Harnessing the Oil Palm Genome for Breeding - ISOPBisopb.mpob.gov.my/pdfFile/8th/ISOPB 2014 SOUVENIR PROGRAMME and PAPER… · International Colloquium on Harnessing the Oil Palm

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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.

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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

http://www.isopb.org/



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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



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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)



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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)



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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

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



SPEAKERS BIOGRAHPY &

ABSTRACT/PAPER



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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.



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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.



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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)



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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.



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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: [email protected] 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

mailto:[email protected]



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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.



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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.



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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 : [email protected]

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

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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



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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



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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

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LIST OF PARTICIPANTS AS AT 12 JUNE 2014



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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



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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



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



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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



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





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51 Dr ZulkifliYaakub MPOB, 6 PersiaranInstitusi, Bandar BaruBangi, 43000 Kajang, Selangor, Malaysia

52 Dr Zuraidah Yahya



53 Ms ZurainiShaharudin Borneo SamuderaSdnBhd, Jln. KelapaSawit, Off Km 4, JlnTuaran, 88300 Kota Kinabalu, Sabah, Malaysia

Documents

Harnessing the Oil Palm Genome for Breeding - ISOPBisopb.mpob.gov.my/pdfFile/8th/ISOPB 2014 SOUVENIR PROGRAMME and PAPER… · International Colloquium on Harnessing the Oil Palm