Coconut - Genomics of Cultivated Palms - page 17

coconut. One is a set developed as CnZ series in the Philippines [22] ; another set is
the CAC series developed in Scotland [17-20] ; and a third is a set of SSRs devel-
oped in France as the CnCir series [23] . Primers and sequences of these SSR loci
are available at Genbank database, and map positions are at the Link2palm website
( http://www.neiker.net/link2palm/Coco/DefCOCO.htm ). Microsatellite markers are
currently used widely in the characterization of coconut germplasm belonging to
different countries such as China [24] , India [21] , Sri Lanka [17] , Philippines [22] ,
Dominican Republic [25] , and USA (Florida) [20] .
2.3 Maker-Trait Associations, QTL Mapping on Coconut
Markers associated with important traits can increase the breeding efficiency and
save time in a perennial crop like coconut. Resistance to eriophyid mite [37] , lethal
yellowing disease [38] , and lethal disease [39] are associated with selected alleles
of SSR or RAPD markers ( Table 2.2 ). These markers, after further validation and
conversion as SCAR markers and kit or chip, serve as an efficient tool for coconut
breeding. QTL mapping of important traits such as early flowering [40] , yield [41] ,
fruit components [43] , and composition of cuticular wax [44] are identified so far
( Table 2.2 ). Strong QTLs and saturation of coconut linkage map with an additional
set of markers can increase the breeding efficiency of coconut for the traits of inter-
est. AFLP markers are the favorable choice in QTL mapping experiments [40-43]
as they generate a large number of scorable bands. All other marker systems such as
ISTRs [40] , ISSRs [41] , RAPDs [37,38,40] , RFLPs [42] , and SSRs [37,39,41-43]
were also useful in trait association/QTL mapping in coconut. Details of the knowl-
edge available on mapping of genes and markers with traits are as given in Table 2.2 .
2.4 Genome Biology of Coconut Endosperm and
Fatty Acid Biosynthesis
Endosperm is the most important economic part of the coconut palm and provides
a refreshing health drink during the immature stage and edible grade oil during the
mature stage. Little information is available on the coconut endosperm, from the
experiments on cDNA library [44] , X-ray diffraction studies of cocosin [45] , gene
[7] and promoter [46] cloning of LPAAT, miRNA chip [47] on mature and imma-
ture endosperm, free nucleotides [48] , and biochemistry [50] of a mutant endosperm.
Sequencing of the transcriptome of the 8- and 15-month-old endosperm revealed that
41% of genes are homologous to those having known gene function. Expression of
oleosin and globulin genes (similar to oil palm ones) is specific to 15-month-old pulp
and not in 8-month-old pulp. One unique gene, KIAA 1239 protein, 322 amino acids
long, which is otherwise known only in mammalian systems like humans, is overex-
pressed at the endosperm development stage of coconut [44] . Coconut endosperm
contains a storage protein known as cocosin. Cocosin was purified, crystallized,