Produce Degradation Pathways and Prevention

Genomic Exploration of Produce Degradation 13

quantitative analysis. Arrays have been fabricated on a variety of different materials,
but the most common are oligonucleotide- or DNA-based arrays fabricated on glass
slides or nylon membranes.
Fessehaie et al. (2003) recently applied an oligonucleotide array for the identi-
fication and differentiation of bacteria pathogenic in potatoes. In their study, oligo-
nucleotides 16 to 24 bases long were selected from the 3′ end of the 16S gene and
the 16S–23S intergenic spacer regions of bacteria pathogenic in potatoes, including
Clavibacter michiganensis subsp. sepedonicus, Ralstonia solanacearum, and the
pectolytic erwinias, including Erwinia carotovora subsp. atroseptica and carotovora
and E. chrysanthemi. Genomic DNA from bacterial cultures was amplified by PCR
using conserved ribosomal primers and labeled simultaneously with digoxigenin-
dUTP for the hybridization experiment. Subsequent serological detection of the
digoxigenin label revealed different hybridization patterns that were distinct for each
species and subspecies tested. Preliminary tests also show that bacteria could be
detected by hybridizing to the array amplicons from mixed cultures and inoculated
potato tissue.

FIGURE 1.1A graphical illustration of the concept of population genomics. The solid circle
on the left represent the population genome of soft rot erwinia, which is the compilation of
whole and partial genome sequences. The two complete genome sequences (Eca SCRI1043
= Erwinia carotovora subsp. atroseptica SCRI1043 and Ec 3937 = Erwinia chrysanthemi
3937) serve as the system core. The leftward direction of the central line outlines the strategy
to obtain the population genome. The ultimate goal of population genomics is, however, in
the rightward direction (i.e., to help to resolve problems associated with strains in the fields
or production).

Eca Randomly

SCRI1043Ec 3937EcaSCRI1039sampled strains

Soft rot erwina

genome

Field strains