3.1. DEGs functionally involved in cell wall modification,
drought response, ABA and ethylene hormone signals in fruits undergoing
abscission following cold stress
To investigate differences in fruits in-field under the abscission
process before any additional physiological changes after falling, we
conducted RNA-seq analysis to compare the physiological response of
fruits with pedicel under abscission with the control (Supporting
Information Figure S1). We identified 439 DEGs using both a FDR value
< .05 and |log2 fold change| >
1 as cut-offs. 324 genes were up-regulated, and 115 genes were
down-regulated (Supporting Information Figure S2). The major gene
ontology (GO) classification included the stress response (GO:0006950),
process of oxidation-reduction (GO:0055114, GO:0016705, and GO:0016491),
protein binding (GO:005515), and flavin adenine dinucleotide binding
(GO:0050660). Among 439 DEGs, 269 genes were annotated to the InterPro2
database for the functional enrichment analysis. Based on the
annotation, we selected 92 DEGs and classified them into nine functional
groups (Supporting Information Table S1). In the cell wall modification
class, genes encoding pectinesterase (MD08G1195600 ,MD04G1008100 , etc), polygalacturonase (MD07G1011600 ,MD10G1179100 ), and expansin (MD06G1195100 ) were
differentially expressed in the ‘Abscission’ group.
DEGs related to oxidation-reduction included some down-regulated
polyphenol oxidases (e.g. MD10G1298700) and a few up-regulated ribulose
biphosphate carboxylases (RuBPC) (e.g. MD13G1041900 ). This
category also included genes encoding
UDP-glucuronosyl/UDP-glucosyltransferase homologs.
The senescence-related DEGs included the down-regulated senescence
regulator 40 (S40 ; MD10G1269600 , MD00G1093200 ) and
the up-regulated desiccation protectant protein homolog
(MD01G1072000 ). The up-regulation of both dehydrin 1(DHN1 ; MD02G1140100 ) and LEA14 (MD
00G1127700 ) homologs indicated drought stress response of fruits under
abscission and the dehydrin xero 1 (XERO1 ) was found to be
down-regulated.
In the DNA-binding group, most DEGs were members of transcription factor
families that contained either NAC (NAM, ATAF1/2, and CUC2) or bHLH
(basic helix-loop-helix) domain. Interestingly, a SHORT-ROOT(SHR ) homolog (MDP04G1046000 ) was found up-regulated in
the tissues under abscission.
In the class of phytohormone signal transduction, genes involved in both
ABA and ethylene signal pathways were detected. A few ABA signal-related
genes were annotated to either ABA metabolism (MD15G1082600 ;ABA 8’-hydroxylase 4 ) or downstream response
(MD10G1029100 ). The ethylene receptor Reversion-to-Ethylene
(RTE ) 1 homolog (MD15G1250900 ) was up-regulated in
the ‘Abscission’ group.