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with more lines than the 60 or so produced so far are needed for finer-scale
mapping to detect more closely linked genetic effects (McCallum et al ., 2005b).
The development of male-fertile, seed-reproduced garlic has enabled the first
genetic linkage map for garlic to be derived (Zewdie et al ., 2005). The genetic
markers used were developed from expressed DNA sequences from onion (Kuhl
et al ., 2004). A gene locus for fertile seed production was located on the linkage
map.
Molecular markers are useful for surveys of genetic diversity both within
and between allium species (Klaas and Friesen, 2002; McCallum et al ., 2005b).
Markers are already finding practical applications within the onion industry;
for example, markers from chloroplast DNA characteristic of male-sterile
cytoplasm are widely used to quickly classify cytoplasm in the development of
maintainer and male-sterile lines during the breeding of onion hybrids (see
below) and for quality control (i.e. confirming genetic identities) in breeding
and hybrid-onion seed production (Havey, 2002; Jakse et al ., 2005).
GENOMICS
The collection of DNA sequences and, for some organisms, the sequencing of
all the genetic material, has made possible the comparison of DNA sequences
within and between taxonomic groups (Havey et al ., in press). The function of
a DNA sequence can be tentatively inferred from knowledge on what enzyme
or other protein it, or similar sequences, code for in other species. Taxonomic
groups showing high similarity in their arrangement of DNA subsequences
along the chromosomes are said to show high synteny or colinearity.
The study of genomes investigating how they function as a whole system
in controlling growth, development and adaptation - and also to clarify the
phylogenetic relationships between species - is a central concern of current
biological research. Such genomic studies in the alliums are in their infancy,
but a library has been created of 11,008 DNA sequences derived by sequencing
DNA complementary to the RNA isolated from bulb, root, leaf and callus tissue
of onion (Kuhl et al ., 2004). The sequence information is freely available online
at http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=onion.
Since they are derived from RNA found in the tissues, these are the DNA
sequences that are actively transcribing for RNA and hence they are termed
'expressed sequence tags' (EST). They should encompass the active genes in
their respective tissues. Sixty per cent of these sequences matched proteins
from other organisms, of which nearly 24% could be tentatively assigned to
some gene functionality, mostly involved with metabolism. EST markers show-
ing similarities to EST markers from rice were selected and linkage mapped
using the lines derived from the 'Ailsa Craig'
'Brigham Yellow Globe' cross
mentioned above under linkage maps. Physical locations for these markers on
the chromosome were determined using the monosomic addition lines also
 
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