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.