Iita yam breeding 2005-2015

A member of CGIAR consortium www.iita.org

Workshop on Implementation of IITA’s Genetic Improvement StrategyAntonio 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

http://www.exotic-plants.de/auktionsbilder/Dioscorea_sylvatica1_large.jpg


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 KNOWLEDGEAND 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 AreasWith 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 metabolitesImpact 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 YamFood

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 andGenotyping Spp.

Core collection and Core Diversity set

Inter-specific Hybridization

Aneuploidy

Re-

defin

ition

Of E

nviro

men

tsS

peed

ing

upth

e se

lect

ion

Kno

wle

dge

and

use

of d

iver

sity

STRUCTURE OF THE PROGRAM

Acc

eler

ate

adop

tion


Redefinition of environments: Yam production systems

Characterization

Livelihood

• Food Security • Income Level • Income Flows • Employment • Poverty-capability • Well-being • Gender Effects Resilience

• Production Risk • Market Risk • Response to Shocks Natural Resources

Base

• Water Resources • Soil Resources • Forest Resources

•

Impact

Livelihood Strategies

Agricultural Intensification

Agricultural Extensification

Agricultural Diversification

Agricultural Specialization

Non-agricultural

Process of Change

Differentiated Social Actors

Livelihood Resources

Production System

• Weather (Rainfall and Temperature) • Soil Units scale less than 1:300.000 • Land use with yam species • Length Growing season

Economic Financial

• Savings and Loans • Productive Assets • Land • Labor • Markets Human

• Formal Education • Capabilities • Agency • Gender • Leadership • Values • Origin and Ethnicity • Family Characteristics Social:

• Participation and Role in Organizational Processes

• Personal Contacts • Influential People • Knowledge Sharing

Opportunities • Service Providers • Collective Action • Community Characteristics

Endow

men

ts and

En

titlem

ents

Support Institutions and

External Intervention

Development State

Livelihood 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


TYPE 1 TYPE 2 TYPE 3 TYPE 40%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

WomenMen

GENDER

FARMERS’ CHARACTERISATION: TYPES….


GENDER CATEGORIES

Women: Young Old

Men: Young Old

FARMERS’ CHARACTERISATION: TYPES…


2 - 4 months

8-10 months10-20 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 10 20 30 40 50 60 70 80 90 100

12 15 74 RTS

Pathogen survey Pathogen Diversity analysis More Virulent strains

TDa F1 selection 2011-2012

ANTRACHNOSE SCREENING PROTOCOL USING VINE CUTTING



D. a

lata

and

D. r

otun

data

Improving meristem culture

D. a

lata

and

D. r

otun

data

Vine propagation

D. a

lata

and

D. r

otun

data

Minituber propagation

Propagation



Years Phenotypic Selection at IITA5-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 sacksViruses: 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 accessionsSource: Asiedu, 2010

Africa: 90-95% accessions

Asia:…..accessions

Pacific…..accessions


METHODS USED (CONVENTIONAL AND MOLECULAR/GENOMICS-ASSISTED BREEDING )



Inter-specific HybridizationRefinement 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

BreedingObjective

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 maturityLonger tuber

dormancy

x Objective 2

Objective 5


Inbreeding

Monoecious Haploids

Diallel crosses

Back crosses4120 Progenies

Anther cultureCharacterization 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 alata100 Elite materials characterization

5. Tuber micronutrient density

5.1. Screening germplasm for tuber iron and zinc contents5.2. 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) content5.7. 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 cloneSelection within each blockReps allow for a Statistical phenotypic selection (Gardner (1961)Replicated information for each familySelection Index (SI)

Information use to derive the relative values of the parents that generated the families

General Combining AbilityGCA

Specific Combining AbilitySCA

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

MF

1 2 3 4 5 6 7 8 9 10 11 12 13 141 28 8 23 18 26 7 21 25 17 9 22 4 18 262 25 27 11 12 10 6 20 1 15 5 24 13 9 143 22 14 15 9 16 4 13 14 23 12 2 27 11 254 20 3 24 19 5 2 18 3 6 7 8 19 10 165 17 2 7 1 6 8 10 9 13 4 3 20 6 216 21 18 16 4 3 7 13 21 17 11 15 1 5 237 12 13 6 10 11 5 14 1 3 9 24 7 2 108 1 14 23 19 9 22 15 25 16 6 10 8 22 39 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 2511 17 12 13 10 19 8 4 8 1 13 3 12 4 1612 21 4 18 5 22 15 26 5 18 15 7 23 1 413 8 23 6 20 14 9 17 11 19 21 16 6 14 2614 3 5 11 2 24 7 13 12 20 8 24 11 27 215 7 1 9 16 8 10 5 1 9 4 6 2 5 1816 10 17 3 2 1 14 6 13 17 1 22 15 3 1217 22 12 19 4 15 12 4 19 14 25 10 7 13 1918 25 14 6 21 28 18 7 8 5 18 11 23 16 819 24 11 20 13 9 10 2 3 13 12 4 14 20 1720 2 26 8 23 16 5 27 11 15 21 24 6 9 2

(HSMRS)

M

M M

M M

MFM

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….










Additive

Dominance



A member of CGIAR consortium www.iita.orgA member of CGIAR consortium www.iita.org

Yam: USAID-Linkage projectFocus: 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 studentPartnership: NRCRI, Nigeria; USDA-ARS, Stoneville, USA; Clemson University, Clemson, USA


SSRs from EST-sequencesMore 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 mappingNHsB9_c14199_2_a0.0

Oc_93_a3.3Oc_2671_a3.6Oc_280_a5.6Wc_946_a7.7Oc_917_a8.1Oc_6126_a11.2

Os87_lrc4432_a11.8Wc_1531_a13.1

NHsA8_c4355_5_a13.2Wc_422_a13.7Oc_5893_a15.6Oc_3971_a17.2Oc_3766_b18.9Oc_5267_a36.0Oc_2822_b39.0Oc_6102_a39.2Oc_1655_a39.6Oc_1780_a39.9Oc_2567_a40.3Oc_1923_a40.4Os87_c878_a40.8Oc_3766_a40.9Oc_4872_aNHs87_lrc10426_a41.2Wc_983_a41.4Oc_2822_a41.5NHc_7064_aOs87_c8656_a41.6Ws87_c7372_a41.8Wc_5349_a42.0Oc_6095_a42.1

Os87_c10305_a42.3Oc_827_a42.4Wc_5951_aOc_3442_a42.5Oc_5145_aWc_3253_bOc_170_bOc_509_a42.6Wc_1217_a42.8Oc_5632_a42.9Wc_962_a43.0Wc_2471_b43.1Oc_5610_a43.3Oc_715_aOc_5427_a43.4

NHsA8_c11845_2_a43.6NHsA8_c10400_3_a43.7

NHc_4243_a43.8Oc_6940_a43.9Oc_5040_bOc_6673_a44.1

NHsA8_c12061_3_aNHc_3698_aOc_1852_a44.3

NHsB9_c15621_2_aWs87_lrc3111_a44.5Oc_5847_a44.6

NHsA8_c10860_2_a44.7OsA8_c9342_3_aOc_5183_b44.8

Oc_1889_a44.9Oc_119_aOc_3771_a45.1Wc_775_aOc_3705c45.2

OsA8_c8444_5_a45.4Oc_2415_aWc_1977_a45.6NHc_3405_a45.7NHc_1324_aOc_4996_b45.8Wc_3915_a46.0Oc_5440_aOc_238_a46.1NHc_116_a46.3Oc_582_a46.6Oc_108_bWc_4336_a46.9

NHsB9_c13279_2_a47.0NHs87_c4761_aWc_777_a47.5Oc_5164_aWc_2185c48.0NHc_5720_a48.8Oc_304_a49.4lrc7566cOsA8_c14521_2_a49.7

Oc_2743_a50.6Oc_2999_a60.5

OsA8_c12359_2_a62.5NHc_4781_a74.7NHc_7134_a75.8

NHsA8_c4909_5_a77.5Oc_246_b80.6

NHsA8_c12200_2_a82.3

LG 1 Oc_5890_a0.0

NHsA8_c8784_3_a18.9

Oc_525_a58.6Oc_907_a66.2NHsA8_c13798_2_a66.3Oc_5076_a68.5Oc_3321_a71.6NHsA8_c9294_2_a73.1Oc_913_a75.4Oc_3101_a77.3NHsA8_c12478_2_a78.1NHsA8_c6498_3_a82.1NHsB9_c12106_2_a85.3Oc_3462_b106.4

Oc_2340_a139.5

Oc_6191_a157.1

Wc_3404_a188.6

LG 2Oc_823_a0.0Oc_4253_a7.5Os87_lrc4228_b13.4Oc_5302_a29.8Oc_3618_b45.2NHc_4075_a49.8Wc_1200_a68.7Oc_809_a69.6Oc_3895_a71.1Oc_2852_a87.0Os87_c8742_a92.1NHc_4998c96.5Oc_3758c98.7Oc_5925_a110.4Oc_1099_a119.4Oc_425_a122.6Oc_4418_a134.0

Wc_4410_a164.7NHsA8_c4553_8_a166.1

LG 3Oc_4494_a0.0

Wc_1746_a36.2NHc_1817_a38.3OsA8_c2962_23_a43.3Oc_2051_a55.5Oc_6893_a63.8Oc_2985_a74.8Oc_232_a83.1Oc_2491_a92.8

Oc_2231_a110.6

Oc_5238_a133.7OsA8_c5428_4_a148.4Oc_3654_b159.0Ws87_c12398_a167.2

Oc_446_a200.6

LG 4OsA8_c14040_2_a0.0Oc_2390_a16.0

Oc_345_a33.6Oc_6956_a39.5

Wc_3230_a104.5Oc_4895c108.0NHsA8_c2056_3_a124.1

Os87_c4651_a142.3

OsB9_c15460_2_a162.7

NHc_451_b201.3

Oc_441_a230.4

LG 5Oc_3261_a0.0

NHsB9_c5688_4_a20.8

Oc_1444_a46.4Os87_lrc7943_a46.8

Oc_1547_a75.8

Wc_215_a91.9Oc_3189_a99.7

Os87_lrc10167_a116.4OsA8_c5283_4_a131.1

Os87_c937_a149.8Os87_lrc4003_a157.3NHc_3428c159.1Os87_lrc2126_a166.5Oc_44_a172.2NHc_7097_a183.9Oc_897_a192.7

LG 6Oc_4996_a0.0Oc_469_a1.5Wc_349_a11.5WsA8_c2862_10_a17.6NHs87_lrc10359_a19.7NHc_4375_a24.2Oc_5784_a31.1Oc_2093_a32.7Oc_7219_a37.8Wc_2749_a41.9Oc_3461_a61.8Oc_2019_a86.6NHc_3467_a94.1Oc_3981_a94.7

Oc_6374_a150.1Oc_6374_b151.1NHsA8_c10943_3_a157.1OsA8_c11757_2_a159.3Oc_5573_a162.5NHc_4316_a167.9Oc_4478_a176.6Oc_2445_a177.1NHsA8_c6591_5_a177.2

Oc_2244_a216.6Oc_2506_b222.6Oc_3284_b239.0

LG 7Wc_5986_a0.0Oc_798_a1.3Oc_5988_a4.5Oc_1893_a24.6Oc_1520_a28.7NHs87_c8985_a49.2Oc_315_a56.7Ws87_c5038_a61.0Oc_3418_a62.6Wc_3717_a68.4

Oc_587_a94.5Oc_1854_a115.1NHs87_c10016_a119.2Oc_6143_a127.2Oc_3139_a133.2Oc_2947_b138.6Oc_6057_a143.1NHsA8_c14662_2_a144.9Oc_4953_a147.4OsB9_c10038_2_a156.9

LG 8

Oc_649_b0.0Wc_3659_a1.7Os87_lrc4485_a6.2Oc_5781_a7.5Oc_1259_a9.2Oc_1191_a12.7Oc_6996_a14.0Oc_1786_a24.3Wc_2084_a38.7NHsB9_c12604_2_a51.2NHsB9_c9853_3_a63.2Oc_2473_a87.8Oc_214_a89.3Os87_lrc6408_a90.6Oc_3348_a91.9Oc_5843_a93.8Oc_6461_a95.2Oc_4677_b102.0Oc_2676_b110.2WC_4163_a133.9Ws87_c5895_a134.3

NHsB9_c9943_3_a166.6

Oc_2436c185.9

LG 9Oc_2918_a0.0NHc_5174_a6.0

OsA8_c8687_3_a24.5Oc_4913_a27.8Oc_5458_a36.9Oc_393_b48.6Wc_1967_a59.1Oc_5561_b67.6Wc_5485_a76.5Oc_6343_a79.5

Oc_2912_a109.5Oc_4870_b120.1Oc_437_a133.4

Oc_1712_a182.4

Wc_531_a201.5

LG 10Wc_1972_a0.0NHc_6686_a1.3Oc_3982_a1.9Wc_6827_a31.2OsA8_c6740_3_a32.1

NHc_2230_a54.7Oc_5813_a56.1NHsA8_c10398_2_a74.0Oc_4539_a92.4Oc_5164_b95.7Oc_4740_a96.5Oc_1949_a97.2Os87_c4229_a98.6Oc_4278_a101.1Oc_6227_a102.7Oc_808_a105.1Oc_2845_a125.9NHsB9_c8296_4_a142.7

LG 11NHsA8_c6820_3_a0.0NHs87_c7757_a5.9Oc_4934_a8.4Wc_1831_b12.4

Wc_5531_a42.6Oc_4153_a46.5Oc_5825_a52.1NHsB9_c12502_2_a63.6

Os87_c1577_a85.7Oc_4851_b95.0Oc_3279_a110.1Wc_5474_a125.0

Oc_3885_b148.9OsA8_c3957_8_a152.1Oc_586_a158.3NHc_2801_a162.6

Os87_c2260_a189.7Oc_5183_a198.1Oc_4843_a208.2

LG 12Oc_2590_a0.0

Wc_5598_a34.4Oc_7063_b35.2Oc_2034_a36.3Oc_5879_a47.1Oc_6261_b51.3

NHsB9_c11476_3_a88.8NHc_4784_a97.7Wc_3780_a104.5Oc_30_d106.7Oc_3780_b114.6Oc_1632_a119.1Oc_346_a126.4Oc_3374_a143.0

LG 13Oc_7240_b0.0Oc_1113_a2.9

Os87_c10557_a51.4Oc_2173c60.2Oc_5905_a71.2NHc_6655_a84.7Wc_1981_a97.0Oc_4536_b99.8Oc_2863_b104.3Oc_1176_a117.6Oc_6254_a121.0Oc_4606_a121.8Oc_81_a124.9NHsA8_c12375_2_a125.3Os87_lrc5487_a127.0Oc_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_a75.9Os87_c10801_a80.3Os87_c4483_a81.2OsA8_c3639_17_a86.8

NHsA8_c14455_2_a110.7NHc_941_a113.4Os87_c12339_a115.0

NHsB9_c10590_2_a144.6

LG 15NHsB9_c11075_2_a0.0

Oc_2627_a34.3Oc_4881_a48.7OsA8_c1060_15_a56.1Oc_6491_a59.3

Wc_5539_a77.1

Oc_183c97.8Wc_5003_a100.6Oc_320_b112.5NHsB9_c12667_2_a114.9

Oc_594_b127.7

OsB9_c9685_3_a155.7Oc_3186_a169.9Oc_205_a173.6

Oc_2065_a195.0

LG 16Oc_5095_b0.0

Oc_5771_a25.7

Oc_2141_a58.1Oc_5707_a64.5

Oc_763_a108.0

Wc_7052_a135.2Oc_4329_a138.1

LG 17NHsB9_c13489_2_a0.0NHsA8_c11104_2_a12.3Ws87_lrc7506_a16.6

NHsA8_c13522_2_a*60.5

Wc_2196_b91.3Oc_2744_a93.2

LG 18Oc_2589_a0.0Oc_1165_ab6.0Oc_5127_a7.6Oc_1165_a9.2Oc_1165_ac10.3NHs87_lrc8239_a25.0

Oc_2547_a54.6

LG 19Oc_4991_a0.0

Oc_2132_a28.2Oc_664_a37.9Oc_5740_a42.6Oc_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)Significance 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 22041 SSRs matched but

monomorphic572 SSRS matched

503 SSRs did not match to the other parent

Parent 2 vs Parent 12027 SSRs matched but

monomorphic573 SSRS matched

515 SSRs did not match to the other parent

Test results of 572 genomic-SSRs primers on Parent 1 and

Parent 292 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

filterchi-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, Ibadan

Male Inflorescenc

e

Female Inflorescenc

e

Monoecious

Fruits


Leaf Shape and Area; SPAD; Stomata Density

Flowering Fruit bearing Viruses Anthracnose


Phenotyping of GBS materials


Phenotyping: ResultsVine 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 portion

Flowering (female)

Fruiting (female)

Correlation

Head 115 51 0.443

Middle

74 31 0.419

Tail 76 31 0.407

Tuber portion

Vine number

Tuber number

Correlation

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 extraction800ul MeOH:H2O (1:1)1hr @ RT800ul 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. bulbeferaOne 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 projectsMAFF: Genotyping parents and mapping population progenies using SSRs and GBS for generating genetic maps and determine associations for traits related to nutrient use efficiencyTraining: 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 24TDr 00/00362 29TDr 95/01932 629TDr 99/02562 23

TDr 89/02157 TDr 95/01932 16

TDr 89/02665

TDr Alumaco 23TDr 00/00362 2TDr 97/00777 16TDr 95/01932 4

TDr 97/00917 TDr 95/01932 37TDa 00/00194 TDa 02/00012 341TDa98/01166 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 projectsDetermination 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

FORM No

TRIAL TYPE

SITE CODE YEAR MONT

H 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

DAYS IN CYCLE

PLANTS / PLOT

PLANTS / HARVESTED PLOT

HARVESTED AREA (M2)

EXPTL ENTRIES/

TRIAL

CHECK

ENTRIES/TR

IAL

YAM SPECI

E

* 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 SPECIE01 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


Fact

or 2

(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_03/00544TDa_07/00003

TDa_07/00026TDa_07/00032

TDa_07/00038

TDa_07/00062

TDa_07/00081

TDa_07/00125TDa_07/00126

TDa_07/00128

TDa_07/00131TDa_07/00133

TDa_07/00141

TDa_07/00146TDa_07/00147

TDa_98/01176

Abuja Ikenne

Ubiaja

AMMI TDA Yield From a RCBD Parents and progenies selection


15 years of breeding data• Parents• Progenies

Genetic Gain










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, GRC2. 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 growth2. Drip irrigation system at SH3. SPAD4. Tablet and Hard copy field book5. In process: Bar code system, Breeding platform

http://www.aliexpress.com/item/Zebra-ZM400-300dpi-Barcode-label-thermal-Printer-machine/546106053.html


USE OF BREEDING MANAGEMENT SYSTEM OF THE INTEGRATED BREEDING PLATFORM.

Data from 2001-2010 in migration process

Use of Yam Ontology


PARTNERSHIPBIOTECHNOLOGY

AND GENETIC IMPROVEMENT

PLANT PROTECTION AND HEALTH

SOCIAL SCIENCES AND

COMMERCIALIZATION

NATURAL RESOURCES

MANAGEMENT

GDT, JIRCAS, IBRC, USDA, GBIFCORNELL UNIV.MISSISIP. UNIV.TOKYO U. AGRICCIRAD-IRDINIVIT-CUBANARSCG-CIAT-CIPNRI-UKMOFA-JapanJHI-UK....

CIRADITCFAOFOOD INDUSTRYMOTI-GHANAM. OF AGRIC.NRI-UKNARESPRIMLAKSYOUTH-IITA.......

NARESPL. PRTC. AGENUC – DAVISNRI-UKUI..........

TOKYO U.AGRICNARESMAFF-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-Montes2. Asrat Amele3. David DeKoeyer4. R. Bhattacharjee5. Saini Himanchu

NRS

6. Edemodu Alex, Res. Assoc.7. Adeosun Tunde, Res. Officer8. Partick Ezighi, Res. Superv.9. Sunday Olajide, Technician10.Kola Odelade, Field assist.11. Nurudin, Pollinator12.Kabiru Ganiyu, Pollinator8. Adewumi Adeyinka , Res. Assoc9. 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 2008TDa 98/01168 Dioscorea alata 2008TDa 98/01176 Dioscorea alata 2008TDa 00/00104 Dioscorea alata 2009TDa 00/00194 Dioscorea alata 2009TDr 89/02602 Dioscorea

rotundata2009

TDr 89/02660 Dioscorea rotundata

2009


2009


2010


2010

TDa 00/00364 Dioscorea alata 2010

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

RegisteredD. rotundataTDr 89/02475TDr 89/02565TDr 89/02665TDr 95/01864TDr 95/18544TDr 95/19156TDr 95/19127TDr 95/19177TDr 96/00629

D. alata TDa 98/01166TDa 98/01176


Production System

Ware Seed, and

Subsistence Yam

EnvironmentDrought

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 9848AVG released variety (TDr 89/02265) 13667 6111 46200 46000 10700 5000 5933 1675 6000 611 11650AVG 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 Yam Production 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 SystemEnvironmentLocalitiesAVG best five improved lines Kg/ha 14628 10970 7090 7997 7700AVG Local and national landraces as Checks Kg/ha 6423 6480 5250 6022 5148AVG 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


2 - 4 months

8-10 months10-20 seed for PT

Speeding up the selection: Reduction of time to develop

From 9 to 4 yrs


NEMATODES

N.U.EANTHRACNOSE

EARLY- LATE MAT

DROUGHT TOLER

Achievement: Selection of Parents II :


D. rotundata: 16 Parents of populations with three years data422 clones in mapping populations including the parents with three years data10 clones under re-sequentiation with more than three years data70 clones actually in crossing blocks, with data of flowering and other traits for more than 5 years 150 elite clones with 8 years data200 clones in Advanced yield trials with three years data100 clones in preliminary yield trials with two years data100 clones in family replicated trials with three years data500 F1C1 Clones with one year data700 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 data2 parents under sequentiation for anthracnose resistance200 clones in three mapping population including the parents with three years data50 clones actually in crossing blocks with data of flowering and other traits for more than 5 years 150 elite clones with 8 years data190 clones in Advanced yield trials with three years data150 clones in preliminary yield trials with two years data110 clones in family replicated trials with three years data500 F1C1 Clones with one year data500 clones from core collection with 5-10 years data.. To be confirmed

POPULATIONS AND ELITE MATERIAL

YIIFSWA: 23 EliteAFRICA YAM: SeveralJIRCAS: 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

FarmersProcessorsHouseholdsTradersIndustry

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-DEFINITIONOF ENVIROMENTS

ACCELERATE ADOPTION

KNOWLEDGE AND USE OF DIVERSITY

SPEEDING UPTHE

SELECTION

IITA’s STRATEGICOBJECTIVE 1

F. SECURITY


SUST. NRM


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 countries2. To develop a n implementation plan for yam breeding for each country3. Genome sequence of TDr and TDa4. GBS for actual parents5. Start a new breeding cycle in 2014 using GCA and SCA6. Determine feasibility of genomic selection7. Develop bi-parental and multi-traits population for TDa, TDr, TDd8. 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 VisionITA 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 Vision1. Increase the germplasm collection, efficient evaluation2. 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 recessive3. Efficient Methods for the improvement of complex traits

4. Use of appropriate Breeding tools to improve Genetic Gain, incorporating farmers criteria from early generations5. 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 annotationTo effectively mine information from the available WGSTo 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 traitsThere 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 populationsThe 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 selectionExperiences 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 Vision14. 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


TEAMBIOTECHNOLOGY

AND GENETIC IMPROVEMENT

PLANT PROTECTION AND HEALTH

SOCIAL SCIENCES AND

COMMERCIALIZATION

NATURAL RESOURCES

MANAGEMENT

M. AbbertonR. BhattacharjeeA. Lopez-MontesG. BadaraN. MaroyaB. AighewiT. GirmaH. Kikuno (2012)A. AmeleD. DeKoeyer

R. MatsumotoK. Yukiko

M. DjanaA. TahirouM. Dixon

L. KumarD. CoyneR. BandiopadhayJ. Augusto

S. HauserJ. Martin

R. Matsumoto


TEAM and CAPACITIESThe 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

Government & Nonprofit

Transcript of Iita yam breeding 2005-2015