (GBS); high-throughput phenotyping (metabolomics);
morphological characterization; breeding applications (inter- and intra-specific crosses)
Partnership: Cornell university, USA; Royal Holloway university laboratory, UK
 810 D. rotundata genotypes selected (core collection = 470 landraces; breeding lines =
307 genotypes; varieties from markets = 33)
 Pst I restriction enzyme to digest DNA
 GBS analysis completed on 553 genotypes using UNEAK analysis pipeline
Summary of TagPairs and
resulting SNPs (before annotation with WGS)
 6336738 total tags after merging
 HapMap SNPs (unfiltered): 4915
 HapMap SNPs (filtered): 416
Summary (after annotation with WGS)
(550 out of 553 sequences used)
 Only 48% of GBS sequences mapped to
reference genome (4531 scaffolds)
 23760 SNPs recorded (unfiltered)
 10950 SNPs (filtered)

Phenotyping of GBS materials
 All 810 genotypes planted in an augmented design
using three checks
 Each tuber was cut into three sections (head, middle
and tail) for planting
 Planting in two locations including Ibadan and Ikenne,
in May and June, 2014 respectively
 Observations on following above ground traits such as:
- Days for germination (Earliness)
- Number of vines per portion of the tuber
- Pests and diseases (anthracnose, virus, and
nematodes)
- Leaf shape and number of internodes
- Flowering traits (monoecy, dioecy, no flowering)
 For below ground observations:
- Tuber number and shape
- Tuber weight
 Soil samples from around each tuber and sent for
analysis
GBS Field Evaluation 2014, Ibada
Male
Inflorescenc
e
Female
Inflorescenc
e
Monoeciou
s
Fruits

Leaf Shape and Area; SPAD; Stomata Density
Flowering Fruit bearing Viruses Anthracnose
Phenotyping of GBS materials

Phenotyping: Results
Vine number
Head (38%)
Middle (30%) Tail (32%)
Tuber number
Head (39%)
Middle (29%) Tail (32%)
Tuber yield/kg
Head (44.8%)
Middle (26.6%)
Tail (28.5%)
Tuber
porti
on
Floweri
ng
(female)
Fruitin
g
(femal
e)
Correlatio
n
Head 115 51 0.443
Middle 74 31 0.419
Tail 76 31 0.407
Tuber
portio
n
Vine
numb
er
Tuber
numb
er
Correlatio
n
Head 1248 1048.9 0.84
Middle 984 776 0.788
Tail 1065 870.5 0.817

Metabolomics
 49 accessions from IITA breeding program
 5 species (D. alata, D. bulbifera, D. cayenensis, D. dumetorum, D.
rotundata)
 Tuber material (Head, middle and tail; selected leaf material)
10mg lyophilised tissue
phase separation
polar
standard
extraction
800ul MeOH:H2O (1:1)
1hr @ RT
800ul CHCl3
non-
polar
GC-MS
LC-MS/MS (UP)LC-PDA/MS
Polar = up to ~500 features
Non-polar = up to ~300
features

Metabolomics
D. rotundata clustered with wild relatives
 Non-polar analysis did not separate the
species well
 Polar analysis showed good species variation
 Limited variation in all species except D.
dumetorum and D. bulbefera
One major outlier in TDd 3774 based on
fatty acid profiles

Support to yam breeding at IITA
 Genotyping of 333 core genotypes (alata and rotundata) and 200 crossing block
materials (alata, rotundata, dumetorum, bulbefera and cayenensis) using 100
SSR markers
 Genotyping of 221 elite lines (D. rotundata = 50; D. alata = 73; D. dumetorum =
65; D. esculenta = 32; and D. cayenensis = 6) using 50 SSR markers
 Genotyping of mapping populations
- 4 female and 4 male (12 crosses and 460 progenies) (anthracnose)
- 2 alata and 5 rotundata populations (YMV)
 Genotyping of parents of inter- and intra-specific crosses
- 6 female and 6 male (D. alata) (tuber shape)
- 4 female and 6 male (D. alata), 2 female and 5 male (D. rotundata)
(monoecious plants)
- 7 female and 4 male (D. rotundata) (high carotene content)
- D. alata x D. rotundata; D. bulbefera (wild) x D. alata; D. rotundata x D.
cayenensis

Results
Population structure and UPGMA clustering based
on modified roger’s distances among 333 core
accessions and 221 elite lines
 Integration of genotypic
and phenptypic data to
assess pattern of genetic
diversity
 Complete genotyping of
breeding populations
 Genotyping with larger sets
of molecular markers (SSRs
and SNPs)
 GWAS and genomic
selection, where applicable

Other projects
MAFF: Genotyping parents and mapping population progenies using SSRs and GBS for
generating genetic maps and determine associations for traits related to nutrient use
efficiency
Training: 1 M.Sc. student (Nigeria); 1 M.Sc. student (Ghana); 1 Ph.D. student (Nigeria)
Trait of
Interest
No. of
female
No. of
male Crosses Progenies
NUE 6 6
TDr 04-219
TDr Alumaco 24
TDr 00/00362 29
TDr 95/01932 629
TDr 99/02562 23
TDr 89/02157 TDr 95/01932 16
TDr 89/02665
TDr Alumaco 23
TDr 00/00362 2
TDr 97/00777 16
TDr 95/01932 4
TDr 97/00917 TDr 95/01932 37
TDa 00/00194 TDa 02/00012 341
TDa98/01166 TDa 02/00012 4
Additional 225 genotypes from Ghana (4 parents with 2 crosses and progenies)
 A set of 150 SSRs are being tested on parents for polymorphism
 Two of the mapping populations parents and progenies will be sent for GBS analysis
at
Clemson University

Other projects
Determination of ploidy levels in different Dioscorea sps. (Dr. Jaroslav’s lab, Czech Republic)
TDc 4712; 2n = 6x = 60 TDd 3106; 2n = 6x = 60

Other initiatives
Whole genome sequencing of Dioscorea rotundata completed; re-sequencing of
additional 10
lines completed; RAD-sequencing of mapping population for sex completed
The Genome Analysis Center (TGAC): transcriptomic analysis (RNAseq and small
RNAseq) for
anthracnose disease; DNAseq of parents and the pathogen (Colletotrichum
gloesporoides)
- Leaf samples from non-infested and infested plants (resistant and susceptible
parent; and 4 progenies: HR, MR, R and S)
- DNAseq of resistant parent (250 bp forward and reverse reads)
- Genome assembly using the new DISOCOVAR de novo workflow
African Orphan Crops Consortia (AOCC): Agreement signed between IITA and ICRAF
for DNA
sequencing and re-sequencing of three Dioscorea spp.
- D. dumetorum (whole genome sequencing)
- D. alata, D. rotundata and D. dumetorum (Re-sequencing of 100 lines each)

FIELD BOOK: TRIAL
DESCRIPTION
PLANTING DATE HARVEST DATE
PROJECT
CODE
YEAR
FORMNo
TRIALTYPE
SITECODE
YEAR
MONTH
DAY
YEAR
MONTH
DAY
1
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
OTHER CODES
DAYSIN
CYCLE
PLANTS/
PLOT
PLANTS/
HARVESTED
PLOT
HARVESTED
AREA(M2)
EXPTL
ENTRIES/
TRIAL
CHECK
ENTRIES/TRIA
L
YAMSPECIE
*
24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54
TRIAL TYPE SITE YAM SPECIE
01 CORE COLLECTION 08 ADVANCED YIELD TRIAL 01 IBADAN 07 01 TDr
02 POLYCROSS 09 REGIONAL TRIAL 02 ABUJA 08 02 TDa
03 CONTROLLED CROSS 10 PVS TRIAL 03 UBIAJA 09 03 TDd
04 F₁ 11 OTHER BREEDING TRIAL 04 IKENNE 10 04 TDc
05 F₁C₁ 12 SEED INCREASE 05 MOKWA 11 05 TDb
06 SINGLE ROW TRIAL 13 THESIS 06 KANO 12 06 TDsc
07 PRELIMINARY YIELD TRIAL 07 INTER spp
08 OTHER
DATA MANAGEMENT METHODS

Factor2(34.1%)
-1.0
-0.6
-0.2
0.2
0.6
1.0
Factor 1 (54.8%)
-1.0 -0.6 -0.2 0.2 0.6 1.0
TDa_02/00092
TDa_02/00151
TDa_03/00010
TDa_03/00132
TDa_03/00135
TDa_03/00203
TDa_03/00275
TDa_03/00497
TDa_03/00544
TDa_07/00003
TDa_07/00026
TDa_07/00032
TDa_07/00038
TDa_07/00062
TDa_07/00081
TDa_07/00125
TDa_07/00126
TDa_07/00128
TDa_07/00131
TDa_07/00133
TDa_07/00141
TDa_07/00146
TDa_07/00147
TDa_98/01176
Abuja
Ikenne
Ubiaja
AMMI TDA Yield From a RCBD
15 years of breeding data
• Parents
• Progenies
Genetic Gain

GCA
SCA
Additive
Dominance

A. Selection of half-sib families based on progeny tests.
Example: i) OP seed used to establish tests, ii) orchard is not rogued, iii) but on the
basis of progeny tests, seed collections are made only from healthy plants.
Predicted gain is specific to that directed seed collection.
B. Linear Model for Observations (Assume OP, RCB progeny test)
yijkl = µy + Ei + Bij + fk + feik + pijk + eijkl
where µy, Ei, Bij = fixed effects for overall mean, test, and block
fk, feik, pijk, eijkl = random effects for family, family x environment, plot and within-
plot (random effects have expected values of zero and some variance)
The covariances between all pairs of factors are assumed zero, Σ Ei = 0, and Σ Bij
in any one test = 0.
C. Prediction Equation 1. Observational unit is half sib family mean (..k.) y¯..k. =
µy + fk + (fe.k/t) + (p..k/tb) + (e..k./tbn)
Family Selection from FRT and OP Crossing Blocks

LOGISTIC REGRESSION ANALYSIS
FARMERS’ PVS

FARMERS’ PVS

PRODUCTION AND MAINTENANCE OF SEED FOR TRIALS AND
OF BREEDER (PRE-BASIC) SEED OF RELEASED VARIETIES
TRIALS and BREEDER SEED
1. MINISET TECHNIQUE (50-70 g)
To produce : YAM SEED (150-200)
2. VERTICAL SACKS: Vine cutting to
produce 80 -100g YAM SEED
RELEASED VARIETIES
1. IN VITRO MAINTENANCE, GRC
2. CLEANING FOR VIRUSES
-Establishment of virus-free clones of landrace and
breeding collection
-Characterization of viruses infecting yams in West Africa
-Surveys for incidence and prevalence of major pest and
diseases in West Africa
-Development of versatile diagnostic tools for all the major
yam infecting viruses in West Africa
-Characterization of YMV in D. rotundata diversity set
-Phenotyping germplasm and mapping populations for YMV
resistance, and understanding genetic and molecular basis
of host-virus interactions (mechanisms)
-Phenotyping germplasm and landraces for anthracnose
resistance
-Understanding etiology and rate of seed yam degeneration,
including modes and rate of virus infections
-Deep sequencing of smallRNA profiles for discovery of
viruses in yam, including the impact of integrated
badnaviruses

USE OF MECHANIZATION AND AUTOMATION
INCLUDING ELECTRONIC DATA CAPTURE
1. Land preparation: depth, tuber growth
2. Drip irrigation system at SH
3. SPAD
4. Tablet and Hard copy field book
5. In process: Bar code system, Breeding platform

USE OF BREEDING MANAGEMENT SYSTEM OF THE
INTEGRATED BREEDING PLATFORM.
Data from 2001-2010 in migration process
Use of Yam Ontology

PARTNERSHIP
BIOTECHNOLOGY
AND GENETIC
IMPROVEMENT
PLANT
PROTECTION
AND HEALTH
SOCIAL SCIENCES
AND
COMMERCIALIZATION
NATURAL
RESOURCES
MANAGEMENT
GDT, JIRCAS,
IBRC, USDA, GBIF
CORNELL UNIV.
MISSISIP. UNIV.
TOKYO U. AGRIC
CIRAD-IRD
INIVIT-CUBA
NARS
CG-CIAT-CIP
NRI-UK
MOFA-Japan
JHI-UK
.
.
.
.
CIRAD
ITC
FAO
FOOD INDUSTRY
MOTI-GHANA
M. OF AGRIC.
NRI-UK
NARES
PRIMLAKS
YOUTH-IITA
.
.
.
.
.
.
.
NARES
PL. PRTC. AGEN
UC – DAVIS
NRI-UK
UI
.
.
.
.
.
.
.
.
.
.
TOKYO U.AGRIC
NARES
MAFF-JAPAN
.
.
.
.
.
.
.
.

Partners (Genomics)
- USDA-ARS, Mississippi, USA
- Clemson University, USA
- Virginia State University, USA
- Iwate Biotechnology Research Center, Japan
- JIRCAS, Japan
- The Genome Analysis Center, UK
- African Orphan Crops Consortium: ICRAF, Nairobi and UC Davis,
USA
- Royal Holloway University of London, UK
- Institute of Experimental Botany, Czech Republic
- Michigan State University
PARTNERSHIP

RESOURCES
HUMAN CAPITAL
IRS
1. A. Lopez-Montes
2. Asrat Amele
3. David DeKoeyer
4. R. Bhattacharjee
5. Saini Himanchu
NRS
1. Edemodu Alex, Res. Assoc.
2. Adeosun Tunde, Res. Officer
3. Partick Ezighi, Res. Superv.
4. Sunday Olajide, Technician
5. Kola Odelade, Field assist.
6. Nurudin, Pollinator
7. Kabiru Ganiyu, Pollinator
8. Adewumi Adeyinka , Res. Assoc
9. Adejuwon Ebunutti, Technician
FINANCIAL CAPITAL
1. CG-Consor. 2005-2015
- 50 -100K to < 30K operative
- 1 IRS and 6 NRS
2. Bilateral 2012-2015
- MAFF Jap. ~ 230K (Breed/SF)
- YIIFSWA- 12.5 M ~ 300K (PVS)
- AF. YAM. 13.5 M. Breeding
- MOFA Jap: 50-100K Breeding
- TUA: < 20K Breeding
- JIRCAS: < 10K Breeding
- IFAD : 130K Breeding
- ITC : 50K
- PRIMLAKS: 40K.

Achievements over the last decade (international exchange of germplasm; genetic
gain realised; varieties released by partners; important traits added to improve
resilience or end-user preference; parents used by private sector; area under
improved varieties from program)
IITA designation Species Year of Release
TDa 98/01166 Dioscorea alata 2008
TDr 89/02602 Dioscorea rotundata 2009
Eleven (11) IITA-bred yam varieties officially released
in Nigeria in 2008, 2009 and 2010

Distributed in Benin
The D. alata genotypes include (10):
TDa 98/01166, TDa 99/01169, TDa
01/00012, TDa 01/00018, TDa 00/00064,
TDa 01/00090, TDa 98/01168, TDa
01/00092, and TDa 00/00103
(introduced from IITA), and Florido
(introduced from Puerto Rico).
Among the selected D. rotundata are (6):
TDr 747, TDr 99/00632, TDr 95/19158,
TDr 95/11531, TDr 89/00665 and TDr
95/18544 (introduced from IITA).
Distributed in Togo
two D. rotundata varieties (TDr 89/02665
and TDr 747)
Popularization of ‘Florido’, an introduced
D. alata which originated from Puerto
Rico.
Three other IITA developed varieties
comprising of two D. rotundata (TDr
95/19156 and TDr 97/00903), and one
D. alata (TDa 99/01169)

GHANA 2005
Three new varieties – CRI Pona, CRI
Kukrupa and Mankrong Pona (TDr
89/02665)
COTE D’ Ivoire, 2012
Registered
D. rotundata
TDr 89/02475
TDr 89/02565
TDr 89/02665
TDr 95/01864
TDr 95/18544
TDr 95/19156
TDr 95/19127
TDr 95/19177
TDr 96/00629
D. alata
TDa 98/01166
TDa 98/01176

Production System
Ware Seed,
and
Subsistence
Yam
Environment
Drought
Environment
Localities Abakaliki, Ebonyi stateTegina, Niger State Iseyin, Oyo State
Staked/No staked
Kg/ha
Staked No staked Staked No staked Staked No staked Staked Staked Staked No staked Staked
AVG best five
improved lines 10101 10610 32100 28940 6740 5420 6932 1131 10130 8051 9848
AVG released variety
(TDr 89/02265) 13667 6111 46200 46000 10700 5000 5933 1675 6000 611 11650
AVG Local and
national landraces as
Checks
4436 2897 15640 13660 3333 3500 4980 418 3763 4302 6079
% of Yield Increase
from improved lines
on Local checks
128 266 105 112 102 55 39 170 169 87 62
% of Yield Increase
from improved lines
on released variety
check
-26 74 -31 -37 -37 8 17 -33 69 1218 -15
Ware YamProduction System
Low Fertility Soil environment
Ware and Seed Yam
Production System
Igbariam, Anambra
state
Zaki Biam, Benue state Makurdi, Benue state Oria-Iluchi, Edo state
Low Fertility Soil environment
PVS_YIIFSWA NIGERIA, 2012-2015

Production System
Environment
Localities
AVG best five
improved lines Kg/ha 14628 10970 7090 7997 7700
AVG Local and
national landraces as
Checks Kg/ha 6423 6480 5250 6022 5148
AVG released
varieties Kg/ha
TDr 89/02265 3127 TDr 89/02265 1133 TDr 89/02265 6333 TDr 89/02665 9650 TDr 89/02265 5100
% of Yield Increase
from improved lines
on Local checks 128 69 35 33 50
% of Yield Increase
from improved lines
on released variety 368 868 12 -17 51
TOLON SAVELUGU EJURA ATEBUBU KINGTAMPO
Low fertility soil Drought Low fertility soil
Yam No-Staked system Yam staked system
PVS_YIIFSWA GHANA, 2012-2015

SELECTED CLONES’ TRAITS (TUBERS)
BY FARMERS

SELECTED CLONES’ TRAITS ABOVE GROUND
BY FARMERS

NEMATODES
N.U.EANTHRACNOSE
EARLY- LATE MAT
DROUGHT TOLER
Achievement: Selection of Parents II :

D. rotundata:
16 Parents of populations with three years data
422 clones in mapping populations including the parents with three years data
10 clones under re-sequentiation with more than three years data
70 clones actually in crossing blocks, with data of flowering and other traits for more than 5 years
150 elite clones with 8 years data
200 clones in Advanced yield trials with three years data
100 clones in preliminary yield trials with two years data
100 clones in family replicated trials with three years data
500 F1C1 Clones with one year data
700 clones from core collection with 5-10 years data. To be confirmed
Total = 2268 from the first year of the project
D. alata
8 parents of popluations with three years data
2 parents under sequentiation for anthracnose resistance
200 clones in three mapping population including the parents with three years data
50 clones actually in crossing blocks with data of flowering and other traits for more than 5 years
150 elite clones with 8 years data
190 clones in Advanced yield trials with three years data
150 clones in preliminary yield trials with two years data
110 clones in family replicated trials with three years data
500 F1C1 Clones with one year data
500 clones from core collection with 5-10 years data.. To be confirmed
POPULATIONS AND ELITE MATERIAL
YIIFSWA: 23 Elite
AFRICA YAM: Several
JIRCAS: Earliness

** Development of Genomic Simple Sequence
Repeat Markers for Yam.
Crop science, vol. 55, september– october 2015
** Yam Genome sequence: Submitted to Nature-Genetic
** Three TDr Varieties for Yam Fries-PRIMLAKS
** Three TDr Varieties for yam Flour- PRIMLAKS
** Ten TDa Varieties for ICE Cream – Fan-MILK
** Interspecific Hybrids
** PVS Methodology for Yam
** Yam Ontology
** 1000 Progenies to INIVIT-Cuba

CONSTRAINTS AND MITIGATION PLAN
1. HUMAN CAPITAL
- Capacity building
- Increase – quality
- Breeder by specie
2. FACILITES AND EQUIPMENT
- Management strategy-fund raising
3. PREBREEDING
- IRS, Univ.-partnership for research
- GRC
4. BREEDING
- Capacity building: Africa yam
- IRS, Univ, Private setcor-Partnership
- Fund raising
5. . VARIETY DEVELOPMENT-DELIVERING
- Strengthening community of practice
- Release system-inclusive
-Market oriented-Participatory

Accelerate adoption : Variety Development and Delivering
Variety Development
NARIs to selectF1C1 and PT
PVS
Farmers
Processors
Households
Traders
Industry
P. Systems
RELEASE
Delivering = National Systems
Proposed action plan
1. Priority setting for
yam at country level
2. Yam breeding
process
3. Capacity Building
and research process
To make a significant improvement in yam breeding with NARS partners

RE-DEFINITION
OF ENVIROMENTS
ACCELERATE
ADOPTION
KNOWLEDGE AND
USE OF DIVERSITY
SPEEDING UP
THE
SELECTION
IITA’s STRATEGIC
OBJECTIVE 1
F. SECURITY
IITA’s STRATEGIC
OBJECTIVE 3
SUST. NRM
IITA’s STRATEGIC
OBJECTIVE 2
F. PROFITABILITY
Future Vision

Priority activities and expected outputs in the
next 3-5 years
Priority activities
1. Renovate the collaboration and the MoU terms
between IITA and yam producers countries
2. To develop a n implementation plan for yam
breeding for each country
3. Genome sequence of TDr and TDa
4. GBS for actual parents
5. Start a new breeding cycle in 2014 using GCA
and SCA
6. Determine feasibility of genomic selection
7. Develop bi-parental and multi-traits population for
TDa, TDr, TDd
8. Deliver at least 20 clones per year (starting in
2015) to Nigeria, Ghana, Benin, Togo and Ivory
Coast to be tested in pre-released trials. Seed set
will be produced in 2014
9. To support PVS-Yam establishment in West
African countries
Expected outputs
1. Marker assisted and genomic
selection is feasible and
2. Number of released varieties in
Nigeria, Ghana and Ivory Coast is
increased at least one variety per
year
3. Breeding cycled reduce from 5
to 2 years
4. Multi-traits population delivered
5. Yam breeding programs in
Nigeria and Ghana Strengthened
6. Released varieties are selected
by farmers and breeders trough
PVS

Future Vision
ITA aims to lead an inclusive global consortium of partners to
effectively develop and apply modern approaches to yam breeding and
the deployment of novel varieties.
West Africa is the most important geographic region for the research
Work in other regions will increase, especially through partnership with
national and regional agencies.
East and Central Africa; Latin America & Caribbean; and the Asia-Pacific
region.
Dioscorea rotundata (most cultivated yam species) and D. alata (the most
cosmopolitan) will continue to receive the most attention
Partners in other regions would be supported with species-neutral
technologies for other species that may be specific or more important in
their regions.

Future Vision
1. Increase the germplasm collection, efficient evaluation
2. Increased emphasis on complex traits
Higher yield, Postharvest losses
Early bulking, NUE, Drought tolerance
Viruses resistance, Easy propagation by vine
Value addition traits- starch types-quality
Exploring the advantages of inbreeding in monoecious: unveil recessive
3. Efficient Methods for the improvement of complex traits
4. Use of appropriate Breeding tools to improve Genetic Gain,
incorporating farmers criteria from early generations
5. National systems using participatory yam breeding approach
6. Use of genome sequence data to generate useful genetic information
to increase speed and precision of breeding programmes.
To generate databases for whole genome annotation
To effectively mine information from the available WGS
To connect genotype-phenotype through the integration of linkage mapping
and association analysis.

Future Vision
7. Molecular characterization of germplasm
Fingerprinting of accessions to definitively identify genetic
diversity in the collection and to screen incoming germplasm
for uniqueness
Identification of diverse parents for key traits to develop
populations to feed into the breeding programmes
8. Conservation and characterization of crop wild relatives
and their use in introgression programmes
9. Enhanced phenotyping methods for key traits
There is a need to use high throughput phenotyping
techniques such as metabolomics, to enhance the
multispecies potential of Dioscorea

Future Vision
10. Availability of mapping populations
The most straight forward way of finding the quantitative trait loci (QTL)
underlying traits that are of interest in yam breeding (diseases, quality, etc) is
through genetic linkage analysis.
11. Setting the stage for genomic selection
Experiences can be shared between yam and cassava breeding program at
IITA, which is already implementing genomic selection.
12. Clean yam systems
To generate virus-free planting materials for free movement of germplasm
across borders.
13. Use of tissue culture techniques/transformation
To assist crop improvement like genetic transformation, embryo rescue,
chromosome doubling.
To produce further variations in Dioscorea species, inter-specific hybridization
Anther culture can be used to produce homozygous – haploids

Future Vision
14. Core competencies and Partnerships
Many strong partnerships have already been developed between IITA and West African
NARS, which needs to be strengthened and aligned with the objectives above and
different breeding programs of NARS.
At the same time global partnerships (including, as examples, India and the Pacific) need
to be developed which will allow more rapid progress through the sharing of information,
germplasm and expertise
Working together to enhance both side capacities

TEAM
BIOTECHNOLOGY
AND GENETIC
IMPROVEMENT
PLANT
PROTECTION
AND HEALTH
SOCIAL SCIENCES
AND
COMMERCIALIZATION
NATURAL
RESOURCES
MANAGEMENT
M. Abberton
R. Bhattacharjee
A. Lopez-Montes
G. Badara
N. Maroya
B. Aighewi
T. Girma
H. Kikuno (2012)
A. Amele
D. DeKoeyer
R. Matsumoto
K. Yukiko
M. Djana
A. Tahirou
M. Dixon
L. Kumar
D. Coyne
R. Bandiopadhay
J. Augusto
S. Hauser
J. Martin
R. Matsumoto

TEAM and CAPACITIES
The essential requirements for IITA to create the ‘best modern breeding
program for yam include:
 Well trained and motivated human resources
 Adequate and modern field and laboratory facilities and equipment
 Capacity for: bioinformatics and application of genomic tools,
modern pre-breeding approaches, application of modern approaches to
linking phenotype-genotype, mass propagation and reliable virus cleaning,
efficient and accurate data collection.
 Capacity to store, manage and analyze large data sets including development of
a user-friendly yam database, and the curation and management of the
database (similar to cassavabase or using the same platform)
 Effective collaboration with other scientists or partnerships with relevant
advanced research institutes
 Effective strategies and methods for breeding based on modern and more
efficient tools

THANKS
Future Vision

Iita yam breeding 2005-2015

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