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Spring security x.509 authentication - accept certificates based on their issuer Certificate Authority

I am using Spring Security to authenticate using an x.509 certificate, and it works only when the client certificate which is configured in the browser key-store is present in server trust-store.
How it is working currently:
I have configured the SSL client authentication as optional (server.ssl.client-auth=want , like in this post)
I have configured a server trust-store that contains all client certificates. If the certificate presented by the client is in the trust-store, the mutual SSL connection is created.
When I have the client certificate(s) present in the server-side trust-store, Firefox opens a popup with my client-side certificate(s), which I can choose and the mutual SSL connection is established.
I have configured Spring Security to extract the username from the SubjectDN of the client certificate and check it against a UserDetailsService. If a UserDetails object is returned for that username, the authentication process completes successfully
The problem is that if I remove the client-certificate from the server-side trust-store, Firefox doesn't open this popup anymore, and only a one-way SSL connection is made. Even if the Root CA cert is present in the server trust-store.
What I want:
store in the server trust-store only the certificate of a Root Certificate Authority
allow mutual SSL connection when the client presents a certificate issued by the Root CA in the server trust-store (even if the client certificate isn't present in the server trust-store)
I am also intrigued by two resources on the internet. In this tutorial on Baeldung, it says that all client certificates must be stored in the server trust-store for X.509 auth to work (which confirms my experience).
You must remember that for each user that should be verified by the server, its own certificate needs to be installed in the configured truststore. For small applications with only a few clients, this may perhaps be practicable, with an increasing number of clients it may lead to complex key-management for users.
However, this tutorial by #robinhowlett says that
The client will present its certificate in its keystore to the server, and the server will validate the client certificate’s chain using the CA certificate in the server’s truststore.
This is basically what I want to achieve, but am not able to.
Bottom line: did someone manage to store one or more Root CA certificates in the server trust-store and use client certificates issued by these Root CAs to authenticate via X.509 mutual SSL handshake in Spring Security?
I am using Spring Boot 1.5.2.RELEASE (spring-security-web 4.2.2.RELEASE). I have tested my working SSL authentication with Firefox 53.

I found my problem - I was modifying the trust-store (removing the client cert and leaving only the CA cert) while the server was up (Tomcat, in my case). But the trust-store is kept in memory and gets read only once, when the JVM is initialized (details on this ServerFault post). So trust-store changes are not being read during runtime by Tomcat.
So the answer is simple: yes, if only CA certs are present in the trust-store, during the SSL handshake the server communicates to the browser it wants client certificates issued by the trusted CAs and then the browser prompts the user to select a certificate that is issued by a trusted CA (if such a cert is present in the browser keystore).
However, if a CA is added dynamically to the server trust-store while the server is up and running, it won't be detected. The new CA will only be recognized after the server reboots (and the JVM is re-initialized).

TLS Client Authentication between .NET Console Application Client and Java RESTful Service

Background
I have a .NET console application client that consumes a Java RESTful Service with TLS Client Authentication enabled (aka Mutual Authentication).
It should be the reverse of this SSL Socket between .Net and Java with client authentication
Problem
I am always getting this error: Could not establish trust relationship for the SSL/TLS secure channel
I have no idea how to configure this correctly both on the client and server.
Steps Performed
The .NET console application is already including the CA, intermediate, and server certificates but the same error is being thrown.
I provided the server a Certificate Signing Request (CSR).
The server signed and provided a signed certificate back to me. The signed certificate is being included in the communications between the client and the server. However, the same error is being thrown.
Can anyone enlighten me on how to get a successful handshake?

This has been resolved.
Here are the steps:
Create a Certificate Signing Request (CSR).
Have the CSR signed by the server.
Get the signed certificate.
Include the signed certificate in the HTTP request.
Make sure to put the Self-Signed CA Certificate in the Local Computer's Trusted Root CA store.
Troubleshooting steps in order (do not skip if a certain step is not successful):
Test with HTTP
Test with HTTPS (one-way authentication)
Test with HTTPS (mutual authentication)

Why the SOAP request has been accepted from SoapUI without configuring trust-store location?

I built a Web-Service application in Jdeveloper 11.1.1.7 and deployed it on weblogic 10.3.6 with all Key-store and SSL configuration.
SSl Configuration:
Use Server Certs : Checked
Two Way Client Cert Behavior: Client Certs Not Requested. [That is means it is one-way ssl.
Correct me if that wrong]
SSL Listen Port Enabled: Checked
Key-store Configuration:
Custom Identity and Custom Trust. The file path has been specified for those custom key store
A sample client application has been created and everything seems to be fine; I mean the client can not access the server application without specifying the trust store file location where the server certificate is stored and it is trusted at the client end.
By the server certificate I mean the same certificate that has been configured in server Key-store Configuration
for your information the client application referring to trust store as follow:
System.setProperty("javax.net.ssl.trustStore",[Trust-store location goes here]);
System.setProperty("javax.net.ssl.trustStorePassword", [password goes here]);
Till now nothing wrong. Next is the problem details:
For the purpose of testing I tried to access the deployed web-service application using the SoapUI (open source software). What is confusing is the request has been sent, accepted at the server and proceed without specifying any thing for server certificate nor trust store location in SoapUI project configuration !!
Why the SOAP request has been accepted from SoapUI without referring to server certificate? The request should be rejected in this case.

My experience with SoapUI is that it is quite lenient. For example, if it doesn't check if the CN of server certificate matches the fully qualified domain name in the URL. In your case, your server most likely uses a CA signed certificate. Most of the root and intermediate certificates of well known CA's (e.g. VeriSign/Symantec) are already included in the default truststores for most systems. If your server had used a self-signed certificate, then SoapUI would have incurred SSL error unless you import the self-signed certificates into the truststore of the host where SoapUI is running.

Is there a way to test 2 way ssl through browser?

If so, How do you set certificate for authentication, what files do you need? is it .pfx? How would you install that in browser? Been stuck trying to test 2 way ssl through browser. I have a webservice, and trying to connect always returns certification authentication failed.

Expanding on nickrak's answer. 2-way SSL means that the client trusts the webservice, and that the webservice trusts/authenticates the client.
On the webservice side:
Add the client's CA cert into the webservice's trusted certificates. The "CN" in the webservice server certificate must match the URL of the webservice. The webservice server certificate must not be expired. The webservice may choose to do further authentication based on the client certificate...for example, is the client certificate in a "whitelist" of authorized clients. Perhaps the webservice has multiple levels of access, so the client certificate is checked to determine how much access to give the client.
On the client side:
The CA that signed the webservice server certificate will need to be added to the client's trusted certificate list. In a browser, this will be in the "Trusted Root Certification Authorities" section (IE, Chrome) or "Authorities" section (Firefox). The extensions for these certificates are usually .der, .cer, .crt, or .pem. Also, the client's own private key/certificate combination need to be added to the client browser. This will be in the "Personal" section (IE, Chrome) or "Your Certificates" (Firefox). The extensions for these keystores are usually .p12 or .pfx.

Add the client's CA's public certificate to the Trusted Root Certificate Store.
Add the client's public and private key to the browser's Personal Certificate Store. (usually a pfx, but might also be a der/pem/crt/cer.)
Navigate to page requiring certificate
Optionally, depending on browser: select the certificate you want to use for this connection.
Hopefully, success.

Java certificate based authentication

I have a thrift endpoint that someone created who is not longer with our company. They implemented the authentication via client side certs, but I having a hard time wrapping my head around how it all works. Does anyone know of a tutorial, or howto on this topic.
All I really have is a sample client class. Here are a list of things that I need help with:
Can a server cert and the client cert both be contained in the same trust store
How do you create a new client side cert?
How do you add that client side cert to the server trust store?
Do you need to set the client trust store, and set the java trust (assuming the server is a self signed endpoint)
What does the following error mean?
ERROR[com.cada.CadaDaoTest][main] - Error:
org.apache.thrift.transport.TTransportException: javax.net.ssl.SSLHandshakeException: Received fatal alert: bad_certificate

The truststore (on Tomcat it's configured forthe SSL connector in server.xml) can hold the root of the certificate chain of the client certificate, not the certificate itself. That is, when a certificate is created, it is signed by a CA - certificate authority. If the CA cert is trusted, all certs singed by the CA are trusted as well.
You can create certificates using either keytool (in jdk/bin/) or openssl. There are GUIs for that, like portecle.
The tomcat ssl tutorial might be helpful.