Finally resolved "unknown certificate"

Added both the certificates to ${USER_INSTALL_ROOT}/etc/DummyServerKeyFile.jks

Added both the certificates to ${USER_INSTALL_ROOT}/etc/DummyServerTrustFile.jks

Added both the certificates to ${USER_INSTALL_ROOT}/java/jre/lib/security/cacerts ??

Example command
/opt/WebSphere/AppServer/java/jre/bin/keytool -import -file -keystore -alias server.com01 –trustcacerts

If I add the certificate elsewhere need some more configuration in WAS.
http://www-128.ibm.com/developerworks/websphere/techjournal/0502_benantar/0502_benantar.html