Certificate Chains
keytool can create and manage keystore "key" entries that each contain a private key and an associated certificate "chain". The first certificate in the chain contains the public key corresponding to the private key.
When keys are first generated (see the -genkeypair command), the chain starts off containing a single element, a self-signed certificate. A self-signed certificate is one for which the issuer (signer) is the same as the subject (the entity whose public key is being authenticated by the certificate). Whenever the -genkeypair command is called to generate a new public/private key pair, it also wraps the public key into a self-signed certificate.
Later, after a Certificate Signing Request (CSR) has been generated (see the -certreq command) and sent to a Certification Authority (CA), the response from the CA is imported (see -importcert), and the self-signed certificate is replaced by a chain of certificates. At the bottom of the chain is the certificate (reply) issued by the CA authenticating the subject's public key. The next certificate in the chain is one that authenticates the CA's public key.
In many cases, this is a self-signed certificate (that is, a certificate from the CA authenticating its own public key) and the last certificate in the chain. In other cases, the CA may return a chain of certificates. In this case, the bottom certificate in the chain is the same (a certificate signed by the CA, authenticating the public key of the key entry), but the second certificate in the chain is a certificate signed by a different CA, authenticating the public key of the CA you sent the CSR to. Then, the next certificate in the chain will be a certificate authenticating the second CA's key, and so on, until a self-signed "root" certificate is reached. Each certificate in the chain (after the first) thus authenticates the public key of the signer of the previous certificate in the chain.
Many CAs only return the issued certificate, with no supporting chain, especially when there is a flat hierarchy (no intermediates CAs). In this case, the certificate chain must be established from trusted certificate information already stored in the keystore.
A different reply format (defined by the PKCS#7 standard) also includes the supporting certificate chain, in addition to the issued certificate. Both reply formats can be handled by keytool.
The top-level (root) CA certificate is self-signed. However, the trust into the root's public key does not come from the root certificate itself (anybody could generate a self-signed certificate with the distinguished name of say, the VeriSign root CA!), but from other sources like a newspaper. The root CA public key is widely known. The only reason it is stored in a certificate is because this is the format understood by most tools, so the certificate in this case is only used as a "vehicle" to transport the root CA's public key. Before you add the root CA certificate to your keystore, you should view it (using the -printcert option) and compare the displayed fingerprint with the well-known fingerprint (obtained from a newspaper, the root CA's webpage, etc.).