I have got one Atmega1280V board with programming connector with pin connections as follows
1. Pin1 : gnd
2. Pin2 : reset
3. Pin3 : PB1 SCK/PCINT1 (SPI Bus Serial Clock or Pin Change Interrupt 1)
4. Pin4 : MOSI/PCINT2 (SPI Bus Master Output/Slave Input or Pin Change Interrupt 2)
5. Pin5 : MISO/PCINT3 (SPI Bus Master Input/Slave Output or Pin Change Interrupt 3)


What kind of debugger/programmer should be connected here. IO have to identify that programmer/debugger.

 

Any programmer that supports Atmel AVR.

Google Atmel AVR programmer.

Here is one example:

http://www.aliexpress.com/item/Free-Shipping-New-1pc-USB-ISP-Programmer-For-ATMEL-AVR-ATMega-ATTiny-51-Development-Board/1813921450.html

 

This board is pre-assembled & have programmer connector containg SPI port. That's why I have asked which debugger/programmer to choose.

Debugger like AVR-One support JTAG