Thank you for your help @westfw. I can use Serial to communicate with RS-485 after using either Atmel mEDBG or Arduino as ISP (ATmega32U4). However, Serial1 still does not work. I attach all programmers in this post. Thank you
Programming using AVRISP mkII, USBasp, USBtinyISP (MiniCore), USBasp (MiniCore), Arduino as ISP, or Atmel JTAGICE3 (ISP mode) does not work with Serial1 either. I tried to follow this post atmega328pb xplained mini with Arduino IDE 1.8.5 and USBasp - Microcontrollers - Arduino Forum, but could not resolve this issue.
Arduino as ISP (ATmega32U4)
Sketch uses 7964 bytes (24%) of program storage space. Maximum is 32256 bytes.
Global variables use 723 bytes (35%) of dynamic memory, leaving 1325 bytes for local variables. Maximum is 2048 bytes.
/Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude -C/Users/tkawinf/Library/Arduino15/packages/MiniCore/hardware/avr/2.0.4/avrdude.conf -v -patmega328pb -carduino -P/dev/cu.usbmodem14102 -b9600 -D -Uflash:w:/var/folders/zl/p4_y2q992b97kfkhgq51yr9h0000gn/T/arduino_build_717934/sensor-hub.ino.hex:i
avrdude: Version 6.3-20190619
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch
System wide configuration file is "/Users/tkawinf/Library/Arduino15/packages/MiniCore/hardware/avr/2.0.4/avrdude.conf"
User configuration file is "/Users/tkawinf/.avrduderc"
User configuration file does not exist or is not a regular file, skipping
Using Port : /dev/cu.usbmodem14102
Using Programmer : arduino
Overriding Baud Rate : 9600
AVR Part : ATmega328PB
Chip Erase delay : 9000 us
PAGEL : PD7
BS2 : PC2
RESET disposition : dedicated
RETRY pulse : SCK
serial program mode : yes
parallel program mode : yes
Timeout : 200
StabDelay : 100
CmdexeDelay : 25
SyncLoops : 32
ByteDelay : 0
PollIndex : 3
PollValue : 0x53
Memory Detail :
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
eeprom 65 20 4 0 no 1024 4 0 3600 3600 0xff 0xff
flash 65 6 128 0 yes 32768 128 256 4500 4500 0xff 0xff
lfuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
hfuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
lock 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
calibration 0 0 0 0 no 1 0 0 0 0 0x00 0x00
signature 0 0 0 0 no 3 0 0 0 0 0x00 0x00
efuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
Programmer Type : Arduino
Description : Arduino
Hardware Version: 3
Firmware Version: 8.0
Vtarget : 0.3 V
Varef : 0.3 V
Oscillator : 28.800 kHz
SCK period : 3.3 us
avrdude: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.01s
avrdude: Device signature = 0x1e9516 (probably m328pb)
avrdude: reading input file "/var/folders/zl/p4_y2q992b97kfkhgq51yr9h0000gn/T/arduino_build_717934/sensor-hub.ino.hex"
avrdude: writing flash (7964 bytes):
Writing | ################################################## | 100% 9.52s
avrdude: 7964 bytes of flash written
avrdude: verifying flash memory against /var/folders/zl/p4_y2q992b97kfkhgq51yr9h0000gn/T/arduino_build_717934/sensor-hub.ino.hex:
avrdude: load data flash data from input file /var/folders/zl/p4_y2q992b97kfkhgq51yr9h0000gn/T/arduino_build_717934/sensor-hub.ino.hex:
avrdude: input file /var/folders/zl/p4_y2q992b97kfkhgq51yr9h0000gn/T/arduino_build_717934/sensor-hub.ino.hex contains 7964 bytes
avrdude: reading on-chip flash data:
Reading | ################################################## | 100% 9.26s
avrdude: verifying ...
avrdude: 7964 bytes of flash verified
avrdude done. Thank you.
Atmel mEDBG
Sketch uses 7964 bytes (24%) of program storage space. Maximum is 32256 bytes.
Global variables use 723 bytes (35%) of dynamic memory, leaving 1325 bytes for local variables. Maximum is 2048 bytes.
/Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude -C/Users/tkawinf/Library/Arduino15/packages/MiniCore/hardware/avr/2.0.4/avrdude.conf -v -patmega328pb -carduino -P/dev/cu.usbmodem14102 -b9600 -D -Uflash:w:/var/folders/zl/p4_y2q992b97kfkhgq51yr9h0000gn/T/arduino_build_717934/sensor-hub.ino.hex:i
avrdude: Version 6.3-20190619
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch
System wide configuration file is "/Users/tkawinf/Library/Arduino15/packages/MiniCore/hardware/avr/2.0.4/avrdude.conf"
User configuration file is "/Users/tkawinf/.avrduderc"
User configuration file does not exist or is not a regular file, skipping
Using Port : /dev/cu.usbmodem14102
Using Programmer : arduino
Overriding Baud Rate : 9600
AVR Part : ATmega328PB
Chip Erase delay : 9000 us
PAGEL : PD7
BS2 : PC2
RESET disposition : dedicated
RETRY pulse : SCK
serial program mode : yes
parallel program mode : yes
Timeout : 200
StabDelay : 100
CmdexeDelay : 25
SyncLoops : 32
ByteDelay : 0
PollIndex : 3
PollValue : 0x53
Memory Detail :
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
eeprom 65 20 4 0 no 1024 4 0 3600 3600 0xff 0xff
flash 65 6 128 0 yes 32768 128 256 4500 4500 0xff 0xff
lfuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
hfuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
lock 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
calibration 0 0 0 0 no 1 0 0 0 0 0x00 0x00
signature 0 0 0 0 no 3 0 0 0 0 0x00 0x00
efuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
Programmer Type : Arduino
Description : Arduino
Hardware Version: 3
Firmware Version: 8.0
Vtarget : 0.3 V
Varef : 0.3 V
Oscillator : 28.800 kHz
SCK period : 3.3 us
avrdude: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.01s
avrdude: Device signature = 0x1e9516 (probably m328pb)
avrdude: reading input file "/var/folders/zl/p4_y2q992b97kfkhgq51yr9h0000gn/T/arduino_build_717934/sensor-hub.ino.hex"
avrdude: writing flash (7964 bytes):
Writing | ################################################## | 100% 9.52s
avrdude: 7964 bytes of flash written
avrdude: verifying flash memory against /var/folders/zl/p4_y2q992b97kfkhgq51yr9h0000gn/T/arduino_build_717934/sensor-hub.ino.hex:
avrdude: load data flash data from input file /var/folders/zl/p4_y2q992b97kfkhgq51yr9h0000gn/T/arduino_build_717934/sensor-hub.ino.hex:
avrdude: input file /var/folders/zl/p4_y2q992b97kfkhgq51yr9h0000gn/T/arduino_build_717934/sensor-hub.ino.hex contains 7964 bytes
avrdude: reading on-chip flash data:
Reading | ################################################## | 100% 9.26s
avrdude: verifying ...
avrdude: 7964 bytes of flash verified
avrdude done. Thank you.