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IMPORTANCE OF MPOB OIL PALM GENEBANK FOR GENOME RESEARCH

IMPORTANCE OF MPOB OIL PALM GENEBANK FOR GENOME RESEARCH

RAJANAIDU, N., MOHD DIN, A., KUSHAIRI, A. and MAIZURA, I.RAJANAIDU, N., MOHD DIN, A., KUSHAIRI, A. and MAIZURA, I.

MALAYSIAN PALM OIL BOARD

(MPOB)

MALAYSIAN PALM OIL BOARD

(MPOB)

INTRODUCTIONINTRODUCTION

• Irish potato famine (1846)

∗ 2 clones from South America

• 1970s, 50% of corn crop in USA, wiped by

Helminthosporium maydis

∗ single source of cytoplasmic male

sterility factors

• Irish potato famine (1846)

∗ 2 clones from South America

• 1970s, 50% of corn crop in USA, wiped by

Helminthosporium maydis

∗ single source of cytoplasmic male

sterility factors

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OIL PALM GENETIC BASEOIL PALM GENETIC BASE

• 4 Bogor Palms (1848)• 4 Bogor Palms (1848)

Deli duraDeli dura

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Limited Sources of PisiferasLimited Sources of Pisiferas

Major Pisiferas

Group I:Group I:

�� AvrosAvros; SP540T; SP540T

Group II:Group II:

�� MarihatMarihat H5 and EX5 (H5 and EX5 (YangambiYangambi))

�� YangambiYangambi 718718

�� La Me (L2T, L5T, L10T)La Me (L2T, L5T, L10T)

�� CalabarCalabar

�� EKonaEKona

Group III:Group III:

�� URTURTGroup IV:Group IV:

�� African African pisiferapisifera

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SP540SP540

• Elaeis guineensis

West Africa

• Elaeis oleifera

Central – South America

• E.g x E.o hybrids and back-crosses

are increasingly important – oil

quality & disease resistance

• Elaeis guineensis

West Africa

• Elaeis oleifera

Central – South America

• E.g x E.o hybrids and back-crosses

are increasingly important – oil

quality & disease resistance

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Consequence of narrow base:Consequence of narrow base:

• Slow selection progress

• Vulnerable to pests and diseases

• Slow selection progress

• Vulnerable to pests and diseases

MPOB GenebankMPOB Genebank

MPOB / Private Sector CollaborationMPOB / Private Sector Collaboration

• Utilization

• Progeny testing

• Working collection

• Utilization

• Progeny testing

• Working collection

• Identify Priorities (MPOB-Industry Committee)

• Funding

• Identify Priorities (MPOB-Industry Committee)

• Funding

• Collection

• Evaluation / documentation / selection

• Conservation of base collection

• Collection

• Evaluation / documentation / selection

• Conservation of base collection

PRIVATESECTOR

MPOB PUBLIC

SECTOR

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Genetic resources programmeinvolves four major steps

Collection (sampling)

Evaluation

Utilization

Conservation

Genetic resources programmeinvolves four major steps

Collection (sampling)

Evaluation

Utilization

Conservation

Activities of MPOB Oil Palm Genebank:Activities of MPOB Oil Palm Genebank:

• Collection - centres of diversity

• Establishment, evaluation and selection of

elite material

• Progeny testing of elite material

• Distribution of elite material to the industry

• Screening collections (molecular,

biochemical, quantitative) for genetic

variability.

• Collection - centres of diversity

• Establishment, evaluation and selection of

elite material

• Progeny testing of elite material

• Distribution of elite material to the industry

• Screening collections (molecular,

biochemical, quantitative) for genetic

variability.

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Collections and establishmentCollections and establishment

• Inspiration from N.I. Vavilov

• Concept of ‘Geographic Centres of Origin’

• Inspiration from N.I. Vavilov

• Concept of ‘Geographic Centres of Origin’

Collection

&

Sampling Strategy

Collection

&

Sampling Strategy

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Germplasm CollectionsGermplasm Collections

Elaeis guineensisElaeis guineensisNigeria

AngolaZaireCameroon

Guinea

Sierra Leone

Senegal

Gambia

MadagascarGhana

Africa

Tanzania

Honduras Nicaragua

Costa Rica

Panama

Colombia

Surinam

Brazil

Germplasm CollectionsGermplasm Collections

Elaeis oleiferaElaeis oleifera

CentralCentralCentralCentral----South AmericaSouth AmericaSouth AmericaSouth AmericaEcuador

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COLLECTION METHODCOLLECTION METHOD

• No. of explorations in Africa and South America

• Carried out with the cooperation of host countries

• Collected materials shared equally

• Cost borne by MPOB; partly IBPGR

• Oil Palm Descriptors - record information

• No. of explorations in Africa and South America

• Carried out with the cooperation of host countries

• Collected materials shared equally

• Cost borne by MPOB; partly IBPGR

• Oil Palm Descriptors - record information

SAMPLINGSAMPLING

• Sampling method devised using rainfall,

soil, density of palm groves;

• 5-10 palms per site (population) sampled;

• Number of sites visited in a country

depends on density of palm groves;

• A bunch harvested from each sampled

palm;

• Seedlings derived from a bunch are

considered as an ‘open-pollinated’ family.

• Sampling method devised using rainfall,

soil, density of palm groves;

• 5-10 palms per site (population) sampled;

• Number of sites visited in a country

depends on density of palm groves;

• A bunch harvested from each sampled

palm;

• Seedlings derived from a bunch are

considered as an ‘open-pollinated’ family.

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RECENT COLLECTIONSRECENT COLLECTIONS

Elaeis guineensisElaeis guineensis

Country Year No. of AccessionsNigeria 1973 919Cameroons 1984 95Zaire 1984 369Tanzania 1986 60Madagascar 1986 17Angola 1991 54Senegal 1993 104Gambia 1993 45Sierra Leone 1994 56Guinea 1994 61Ghana 1996 58Elaeis OleiferaHonduras 1982 14Nicaragua 1982 18Costa Rica 1982 61Panama 1982 27Colombia 1982 41Suriname 1982 6Ecuador 2004/2006 16

Country Year No. of AccessionsNigeria 1973 919Cameroons 1984 95Zaire 1984 369Tanzania 1986 60Madagascar 1986 17Angola 1991 54Senegal 1993 104Gambia 1993 45Sierra Leone 1994 56Guinea 1994 61Ghana 1996 58Elaeis OleiferaHonduras 1982 14Nicaragua 1982 18Costa Rica 1982 61Panama 1982 27Colombia 1982 41Suriname 1982 6Ecuador 2004/2006 16

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12

13

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Measurements of fruit dimensions Weighing of 10 fruits Weighing of 10 nuts

Washing seeds with bleaching solution Air-drying of seeds Seeds packed in cloth bags

Seed ProcessingSeed Processing

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Taisha

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GERMPLASM COLLECTION

Jessenia, Oenocarpus, Bactris, Euterpe, Babasu

Country Year No. of CollectionAccessions

Peru 1991 50 Rajaniadu

Colombia 1989 182 Rajanaidu

Mexico 1995 20 Rajanaidu

GERMPLASM COLLECTION

Jessenia, Oenocarpus, Bactris, Euterpe, Babasu

Country Year No. of CollectionAccessions

Peru 1991 50 Rajaniadu

Colombia 1989 182 Rajanaidu

Mexico 1995 20 Rajanaidu

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Bactris PlantationsBactris Plantations

Bactris Palm HeartBactris Palm Heart

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Evaluation and ConservationEvaluation and Conservation

• 100,000 accessions individually

phenotyped for >40 traits

• Yield, BNo, Bunch Weight, ABWT

• Bunch analysis (O/B, K/B, M/F)

• Vegetative (FP, RL, Ht, Harvest Index)

• FAC (18:1, 18:2, I.V.)

• Oil yield/palm/yr

• Carotene, Vitamin E

• Molecular traits

• 100,000 accessions individually

phenotyped for >40 traits

• Yield, BNo, Bunch Weight, ABWT

• Bunch analysis (O/B, K/B, M/F)

• Vegetative (FP, RL, Ht, Harvest Index)

• FAC (18:1, 18:2, I.V.)

• Oil yield/palm/yr

• Carotene, Vitamin E

• Molecular traits

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Application of Molecular StudiesApplication of Molecular Studies

• Genetic structure of oil palm population

∗ RAPD

∗ RFLP

∗ AFLP

∗ SSR

• Genetic structure of oil palm population

∗ RAPD

∗ RFLP

∗ AFLP

∗ SSR

Genetic Structure of Oil Palm Populations

(Kularante, 2000)

Hsp = Total genetic diversity

Hpop = Genetic diversity within populations

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UPGMA analysis of simple maching similarities (AFLP)

(Kularatne, 2000)

FAC on 248 RFLP Markers (E. Barcellos, 1997)

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Polymorphism and AllelesPolymorphism and Alleles

Rare AllelesRare Alleles

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Genetic finger-printingGenetic finger-printing

• Oil palm families

• DNA samples being collected from all

palms involved in crossing programme

(breeding population and wild)

• DNA finger printing of all original palms

involved in crossing (e.g. Calabar 32.3005,

Ekona 2/2311, E206, Yangambi 718, L2T,

L5T, L10T, DA115D, etc)

• Oil palm families

• DNA samples being collected from all

palms involved in crossing programme

(breeding population and wild)

• DNA finger printing of all original palms

involved in crossing (e.g. Calabar 32.3005,

Ekona 2/2311, E206, Yangambi 718, L2T,

L5T, L10T, DA115D, etc)

Mayes et al., 2000Mayes et al., 2000

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Linkage and QTL studiesLinkage and QTL studies

• Nigerian T128 self (shell, virescens)

• Colombian Oleifera x T128 (Oil

quality)

• Nigerian T128 self (shell, virescens)

• Colombian Oleifera x T128 (Oil

quality)

Mapping PopulationMapping Population

Fatty acid composition 2118

Oleifera X

Guineensis, T128 (O

X G)

Shell gene1

Fruit color1

136Nigerian tenera

(T128) self

TRAITSNO. OF

PALMS

CROSS

1: Monogenic trait 2: Quantitative trait

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APPLICATION OF GENETIC MAP FOR OIL PALM

BREEDING (MONOGENETIC TRAITS)

APPLICATION OF GENETIC MAP FOR OIL PALM

BREEDING (MONOGENETIC TRAITS)EAAG/MCAC-990.0MT87a5.3G3712.7CIR4616.1EACA/MCTG-17016.7EACA/MCTG-15018.3

G24621.1EAGC/MCTC>330D24.7SFB3128.3EACA/MCAG-12537.4EACT/MCAT>330B37.6EACA/MCAG-12438.3EAAG/MCAT-14841.7CNH0887-164/15942.4EAAG/MCAG-25244.2EACC/MCAT-16045.9EACC/MCAT-16546.7SNPM00012 SNPM0001351.0VIR54.9MET16-ssr58.6KT360.0MET1661.0EAGC/MCAA-18065.3EACC/MCAT-13065.5G22868.3EAAC/MCAG>330A68.4EAAC/MCAG-12575.3EAAC/MCTT>330C82.1SNPM0006682.9EAAG/MCTG>33087.8EGM388.3G22489.7EAAG/MCTA-18090.7EAAG/MCTA-17991.6EAGC/MCAC-9795.5EAAG/MCTC-17598.2EACT/MCAA-118100.1EAAG/MCAC>330H100.9EACT/MCTA-252101.8EAAG/MCTG-225104.0EACC/MCAG-148104.9EACG/MCAT-85106.8EAGG/MCAA-194109.3CB116A110.3EAAC/MCTG-135111.3EACC/MCAA-148117.9P4O17b>330a119.3EAAC/MCTT-230123.4P4O13a-205128.7EACG/MCTT-165131.4EACT/MCTA>330A134.4KD42137.5EACT/MCTT-165144.1

UBC825/5350.0SFB83s3.7SH10.4EAGC/MCTT-25019.4EAAC/MCTC-20024.1P1T12b-20034.5P4T12b-13538.5KT642.6EAAC/MCTT-12846.2EACT/MCTA-29448.3EAAC/MCAA>330B50.0EAGG/MCAA-12851.9EAAG/MCTA>330B53.2EAAC/MCAT-18553.7EACT/MCAA-20454.6EACA/MCAA-11765.8EAAG/MCAC>330D69.2SFB9873.1EAAC/MCTT-21283.1EAAG/MCTG-16586.7TACT/HCAA-12189.1EACG/MCTT-19093.1EAGC/MCTT>330B94.7EAAG/MCTA-13197.5EAAC/MCAC-142102.4SFB95102.8G152104.1MET41106.2EAAG/MCTA-120106.9EAP3339-173108.0EACT/MCAC-120109.3MET4110.1EAGG/MCTC>330E111.7SFB82113.2SFB56II SFB56I114.5EAAC/MCTA-258117.0EACG/MCTA-182120.8EACT/MCAC-235121.5SNPM00059125.5EAGC/MCTC>330E130.4EACA/MCTG-222132.6EAGG/MCAG>330133.6EACA/MCAG-218137.1EACG/MCAT-260143.1EACG/MCAT-270144.9EAGG/MCAA-300148.1MET25c148.5MET25b150.6EAGG/MCTC>330D156.3EAGG/MCTC>330A158.6EAGG/MCAT-225164.1EACA/MCTA-115174.8

Fruit Color(Vir)

Shell Gene (Sh)

Software:

JoinMap

DURA

TENERA

PISIFERA

QTLs ASSOCIATED WITH FAC IN OxGQTLs ASSOCIATED WITH FAC IN OxG

IV C14:0 C16:0 C18:0 C18:1

EAAG/MCTG>330a0.0

EAAC/MCAT-28516.3

EACA/MCAT-15625.8

SFB4137.7TACG/HCTA-18544.4EACA/MCTC-28549.6EACT/MCAA>330b57.6EACA/MCAA>330a64.6EACC/MCAT-24968.4EACA/MCAT-112**77.7EAAG/MCAG-150**78.6EACA/MCAG-168**85.6EAGC/MCAG-165**90.0TACG/HCAA-250***92.3CIR18II****95.1P1AO-310****96.2CNH1537-140****104.5EACC/MCAG>330a**113.9CIR8-212**114.8CB75A125.4

EAGG/MCAT-198*137.4

IV C14:0

C16

:0

C1

8:0

C18:1

1

RD560.0P4T8I P4T8II1.9EAAG/MCAT-221*7.7

EACA/MCAA-330*19.0EACA/MCAG-103**20.8TACC/HCAG-148*26.1

C14

:0

C1

6:1

C18

:0

C18

:1

15

0

2

4

6

8

10

12

14

0 1.9 1.9 6.9 7.7 12.7 17.7 19 20.8 25.8 26.1

Group 15

LO

D s

co

re

Map cM

P<0.05

012345

6789

10

0 1525 .8

37 .749 .4

57 .668 .4

78 .6 9096 .2

109.5119.8

130.4

LO

D s

co

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Group 1

P<0.05

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• Identification

of tissue culture

clones

• Detection of

contaminants

among plants

derived from

� tissue culture

� seeds

DNA FINGER PRINTINGDNA FINGER PRINTING

• DUS-OP Committee

• Guidelines for registering new plant varieties

( distinct, uniform, stable)

• Gross morphology and chemical profiles

• Molecular markers for confirmation and in case of

disputes

PLANT VARIETY ACTPLANT VARIETY ACT

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Verify purity of crossesVerify purity of crosses

• Contamination?

• e.g. T128 self data

• Monitor quality of crosses

before field planting

• Contamination?

• e.g. T128 self data

• Monitor quality of crosses

before field planting

Oil Palm Genome SequencingOil Palm Genome Sequencing

• Deli dura

• Pisifera

• E. oleifera

• Deli dura

• Pisifera

• E. oleifera

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Diversity PanelDiversity Panel

• DNA collected from a cross-section

of palms in the genebank with

various phenotypic attributes to

screen with oil palm sequence data

• DNA collected from a cross-section

of palms in the genebank with

various phenotypic attributes to

screen with oil palm sequence data

CONCLUSIONCONCLUSION

• Genebanks are important source

for molecular studies and breeding

• Integration phenotypic data with

DNA information

• Accelerate the breeding

programme of oil palm which has

long breeding cycle

• Genebanks are important source

for molecular studies and breeding

• Integration phenotypic data with

DNA information

• Accelerate the breeding

programme of oil palm which has

long breeding cycle

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