Correlation between co-expression modules and physiological
changes
The expression data and traits data of all samples were used in Weighted
Gene Coexpression Network Analysis (WGCNA) and the relationships between
them were
visualized
(Supplementary
Figure S7 ). By using hierarchical clustering and dynamic tree cut
method, co-expression modules were obtained
(Supplementary
Figure S8 ); after merging and filtering, a total of 28 modules
remained; among them, the largest module (MEpaleturquoise) contains
2,691 genes while the smallest module (MEdarkorange2) only includes 181
genes
(Supplementary
Table S6 ).
The relationships between modules and physiological traits were examined
(Figure 9 ). Firmness
showed high correlation with the expression levels of genes from
MEdarkorange2 and MEdarkred modules (R > 0.7) and
anti-correlation with those from MElightyellow, MEdarkgrey and MEbrown4
modules (R < -0.7). Ethylene production was
significantly correlated with six modules (P < 0.01),
including MEsaddlebrown, MElightgreen, MEbisque4, MElightsteelblue1,
MEskyblue3 and MEpaleturquoise. MEskyblue3 module was positively
correlated with LOX2 (R = 0.86) but negatively correlated with
ASA (R = -0.7). MEgrey module had no significant (P< 0.05) correlation with all physiological changes. Notably,
the levels of AAO, AMS, LOX2, O2- and
β-Gal displayed similar correlations with ethylene in many modules.
To further explore the biological function of each module, GO annotation
and enrichment analysis were performed. As shown
(Supplementary
Figure S9 ), MEdarkgrey module was enriched in the GO term of
endopeptidase Clp complex in cellular component category; MEskyblue3
module was enriched in the GO term of amino acid kinase activity;
MElightyellow module was enriched in catalytic activity in molecular
function category. Moreover, the sub-network involving all the above
genes was extracted from the whole co-expression network
(Supplementary
Figure S10 ). The sub-network is roughly parted into two clusters: the
cluster in the upper side contains genes mostly from MEskybule module
and the cluster in the lower side contains genes from other modules. The
genes AUX/IAA, SAUR and SAMS3 from the bisque4 module had high degrees
in the sub-network, indicating that they played key roles in the
correlations with other modules.