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Archives
April 1-30, 2003
PCA collaborates with international
institutions to unravel coconut genome
 An
international project on coconut and oil palm biotechnology
is being funded since 2001 by the European Commission
(EC) under its program on International Cooperation
with Developing Countries (INCO-DC). It is jointly carried
out by research laboratories in seven countries, namely,
Germany: MPIZ; Spain: NEIKER; France: CIRAD; Philippines:
PCA-ARC; Indonesia: IOPRI; Malaysia: MPOB; and Indonesia:
SOCFINDO; and three subcontractors, namely, Tanzania:
MARI; Mexico: CICY; and Ivory Coast: CNRA.
The project has five components: 1) construction
of high-density (HD) DNA marker maps on coconut and
oil palm, and QTL analyses on characters of economic
interest; 2) physical mapping; 3) synteny studies; 4)
establishment of field trial systems consisting of several
populations to be used for future marker-assisted breeding;
and 5) bioinformatics and biotechnology transfer through
internet and international workshop/laboratory courses.
For coconut, the first linkage maps to
be constructed were based on MYD x LAGT mapping population
established at PCA-ARC, Guinobatan, Albay. Published
in the 2000 journal issue of Theoretical Applied Genetics
101: 292-300, different PCR-based DNA marker types were
used such as inverse sequence-tagged repeats (ISTR),
randomly amplified polymorphic DNAs (RAPD), and amplified
fragment length polymorphisms (AFLP). Since then, other
coconut mapping populations have been established. To
date, there are five individual maps (including the
MYD and LAGT maps) that are being expanded or saturated
with more AFLP markers. Also, microsatellites or simple
sequence repeats (SSR) screened from genomic libraries
enriched for (GA)n sequences and cosmid (COS) clones
were prepared for genomic studies, gene isolation and
sequencing. The coconut genome size is about 2.15x109
bp.
For physical mapping, two approaches are
applied: 1) association of mapped AFLP markers to COS
clones via amplification of multi-dimensional pools;
and 2) sequencing the ends of randomly picked, individual
COS clones to design primers for single nucleotide polymorphisms
(SNP) that generate segregating amplification products
in the progenies.
SNP markers in coconut are in part available
to the project from the sequencing of putative resistance
and homeotic gene families. These will serve as candidate
genes representing resistance to biotic stress (fungi,
bacteria, viruses, nematodes, and aphids) and for controlling
important processes in plant development and differentiation
such as leaf development, flower induction and organogenesis.
Towards the end of the project (December
2004), the individual maps will be integrated into a
HD reference map with 16 linkage groups representing
the 16 chromosomes of coconut. It is expected to consist
of 1, 200 to 2, 250 DNA markers covering the whole genome
and it will be filled with QTLs co-segregating with
important traits such as early flowering, increased
nut and oil yield, leaf wax composition and possibly
resistance to biotic and abiotic stress. Standard subsets
of primers derived from AFLP, SSR and SNP markers with
good genome coverage will be selected for future applications.
As syntery studies between coconut and oil palm showed
a high degree of homology with respect to linkage order
and sequences, the coconut HD map will be highly informative
for oil palm and vice versa. (PCA Press Release)
For information dissemination and technology
application, research results are made available to
the scientific community through http://www.mpiz-koeln.mpg.de/~rohde/link2palm.html
and http://www..neiker.net/link2palm
April 1-30 2003 Articles:
::
DA
creates open academy for Philippine agriculture
::
PCA
collaborates with international institutions to unravel
coconut genome
::
EU
tariff preferences benefit RP
::
Making
his mark
::
GIS
application in irrigation emphasized
::
BAR
joins Asia IT and C workshop
::
Philippine
agri’l engineering standards launched
::
El
Niño and coping with it
:: What’s
ailing our sweet potatoes?
::
The
world’s first GM peanut
::: More April 2003 articles :::
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