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Venue
Bali Nusa Dua
Convention Center
Bali, Indonesia
ISOPB
16 June 2014 (Monday)
International Colloquium on
JointlyOrganized by:
Harnessing the Oil Palm Genome for Breeding
IOPRI
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
1
COLLOQUIUM ORGANIZING COMMITTEE
Advisor:
Chairperson:
Co-Chairperson:
Secretary:
Treasurer:
Members:
Secretariat :
Dr A. Kushairi Din (MPOB, Malaysia) Dr N Rajanaidu (MPOB, Malaysia) Dr Razak Purba (IOPRI, Indonesia) Dr ZulkifliYaakub (MPOB, Malaysia) Mr Mustafa Kamal (Sime Darby, Malaysia) Mr Musa Bilal (Sime Darby, Malaysia) Mr Noh Ahmad (MPOB, Malaysia) Mr Wong Choo Kien (AAR, Malaysia) MsYurnaYenni (IOPRI, Indonesia) Mr Nanang Supena (IOPRI, Indonesia) Ms Azleha Dollah (MPOB, Malaysia) Mr Mohamad Arif (IOPRI, Indonesia)
ISOPB OFFICIAL WEBSITE
http://www.isopb.org
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
2
ISOPB EXECUTIVE COMMITTEE MEMBERS
President :
Vice President :
Secretary :
Treasurer :
Committee Members :
Editor :
Auditors :
Regional Rep. Asia-Pacific :
Africa :
Europe :
Americas :
Dr A. Kushairi Din MPOB, Malaysia Dr N. Rajanaidu MPOB, Malaysia Ms JunaidahJudin PPNJ, Malaysia Mr Musa Bilal Sime Darby, Malaysia Dr Soh Oik Chin The Univ. Of Nottingham Malaysia Campus Ms Norziha Abdullah MPOB, Malaysia Mr Wong ChooKien AAR, Malaysia Mr Mustafa Kamal Mohamed Sime Darby, Malaysia Dr ZulkifliYaakub MPOB, Malaysia Dr Abdul RazakPurba IOPRI, Malaysia Dr Bakoume Claude Sime Darby, Malaysia Dr Tristan Durand-Gasselin PalmElit SAS, France Dr Hernan Mauricio Romero CENIPALMA, Colombia
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
3
Message from the Director of IOPRI
It gives me a great pleasure to write this message to this gathering of scientists in
“International Colloquium on Harnessing the Oil Palm Genome for Breeding". This event is
held in conjunction with the International Oil Palm Conference (IOPC) 2014, on 17 to 19
June 2014. ISOPB and IOPRI have a long history of having our seminars back to back and
this International Colloquium is the 4th collaboration after 1988 in Pematang Siantar, 2003 in
Medan and 2010 in Yogyakarta.
Oil palm breeding contributes in increasing productivity of the industry through delivering
better planting materials over the decades. In the 1960s, with DxD, DxT or TxD planting
materials, Crude Palm Oil (CPO) obtained was only 4.3 tonnes/ha/year, and now in the
2010s, CPO production may reach up to 8.3 tonnes/ha/year.
However, yield increase is not the only breeding goal we must focus on, the industry is
expecting breeders to produce planting materials which are tolerant to diseases, adaptive to
marginal land, low input, as well as able to produce specialty oils. Luckily, genome
information is abundant and more accessible. Genome research provides significant
contributions to accelerate breeding programmes and progress and to further improve oil
palm productivity.
In this International Colloquium, three papers will be presented, and hopefully they will
stimulate productive discussion amongst all of the participants, both the speakers and the
audience.
I wish you a successful deliberation and hope our foreign guests will have an enjoyable stay
in Bali.
Dr. WitjaksonoDarmosarkoro
Director of Indonesian Oil Palm Research Institute (IOPRI)
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
4
Message from MPOB Director General
On behalf of the Malaysian Palm Oil Board, I would like to extent a warm welcome to all participants of the International Colloquium on ‘Harnessing the Oil Palm Genome for Breeding’. The Malaysian Palm Oil Board is pleased to once again jointly organize the ISOPB international colloquium with ISOPB and IOPRI. It cannot be denied that breeding has produced impressive gains in terms of oil yield for the oil palm industry. However, the major impediment in breeding is the long selection cycle of the oil palm, some 10-12 years. Being a tree crop, large tracts of land are required for breeding trials, which incur substantial labor and maintenance costs. The ability to select palms for particular traits early in the breeding cycle, preferably at the nursery stage before field planting, would represent a major step forward in expediting oil palm breeding with reduced cost. This makes oil palm an attractive candidate for marker assisted selection (MAS). Recently, MPOB scientists have made a breakthrough with the decoding of the oil palm genome that has important implications in yield improvement, encouraging sustainable development of the industry. MPOB led the efforts at sequencing both the oil palm species, Elaeis oleifera and E.guineensis, including the pisifera and dura palm fruit forms. The research reported 1.8-gigabase (Gb) of the Elaeis guineensis genome sequence and identified at least 35,000 genes. Another major breakthrough of MPOB oil palm genome programme was the identification of the shell gene for the three different fruit forms of E.guineensis. This gene is of significant importance in commercial seed production and breeding programmes. The shell marker “SureSawit Shell Kit” is ready for commercialization. It is heartening to note that oil palm breeders now are moving forward to apply genomic selection in oil palm. This new form of marker-assisted selection in which genetic markers covering the whole genome are used, will greatly assist in the development of new and improved varieties. The Colloquium provides an avenue to discuss strategies that will help oil palm meet the increasing global demand for food and biofuels while simultaneously preserving the rainforest. I am confident that this Colloquium will serve as a strategic platform for participants to share information and exchange ideas on oil palm breeding. I would like to record my highest appreciation to all participants, chairperson, speakers and all those who contributed to the success of this International Colloquium on ‘Harnessing the Oil Palm Genome for Breeding’.
Datuk Dr. Choo Yuen May
Director General of Malaysian Palm Oil Board (MPOB)
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
5
Message from the President of ISOPB
On behalf of the International Society for Oil Palm Breeders, I would like to welcome all
participants, and also to thank you for taking your time off to join us in this International
Colloquium on Harnessing the Oil Palm Genome for Breeding.
The theme of this colloquium was decided with the intention of taking a ride on MPOB’s
latest achievements which are very much applicable to the breeders. In the last quarter of
2013, MPOB has successfully sequenced and published three Oil Palm Genome
Sequences, i.e., two Elaeis guineensis oil palm genome sequences and one Elaeis oleifera
oil palm genome sequence. The achievement in oil palm genetics does not end by a mere
understanding of the plant’s DNA sequence; this work could best be metaphorically
described as the tip of the iceberg on the knowledge of oil palm genetics. What is even more
important is on how to harness this knowledge for oil palm breeding. I believe, your
presence here today is to seek answers to this question. For today’s colloquium we have
invited eminent speakers to share their thoughts and to provide the answers.
The society has always been keeping abreast on the advancement of oil palm breeding, and
actively disseminates the most current knowledge in oil palm breeding and genetics to its
members. This is done through seminars, workshops, colloquiums, symposia and field trips
at the frequency of about one event per year. These activities will not materialize without the
active participation and contribution of the members. Hence, in 2013, we have honoured
some of our members who have given significant contribution to the Society by awarding
them the Fellowship of ISOPB during a gala dinner in conjunction with the ISOPB organized
International Seminar on Oil Palm Breeding – Yesterday, Today and Tomorrow, the Society
General Meeting and election of new executive committee members and regional
representatives. You could reach for the details in ISOPB website, www.isopb.org
Last but not least, I would like to take this opportunity to thank the commitment of all of you,
distinguished invited speakers, participants and members of the organizing committee, in
making today’s colloquium possible and may you have a successful deliberation and a
fruitful day.
Dr. Ahmad Kushairi Din
President of the International Society for Oil Palm Breeders (ISOPB)
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
INTERNATIONAL COLLOQUIUM ON HARNESSING THE OIL PALM GENOME FOR BREEDING
BALI NUSA DUA CONVENTION CENTRE (BNDCC), ROOM: ULUWATU 1
16 JUNE 2014 (MONDAY)
0700 am
0830 am
0845 am
0900 am
0945 am
1015 am
1100 am
1145 am
1245 pm
1300pm
Registration Welcome remarks (President of ISOPB) Opening remarks (Director of IOPRI) Paper 1: Oil Palm Genome Sequence and Discovery of the Shell
Gene: Application in Breeding Dr. Rajinder Singh, MPOB, Malaysia
Tea& Coffee Break Paper2: Practical Aspects of Genomic Selection in Oil Palm
Mr. David Cros, CIRAD, France Paper 3 : The rolesof IOPRI’s Oil Palm Breeder in the
Development of Genome Programme Dr.Abdul RazakPurba, IOPRI), Indonesia
Panel discussion Closing remarks (Vice President of ISOPB) Lunch
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
SPEAKERS BIOGRAHPY &
ABSTRACT/PAPER
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
7
BIOGRAPHY FOR RAJINDER SINGH, MPOB, MALAYSIA
Rajinder Singh is currently a Principal Research Officer at the Malaysian Palm Oil Board.
Rajinder has been with the Malaysian Palm Oil Board for the last 18 years. He obtained his
PhD in Plant Genetics from University Putra Malaysia (UPM). Rajinder is currently the Head
of Genomics Unit of the Advanced Biotechnology & Breeding Centre, at the Malaysian Palm
Oil Board (MPOB). His research interests include molecular marker development, genetic
mapping, DNA microarray as well as DNA sequencing and analysis. In the course of his
career Rajinder has developed and patented diagnostic DNA markers/genes for oil palm
tissue culture and breeding.
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
8
OIL PALM GENOME SEQUENCE AND DISCOVERY OF THE SHELL GENE:
APPLICATION IN BREEDING
Rajinder Singh1, Eng-Ti Leslie Low1, Meilina Ong-Abdullah1, Leslie Cheng-Li Ooi1, Ngoot-
Chin Ting1, Jayanthi Nagappan1, Rajanaidu Nookiah1, Mohd Din Amiruddin1, Rozana Rosli1,
Mohamad Arif Abdul Manaf1, Kuang-Lim Chan1, Mohd Amin Halim1,
Norazah Azizi1, Nathan Lakey2, Steven W. Smith2, Muhammad A. Budiman2, Michael
Hogan2, Blaire Bacher2, Andrew Van Brunt2, ChunyanWang2, Jared M. Ordway2, Robert A.
Martienssen3&Ravigadevi Sambanthamurthi1
1Malaysian Palm Oil Board, 6, PersiaranInstitusi, Bandar BaruBangi, 43000 Kajang,
Selangor, Malaysia.
2Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA.
3Howard Hughes Medical Institute–Gordon and Betty Moore Foundation, Cold Spring Harbor
Laboratory, Cold Spring Harbor, New York 11724, USA
MPOB initially attempted to unravel the oil palm genespaceby sequencing the
hypomethylated regions of the genome using the GeneThresherTM methylation filtration
technique. Over 400,000 sequences were generated from nine individual palms. Simple
sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were also
mined and used to construct high density genetic maps for oil palm. Expanding on this, the
Malaysian Palm Oil Board (MPOB) and its partners then sequenced the E. guineensis and
E. oleifera genomes at high coverage by a combination of 454/Roche technology and BAC
end sequencing. Scaffolds from the build were successfully aligned to the 16 linkage groups
of the oil palm genetic map, and sequencing of 35 transcriptomes from various tissues
enhanced the annotation of the assembly. Obtaining high quality sequence assembly proved
to be a valuable resource to identify genes linked to important agronomic traits of oil palm. In
this respect, using a combination of genetic mapping, homozygosity mapping by sequencing
and the oil palm whole genome sequence as a reference, the homologue of the MADS box
gene SEEDSTICK was found to be responsible for the three different fruit forms of E.
guineensis. The identification of the gene responsible for the fruit forms paved the way for
the development of the SURESAWITTM SHELL diagnostic assay kit. The kit advances the
application of molecular diagnostic tools in both oil palm breeding and commercial seed
production.
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
9
BIOGRAPHY FOR MR. DAVID CROS, CIRAD, FRANCE
Full Name : Mr David CROS
Designation :
Organization & address : French Agricultural Research Centre for International
Development (CIRAD)
Nationality : French
Country of residence & address:
CIRAD Department: Biological Systems
Research unit: Genetic improvement and adaptation of mediterranean and
tropical plants (AGAP)
Team:Oil palm breeding
Avenue Agropolis
TA A-108 / 01
34398 MONTPELLIER
FRANCE
Academic Qualification :
Master of Tropical Biodiversity Enhancement (University of the French West Indies and Guiana), 2005
Master in Agricultural Science and Engineering (National Polytechnic Institute of Toulouse), 2002
Work Experience :
In a PhD study about genomic selection in oil palm breeding (2011-2014),
Oil palm breeder in Pobè (Bénin) for Cirad from 2006 to 2011,
Cucumber breeder in Almeria (Spain) for EnzaZaden (2005-2006),
Research assistant working on pineapple for Cirad in the French West Indies (2002-2004)
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
10
Achievements/Awards :
CrosD., Sanchez L., Cochard B., Samper P., Denis M., Bouvet J.M., Fernandez J..2014.
Estimation of genealogical coancestry in plant species using a pedigree
reconstruction algorithm and application to an oil palm breeding population,
Theoretical and applied genetics, 127 (4) : 981-994.
Morcillo F., CrosD., Billotte N., NgandoEbongue G.F., Domonhedo H., Pizot M., Cuellar M.
T., Espeout S., Dhouib R., Bourgis F., Claverol S., Tranbarger T.J., Nouy B., Arondel V..
2013. Improving palm oil quality through identification and mapping of the lipase gene
causing oil deterioration, Nature Communications, 4 (2160).
Carré C., Gamboa F., Cros D., Hickey J.M., Gorjanc G., Manfredi E.. 2013. Genetic
prediction of complex traits: Integrating infinitesimal and marked genetic
effects,Genetica, 141 (4-6) : 239-246.
About the organisation:
CIRAD is a French research centre working with developing countries to tackle international
agricultural and development issues.
The AGAP research unit, which was launched on 1st January 2011, is a joint research unit
between Cirad, Inra and Montpellier SupAgro, focusing on the genetic improvement of
tropical and Mediterranean plants. The unit endeavours to create the most suitable planting
material for farming systems involving the main 20 tropical and Mediterranean species. The
AGAP unit has a permanent staff of over 300. It covers three major research topics: diversity
and domestication dynamics, development and adaptation, plant genetics and breeding.
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
11
PRACTICAL ASPECTS OF GENOMIC SELECTION IN OIL PALM (ELAEIS GUINEENSIS)
D. Cros, M. Denis, L. Sánchez, B. Cochard, A. Flori, T. Durand-Gasselin, B. Nouy,
A. Omoré, V. Pomiès, V. Riou, E. Suryana, J.M. Bouvet
D. Cros (), M. Denis, B. Cochard, A. Flori, V. Pomiès, V. Riou, J.M. Bouvet CIRAD, UMR AGAP (Genetic Improvement and Adaptation of Mediterranean and Tropical Plants Research Unit), 34398 Montpellier, France.e-mail: david.cros@cirad.fr L. Sánchez, INRA, UR0588, UAGPF (Forest Tree Improvement, Genetics and Physiology Research Unit), 45075 Orléans, France E. Suryana, P.T. SOCFINDO Medan, Medan 20001, Indonesia
A. Omoré, INRAB, CRAPP, Pobè, Benin
B. Nouy, T. Durand-Gasselin, PalmElit SAS, 34980 MontferriersurLez, France
Genomic selection (GS) is a form of marker assisted selection that improves
breeding schemes in plants and animals. It relies on dense genome wide marker coverage
to produce genomic estimated breeding values (GEBV) from a joint analysis of all markers.
The GS model is calibrated using individuals with known phenotypes and genotypes
(training set) and predicts the GEBV of selection candidates. GS can increase the genetic
gain in plants. In perennial crops, this can be achieved via shortened breeding cycles and
increased selection intensity. In oil palm (Elaeisguineensis) the main challenge is to obtain
sufficient accuracy to calibrate the GS models, despite small populations.
We obtained empirical estimates of GS accuracy in oil palm for eight yield traits using
real data from an on-going breeding program. We used three parental populations (Deli,
Group B, LaMé) involved in conventional reciprocal recurrent selection (RRS) with 93 to 131
individuals,genotyped with 265 SSR. We estimated the within population GS accuracy when
predicting masked estimated breeding values. We used three methods to sample training
sets and the GBLUP statistical method to obtain GEBV. The results showed that in Group B
and La Mé, GS could achieve higher accuracy than the pedigree-based model, indicating
that GS could account for family effects and Mendelian sampling terms. The GS accuracy
ranged from -0.41 to 0.94 and was correlated with the relationship between training and test
sets (amax). Training sets optimized with CDmean gave the highest amax and accuracies,
ranging from 0.49 to 0.94. Finally, Group B and La Mé individuals could be preselected for
progeny tests by applying GS to key yield traits.
However, many aspects related to the potential of GS are difficult to study with real
data. Wong and Bernardo (2008) carried out a simulation study to evaluate over three
generations the potential of GS to increase yield in oil palm. They concluded that GS gave
the highest annual response to selection. In order to extend their promising results, we
simulated two realistic oil palm breeding populations and compared over four generations
the current RRS with reciprocal recurrent genomic selection (RRGS). The aim was to select
the best individuals in the two parental populations to increase hybrid performance on bunch
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
12
production. For RRGS, we applied the GBLUP method with the phenotype of hybrids as
data records to obtain the parental genomic estimated breeding value. We studied the
effects of four parameters on the selection response in hybrids: (1) the molecular data used
to calibrate the GS model: in RRGS_PAR, we only used parental genotypes and in
RRGS_HYB we also used genotypes of hybrid individuals; (2) frequency of calibration of GS
model; (3) number of candidates; (4) number of genotyped hybrids in RRGS_HYB. We
concluded that both RRGS_PAR and RRGS_HYB could lead to a higher selection response
than RRS because they allowed decreasing the generation interval and increasing selection
intensity.
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
13
BIOGRAPHY FOR DR. ABDUL RAZAK PURBA, IOPRI, INDONESIA
Name : Abdul RazakPurba
Place and date of birth : PematangSiantar/13 March 1961
Institution: Indonesian Oil Palm Research Institute
Specialty : Plant Breeder
Office address : Indonesian Oil Palm Research Institute Jl. BrigjendKatamso No. 51, Medan 20158 Telp. : (061) 7862477 Fax. : (061) 7862488
Educations
Degree University Year Specialty
Bachelor InstitutPertanian Bogor (IPB) 1983 Agronomy
Master of Science UniversitasGadjahMada (UGM) 1990 Agronomy/Specialization on Plant Breeding
Doctor EcoleNationaleSupérieureAgronomique de Montpellier (E.N.S.A-M), France
2000 Genetics and Plant Breeding
Professional experience
- now deputy director in Indonesian Oil Palm Research Institute (IOPRI), - almost 30 years in the career as an oil palm breeder at IOPRI, - focus of research is integration of biology molecular technique into the oil palm
conventional breeding programme in IOPRI.
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
14
THE ROLES OF IOPRI’S OIL PALM BREEDER IN THE DEVELOPMENT OF GENOME PROGRAMME
Abdul RazakPurba*, Sri Wening, Hernawan Y. Rahmadi, YurnaYenni
Plant Breeding and Biotechnology Research Group
Indonesian Oil Palm Research Institute Jl. Brigjend. Katamso 51, Medan, Indonesia
*Corresponding author: e-mail : razak.purba@yahoo.fr
Tel : + (62) 61 7862477 Fax : + (62) 61 7862488
ABSTRACT
Genome information is a compulsory data for achievement of oil palm breeding objectives. The knowledge of oil palm genome is currently progressing fast, which widely opens the possibility of DNA technologies application in oil palm breeding activities. Molecular biologists should work hand in hand with oil palm breeders in the development of oil palm genome programme. This paper reviews the roles of oil palm breeder within the collaboration of molecular biologist, breeder and bioinformatician in IOPRI, as a case study, to achieve the successful oil palm genome programme.
Key words: genome, DNA technologies, oil palm breeding INTRODUCTION
There are some limitations faced by oil palm breeding in achievement of its goals. Knowledge of oil palm genome is a mandatory if molecular breeding will be involved as a tool to achieve the breeding’s objectives. This is the reason why the development of oil palm genome information is very important. Currently, there are some oil palm genome programmes which are being carried out by some institutions.
Genomics is developing and progressing fast with some advances already achieved
in some species, as well as in oil palm. Research has being done resulting knowledge of oil palm genetic map, including linkage map and QTL map (Billotte et al., 2005; Montoya et al., 2013). The sequencing work of oil palm genome is also being done with some results already reported (Sambanthamurthi et al., 2002; SimeDarby, 2009; Singh, 2011; Singh, 2013). The information of oil palm genome will guide the direction of oil palm breeding, rather than just by phenotypic information, and it will imply on the usage of DNA technologies in oil palm breeding activities. It is including information of markers linked with some traits, in which some research have been conducted to find markers for some characters, such as: oil palm clone abnormality (Cheah and Wooi, 1993; Jaligot et al., 2002; Jaligot et al., 2000; Kubis et al., 2003; Lei et al., 2006; Ong-Abdullah, 2011), shell-thickness (Singh, 2013) and oil quality(Montoya et al., 2013). Agronomic performances of parental palms could be assessed by best linier unbiased prediction of phenotypic data (Purba et al., 2001; Yenni et al., 2009) and it could also be done by molecular markers, by usage of genomic selection method (Wong and Bernardo, 2008). The information of DNA markers in the genetic map combined with general knowledge of the polymorphism of the markers across the collection of germplasm allows the usage of the markers for genetic diversity analyzes(Cochard et al., 2009; Wening et al., 2012b) and other DNA fingerprinting purposes, for examples: identification of illegitimate crosses or progenies (Faizah et al., 2013; Wening
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
15
et al., 2013a), confirmation of homozygosity of haploids and doubled haploid of oil palm (Dunwell et al., 2010), variability of haploids (Sitorus et al., 2010), homozygosity of commercial material parents and other breeding populations (Wening et al., 2013b; Wening et al., 2012a; Wening et al., 2013c). There are many DNA technology applications in plant breeding programme which raise a new term of plant breeding called plant molecular breeding.
Application of oil palm molecular breeding will depend on the success of
development of oil palm genome information. Molecular biologist will work on the exploration and exploitation of genome resources which will need supports of oil palm breeder. Both of parties will equally act and be responsible in the project, as well as taking advantage of the deliveries of the programme. Actually it is impossible to only review the role of just one party in this programme, as one party will always be dependent to the other party. This paper reviews, in particular, the roles of oil palm breeder in IOPRI (Indonesian Oil Palm Research Institute) as a case of study, which at the same time should review the collaboration of molecular biologist, oil palm breeder as well as bioinformatician in the development of oil palm genome programme.
ROLES OF OIL PALM BREEDER IN THE DEVELOPMENT OF OIL PALM GENOME PROGRAMME
1. To drive the direction of interests and the molecular approaches
Oil palm breeders have objectives of their breeding programme, which in the end,
it will be generated new generations/varieties which have intended characters. Generally, the current primary targeted character is still high yield. The secondary characters are high quality oil, slow height increment, tolerant to abiotic stress, resistant or tolerant to pest and disease, etc. Actually, the targeted character is driven by market demand. The trend of market demand could be changing because of some reasons, and breeders will try to fulfill the demand. This objective will drive the target of genome research. So many information should be exploited in the oil palm genome and so many data will be generated. There will be priority of task to be done, depend on the objective of the breeding programme. If tolerant to a disease is considered to be more valuable than high yield character, so finding markers for disease tolerance will be prioritized to be exploited.
The application of DNA technologies should be accordant to oil palm breeding
programme. This makes targets to oil palm genome programme in term of milestones and time frame of achievements, to fulfill the needs in oil palm breeding programme. There are some molecular approaches which could be used and should be done based on priority in targeted milestones, such as: - Genetic diversity assessment of germplasm collection - Early detection of shell-thickness character, and other important traits - Determination of parental palm’s breeding value by molecular markers and
application of genomic selection - Marker assisted selection in introgressing of one character in a genetic background,
such as in backcrossing or other approaches - Association mapping to select the best palm for good ortet
In IOPRI, biotechnology group is under the same research group, together with
breeding group, named “Plant breeding and biotechnology research group”. It will ensure that the programme of biotechnology research is along the needs in breeding programme and for the ease of coordination. IOPRI has a roadmap of research, in
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
16
which the generations of new varieties are released from the exploitation of germplasm collection. The effort is achieved by help of biotechnology (molecular breeding, tissue culture and genetic engineering) deliveries. There are many objectives which are needed to be gained with limited resources so works in biotechnology researches are prioritized based on available resources to do and economic value of the deliverables. There are routine meetings to discuss the achievements and strategies of research. The decisions taken in biotechnology research are always in agreement with breeder’s opinions.
2. To provide available material or to develop material for molecular research
There are expectations that advantages will be obtained from oil palm genome
project, but, at the same time, it is also expected some information from oil palm breeder to carry out the development of oil palm genome information. As we understand for example, it is needed DNA of oil palm materials to do novel sequencing, genetic mapping, and other genome exploitations. In this matter, it is needed information of oil palm breeder about the information of their breeding population or their germplasm. In the oil palm genome programme, oil palm breeder should be able to tell molecular biologist about what are available or not available in their materials, which could be used or should not be used for the development of oil palm genome information. Sometimes works on the development of genome information needs populations with certain specifications and number of individuals. If the type of crossing and the number of individuals per progeny are already available in the existing breeding population, they can be used for the purpose, but sometimes the populations are not yet available and breeder should prepare the availability of the material needed. These things happen in IOPRI. There is a molecular biology research, such as linkage mapping, which uses current crossings which are already available in the field as trials. But, there are some materials which should be prepared first, since it is needed a certain amount of individuals per progeny or confirmation of characters.
3. To provide phenotypic data of material for molecular research
The quality of phenotypic data in the field is very important, so oil palm breeder
should has a robust system to generate reliable phenotypic data. The system includes: standard operation procedure and control of works from mating design, crossing, in the nursery and in the field, data collection, data documentation and works in laboratories. There should be defined parameters of phenotypic data for the particular populations used for particular research and defined identity of each individual palm or defined unique code. An organized database leads robust documentation and exploitation of the massive phenotypic data.
In IOPRI, we have the oil palm breeding research for development division which
is certified by ISO 90001:2008 and KNAPPP. All of the trials are documented in a manner so that each research can be monitored the progress. There is a database contains the information of all IOPRI’s varieties, crossings, pedigree, phenotypic data (vegetative parameters, phenology, bunch production and oil quality) and genotypic data (SSR profiles). The database can be accessed internally to provide information needed by research. The role of the bioinformatician is crucial as the bridge between phenotypic and genotypic data and to generate output resulted from data analyzes.
4. To work in conjunction with molecular biologist and bioinformatician so that work flow from field to laboratory, or vice versa is smooth
Regular meeting among the breeder, molecular biologist and bioinformatician are
held in IOPRI to discuss the progress of works, maintenance of SOP and plans of
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
17
research. The application of current results of oil palm genome project is also discussed in the meetings.
EXPECTATIONS FOR IMPROVEMENTS
Description above emphasizes the truth that oil palm breeder should work together with molecular biologist and bioinformatician in a genome programme. In IOPRI, the three expertise are sometimes blended with some facts, such as: molecular biologists should do field breeder tasks, bioinformatician starts his career as oil palm breeder, and field breeder should make decisions together with molecular biologist about research which is being carried out. It is also understood about awareness for breeders to develop their molecular knowledge and for molecular biologist to develop their field management knowledge. However, the development of each expertise should be emphasized since specialization is not less important. The general ability is needed for understanding of the global things to do a research. Moreover, breeding and biotechnology are based on the same subject which is genetics. Specialization is required to handle the detail things in a research.
REFERENCES Billotte N., Marseillac N., Risterucci A.M., Adon B., Brottier P., Baurens F.C., Singh R.,
Herrán A., Asmady H., Billot C., Amblard P., Durrand-Gasselin T., Courtois B., Asmono D., Cheah S.C., Rohde W., Ritter E., Charrier A. (2005) Microsatellite-based high density linkage map in oil palm (Elaeis guineensis Jacq.). Theoretical and Applied Genetics 110:754-765.
Cheah S.C., Wooi K.C. (1993) Application of molecular marker techniques in oil palm tissue
culture, International Symposium on Recent Developments in Oil Palm Tissue Culture and Biotechnology, Kuala Lumpur. pp. 163-170.
Cochard B., Adon B., Rekima S., Billotte N., de Chenon R.D., Koutou A., Nouy B., Omoré A.,
Purba A.R., Glazsmann J.-C., Noyer J.-L. (2009) Geographic and genetic structure of African oil palm diversity suggests new approaches to breeding Tree Genetics & Genomes 5:493-504.
Dunwell J.M., Wilkinson M.J., Nelson S., Wening S., Sitorus A.C., Mienanti D., Alfiko Y.,
Croxford A.E., Ford C.S., Forster B.P., Caligari P.D.S. (2010) Production of haploids and doubled haploids in oil palm. BMC Plant Biology 10:218.
Faizah R., Wening S., Rahmadi H.Y., Yenni Y., Purba A.R. (2013) Analisa legitimasi projeni
kelapa sawit (Elaeis guineensis Jacq.) menggunakan marka Simple Sequence Repeat (SSR), Konferensi Pengembangan Industri Hilir Kelapa Sawit (POIDeC 2013), Jakarta.
Jaligot E., Beulé T., Rival A. (2002) Methylation-sensititve RFLPs: characterisation of two oil
palm markers showing somaclonal variation-associated polymorphism. Theoretical and Applied Genetics 104:1263-1269.
Jaligot E., Rival A., Beule T., Dussert S., Verdeil J.L. (2000) Somaclonal variation in oil palm
(Elaeis guineensis Jacq.): the DNA methylation hypothesis. Plant Cell Reports 19:684-690.
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Organized by ISOPB, MPOB and IOPRI.
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Kubis S.E., Castilho A.M.M.F., Vershinin A.V., Seymour J., Heslop-Harrison P. (2003) Retroelements, transposons and methylation status in the genome of oil palm (Elaeis guineensis) and the relationship to somaclonal variation. Plant Molecular Biology Reporter 52:69-79.
Lei C.P., Jiun K.S., Choo C.S., Singh R. (2006) Analysis of tissue culture-derived
regenerants using methylation sensitive AFLP. Asia Pacifc Journal of Molecular Biology and Biotechnology 14:47-55.
Montoya C., Lopes R., Flori A., Cros D., Cuellar T., Summo M., Espeout S., Rivallan R.,
Risterucci A.-M., Bittencourt D., Zambrano J.R., Alarcón G.W.H., Villeneuve P., Pina M., Nouy B., Amblard P., Ritter E., Leroy T., Billotte N. (2013) Quantitative trait loci (QTLs) analysis of palm oil fatty acid composition in an interspecific pseudo-backcross from Elaeis oleifera (H.B.K.) Cortés and oil palm (Elaeis guineensis Jacq.). Tree Genetics & Genomes 9:1207–1225.
Ong-Abdullah M. (2011) Moving above and beyond the oil palm genome, PIPOC, MPOB,
Kuala Lumpur. Purba A.R., Flori A., Baudouin L., Hamon S. (2001) Prediction of oil palm (Elaeis guineensis,
Jacq.) agronomic performances using the best linear unbiased predictor (BLUP). Theoretical and Applied Genetics 102:787-792.
Sambanthamurthi R., Abdullah S.N.A., Kadir A.P.G. (2002) Genetic manipulation of the oil
palm - challenges and prospects. The Planter 78:547-562. SimeDarby. (2009) Sime Darby makes important discovery in oil palm genome,
http://www.simedarby.com/. Singh R. (2011) Physical map-assisted improvement of the oil palm genome assembly to
enhance productivity, PIPOC, MPOB, Kuala Lumpur. Singh R. (2013) Oil Palm Genome Programme - An Update MPOB Oil Palm Genome
Programme, PIPOC, MPOB, Kuala Lumpur. Sitorus A.C., Alfiko A., Nasution O., Mienanti D., Rusfiandi H., Iswandar H.E., Ananda W.U.,
Wening S., Forster B.P., Nelson S., P.D.S. C. (2010) The production, doubling and genetics of oil palm haploids, International Oil Palm Conference, Yogyakarta.
Wening S., Faizah R., Yenni Y., Purba A.R. (2013a) Aplikasi sidik jari DNA dalam
manajemen plasma nutfah kelapa sawit, Pertemuan Teknis Kelapa Sawit, Pusat Penelitian Kelapa Sawit, Jakarta.
Wening S., Faizah R., Rahmadi H.Y., Yenni Y., Purba A.R. (2013b) Identifikasi kandidat
individu kelapa sawit dengan tingkat homozigositas tinggi melalui analisis sidik jari DNA. Jurnal Penelitian Kelapa Sawit 21:56-63.
Wening S., Fillianti H., Prasetyo J.H.H., Forster B.P., Nelson S.P.C., Caligari P.D.S. (2012a)
Homozygosity of parental palms used in Single Seed Descent programmes. Oil Palm Bulletin 65:1-5.
Wening S., Wilkinson M.J., Fillianti H., Djuhjana J., Forster B.P., Nelson S.P.C., Caligari
P.D.S. (2013c) Genetic diversity of commercial oil palm seed production parents. Oil Palm Bulletin 67:7-10.
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
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Wening S., Croxford A.E., Ford C.S., Thomas W.T.B., Forster B.P., Okyere-Boateng G.,
Nelson S.P.C., Caligari P.D.S., Wilkinson M.J. (2012b) Ranking the value of germplasm: new oil palm (Elaeis guineensis) breeding stocks as a case study. Annals of Applied Biology 160:145–156. DOI: 10.1111/j.1744-7348.2011.00527.x.
Wong C.K., Bernardo R. (2008) Genomewide selection in oil palm: increasing selection gain
per unit time and cost with small populations. Theoretical and Applied Genetics 116:815-824.
Yenni Y., Nasrullah, Purba A.R. (2009) Prediction of Genetic Value for Oil Performance
Using BLUP, International Seminar on Plant Breeding, Kuala Lumpur.
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
LIST OF PARTICIPANTS AS AT 12 JUNE 2014
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
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LIST OF PARTICIPANTS:
NO SAL NAME ORGANISATION & ADDRESS
1 Dr Ahmad Kushairi Din MPOB, 6 PersiaranInstitusi, Bandar BaruBangi, 43000 Kajang, Selangor, Malaysia
2 Mr Anek Limsrivilai Golden Tenera Limited Partnership, 12/9 Naplubpla Rd., Krabiyai, Muang, Krabi, 8100 Thailand
3 Ms Aurelie Grignard Socfin Research, Rue de Romont 24, 1700 Friboourg Switzerland
4 Ms Baitha Santika PT Bina SawitMakmur, Sampoerna Strategic Square, north tower, 28th floor, Jl. Jend. Sudirmankav. 45 Jakarta-Indonesia 12930
5 Mr David Cros CIRAD, UMR AGAP, 34398 Montpellier, France
6 Dr Dwi Asmono PT Bina SawitMakmur, Sampoerna Strategic Square, north tower, 28th floor, Jl. Jend. Sudirmankav. 45 Jakarta-Indonesia 12930
7 Mr Emmanuelle Lamade CIRAD, France
8 Mr Fahmi Wendra PT Bina SawitMakmur, Sampoerna Strategic Square, north tower, 28th floor, Jl. Jend. Sudirmankav. 45 Jakarta-Indonesia 12930
9 Ms Farawahida Mohamad Darus
MPOB, 6 PersiaranInstitusi, Bandar BaruBangi,
43000 Kajang, Selangor, Malaysia
10 Ms Grignard SOCFIN Research, Rue de Romont 24, 1700 Friboourg Switzerland
11 Mr Hairinsyah PT SMART, Plaza Tower 11, 16 th Floor, Jln M. H. Thamrin no. 51, Jakarta 10350, Indonesia
12 Mr Indra Shahputra PT Socfin Indonesia, Jl. KL YosSudarso. No. 106 Medan 20115 , North Sumatera-Indonesia
13 Mr Ivan Mauricio Ayala Diaz Cenipalma, Colombia
14 Ms Jayne Josie James Borneo SamuderaSdnBhd, Jln. KelapaSawit, Off Km 4, JlnTuaran, 88300 Kota Kinabalu, Sabah, Malaysia
15 Mr Joe Pang Thau Sin TSH Biotech SdnBhd,, Bangunan TSH, TB 9, KM 7, Apas Road, 91000, Tawau, Sabah, Malaysia
16 Ms Junaidah Judin Johor Plant Tech Sdn Bhd, Lot 9092, Pusat Pertanian Ayer Hitam, Batu 1, Jalan Ayer Hitam, 86100 Kluang, Johor, Malaysia
17 Dr Kukuh Setiawan Asian Agri, Jl M.T. Haryono No. A1, Uniplaza Building, East Tower 6th floor, Indonesia
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
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NO SAL NAME ORGANISATION & ADDRESS
18 Mr Lalu Firman Budiman PT Astra Agro Lestari Tbk Jln Puloayang Raya blok OR 1, Kawasan Industri Pulogadong, Jakarta 13930, Indonesia
19 Dr Lim Loon Lui IOI Palm Biotech SdnBhd, Level 8, Two IOI Square, IOI Resort, 62502 Putrajaya, Malaysia
20 Mr Mohd Isa Zainol Abidin EPA MagamentSdnBhd,UluTiram Estate, K. B. 705, 80990 Johor Bahru, Johor, Malaysia
21 Dr Mukesh Sharma PT. Tunggal Yunus Estate, Indonesia
22 Mr Nanang Supena IOPRI, Jl. Katamso No. 51, Medan 20158, Indonesia
23 Mr Nicolas Turnbull PalmElit SAS, 2214 BD de la Lironde, ParcAgropolis Bat 14, 34980 Montferriersurlez, France
24 Mr Noh Ahmad MPOB, 6 PersiaranInstitusi, Bandar BaruBangi, 43000 Kajang, Selangor, Malaysia
25 Dr Norbert B illotte CIRAD Research, CIRAD-UMR AGP, Avenue Agropolis, 34338 Montpellier, Cedex 5, France
26 Ms Nordiana Abd Aziz
MPOB, 6 PersiaranInstitusi, Bandar BaruBangi,
43000 Kajang, Selangor, Malaysia
27 Dr Norman Hj Kamaruddin MPOB, 6 PersiaranInstitusi, Bandar BaruBangi, 43000 Kajang, Selangor, Malaysia
28 Ms Patcharin Tanya Golden Tenera Limited Partnership, 12/9 Naplubpla Rd., Krabiyai, Muang, Krabi, 8100 Thailand
29 Mr Peerasak Srinives Golden Tenera Limited Partnership, 12/9 Naplubpla Rd., Krabiyai, Muang, Krabi, 8100 Thailand
30 Dr Portjamarn Suraninpong School of Agricultural Technology Walailak University, 222 Thaiburi, Thasala, Nakhon Si Thammarat, 80160 Thailand
31 Mr Rahmat Basuki PT Agro Indomas, Central Kalimantan, c/o Manara Global Lt. 16, JlSubrotokav. 27, Jakarta, Indonesia
32 Dr Rajanaidu, N MPOB, 6 PersiaranInstitusi, Bandar BaruBangi, 43000 Kajang, Selangor, Malaysia
33 Dr Rajinder Singh MPOB, 6 PersiaranInstitusi, Bandar BaruBangi, 43000 Kajang, Selangor, Malaysia
34 Dr Razak Purba IOPRI, Jl. Katamso No. 51, Medan 20158, Indonesia
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
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NO SAL NAME ORGANISATION & ADDRESS
35 Ms Reni Surbawati Kusumaningtyas PT SMART, Plaza Tower 11, 16 th Floor, Jln M. H. Thamrin no. 51, Jakarta 10350, Indonesia
36 Mr Rizki Akbar Asian Agri, Jl M.T. Haryono No. A1, Uniplaza Building, East Tower 6th floor, Indonesia
37 Ms Seng Tzer Ying FELDA Agricultural Services SdnBhd Tingkat 7, BalaiFelda, Jln. Gurney Satu 54000 Kuala Lumpur
38 Ms Siti Hawa Mohamed Saad FELDA Agricultural Services SdnBhd Tingkat 7, BalaiFelda, Jln. Gurney Satu 54000 Kuala Lumpur, Malaysia
39 Mr Tony Liwang PT SMART, Plaza Tower 11, 16 th Floor, Jln M. H. Thamrin no. 51, Jakarta 10350, Indonesia
40 Dr Tristan Durand-Gasselin PalmElit SAS, 2214 BD de la Lironde, ParcAgropolis Bat 14, 34980 Montferriersurlez, France
41 Mr Veriappan Pangiansarom PT Agro Indomas, Central Kalimantan, c/o Manara Global Lt. 16, JlSubrotokav. 27, Jakarta, Indonesia
42 Mr Wahid Omar
MPOB, 6 PersiaranInstitusi, Bandar BaruBangi,
43000 Kajang, Selangor, Malaysia
43 Dr Xiaohong Hou USA
44 Mr. Yogo A Nugroho PT SMART, Plaza Tower 11, 16 th Floor, Jln M. H. Thamrin no. 51, Jakarta 10350, Indonesia
45 Dr Yohannes Samosir PT Bakrie Sumatera Plantations. Tbk Bakrie Tower lt. 18, Komp. Rasuna Epicentrum, Jl HR Rasuna Said, Jakarta Selatan, Indonesia
46 Mr Yong Yit Yuan PT SMART, Plaza Tower 11, 16 th Floor, Jln M. H. Thamrin no. 51, Jakarta 10350, Indonesia
47 Mr YopyDedywiryanto PT SMART, Plaza Tower 11, 16 th Floor, Jln M. H. Thamrin no. 51, Jakarta 10350, Indonesia
48 Ms YurnaYenni IOPRI, Jl. Katamso No. 51, Medan 20158, Indonesia
49 Mr ZulhermanaSembiring PT BinaSawitMakmur, Sampoerna Strategic Square, north tower, 28th floor, Jl. Jend. Sudirmankav. 45 Jakarta-Indonesia 12930
50 Dr Zulkifli Hashim
MPOB, 6 PersiaranInstitusi, Bandar BaruBangi,
43000 Kajang, Selangor, Malaysia
International Colloquium on Harnessing the Oil Palm Genome for Breeding. 16 June 2014, Bali, Indonesia.
Organized by ISOPB, MPOB and IOPRI.
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NO SAL NAME ORGANISATION & ADDRESS
51 Dr ZulkifliYaakub MPOB, 6 PersiaranInstitusi, Bandar BaruBangi, 43000 Kajang, Selangor, Malaysia
52 Dr Zuraidah Yahya
MPOB, 6 PersiaranInstitusi, Bandar BaruBangi,
43000 Kajang, Selangor, Malaysia
53 Ms ZurainiShaharudin Borneo SamuderaSdnBhd, Jln. KelapaSawit, Off Km 4, JlnTuaran, 88300 Kota Kinabalu, Sabah, Malaysia
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