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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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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
re
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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