Generate a self-signed certificate on the fly

I edited the answer to do the root certificate first and then issue an end entity certificate.

Here is some example of generating a self-signed certificate through Bouncy Castle:

public static X509Certificate2 GenerateSelfSignedCertificate(string subjectName, string issuerName, AsymmetricKeyParameter issuerPrivKey,  int keyStrength = 2048)
{
    // Generating Random Numbers
    var randomGenerator = new CryptoApiRandomGenerator();
    var random = new SecureRandom(randomGenerator);

    // The Certificate Generator
    var certificateGenerator = new X509V3CertificateGenerator();

    // Serial Number
    var serialNumber = BigIntegers.CreateRandomInRange(BigInteger.One, BigInteger.ValueOf(Int64.MaxValue), random);
    certificateGenerator.SetSerialNumber(serialNumber);

    // Signature Algorithm
    const string signatureAlgorithm = "SHA256WithRSA";
    certificateGenerator.SetSignatureAlgorithm(signatureAlgorithm);

    // Issuer and Subject Name
    var subjectDN = new X509Name(subjectName);
    var issuerDN = new X509Name(issuerName);
    certificateGenerator.SetIssuerDN(issuerDN);
    certificateGenerator.SetSubjectDN(subjectDN);

    // Valid For
    var notBefore = DateTime.UtcNow.Date;
    var notAfter = notBefore.AddYears(2);

    certificateGenerator.SetNotBefore(notBefore);
    certificateGenerator.SetNotAfter(notAfter);

    // Subject Public Key
    AsymmetricCipherKeyPair subjectKeyPair;
    var keyGenerationParameters = new KeyGenerationParameters(random, keyStrength);
    var keyPairGenerator = new RsaKeyPairGenerator();
    keyPairGenerator.Init(keyGenerationParameters);
    subjectKeyPair = keyPairGenerator.GenerateKeyPair();

    certificateGenerator.SetPublicKey(subjectKeyPair.Public);

    // Generating the Certificate
    var issuerKeyPair = subjectKeyPair;

    // Selfsign certificate
    var certificate = certificateGenerator.Generate(issuerPrivKey, random);

    // Corresponding private key
    PrivateKeyInfo info = PrivateKeyInfoFactory.CreatePrivateKeyInfo(subjectKeyPair.Private);


    // Merge into X509Certificate2
    var x509 = new System.Security.Cryptography.X509Certificates.X509Certificate2(certificate.GetEncoded());

    var seq = (Asn1Sequence)Asn1Object.FromByteArray(info.PrivateKey.GetDerEncoded());
    if (seq.Count != 9)
        throw new PemException("malformed sequence in RSA private key");

    var rsa = new RsaPrivateKeyStructure(seq);
    RsaPrivateCrtKeyParameters rsaparams = new RsaPrivateCrtKeyParameters(
        rsa.Modulus, rsa.PublicExponent, rsa.PrivateExponent, rsa.Prime1, rsa.Prime2, rsa.Exponent1, rsa.Exponent2, rsa.Coefficient);

    x509.PrivateKey = DotNetUtilities.ToRSA(rsaparams);
    return x509;
}


public static AsymmetricKeyParameter GenerateCACertificate(string subjectName, int keyStrength = 2048)
{
    // Generating Random Numbers
    var randomGenerator = new CryptoApiRandomGenerator();
    var random = new SecureRandom(randomGenerator);

    // The Certificate Generator
    var certificateGenerator = new X509V3CertificateGenerator();

    // Serial Number
    var serialNumber = BigIntegers.CreateRandomInRange(BigInteger.One, BigInteger.ValueOf(Int64.MaxValue), random);
    certificateGenerator.SetSerialNumber(serialNumber);

    // Signature Algorithm
    const string signatureAlgorithm = "SHA256WithRSA";
    certificateGenerator.SetSignatureAlgorithm(signatureAlgorithm);

    // Issuer and Subject Name
    var subjectDN = new X509Name(subjectName);
    var issuerDN = subjectDN;
    certificateGenerator.SetIssuerDN(issuerDN);
    certificateGenerator.SetSubjectDN(subjectDN);

    // Valid For
    var notBefore = DateTime.UtcNow.Date;
    var notAfter = notBefore.AddYears(2);

    certificateGenerator.SetNotBefore(notBefore);
    certificateGenerator.SetNotAfter(notAfter);

    // Subject Public Key
    AsymmetricCipherKeyPair subjectKeyPair;
    var keyGenerationParameters = new KeyGenerationParameters(random, keyStrength);
    var keyPairGenerator = new RsaKeyPairGenerator();
    keyPairGenerator.Init(keyGenerationParameters);
    subjectKeyPair = keyPairGenerator.GenerateKeyPair();

    certificateGenerator.SetPublicKey(subjectKeyPair.Public);

    // Generating the Certificate
    var issuerKeyPair = subjectKeyPair;

    // Selfsign certificate
    var certificate = certificateGenerator.Generate(issuerKeyPair.Private, random);
    var x509 = new System.Security.Cryptography.X509Certificates.X509Certificate2(certificate.GetEncoded());

    // Add CA certificate to Root store
    addCertToStore(cert, StoreName.Root, StoreLocation.CurrentUser);

    return issuerKeyPair.Private;
}

And add to the store (your code slightly modified):

public static bool addCertToStore(System.Security.Cryptography.X509Certificates.X509Certificate2 cert, System.Security.Cryptography.X509Certificates.StoreName st, System.Security.Cryptography.X509Certificates.StoreLocation sl)
{
    bool bRet = false;

    try
    {
        X509Store store = new X509Store(st, sl);
        store.Open(OpenFlags.ReadWrite);
        store.Add(cert);

        store.Close();
    }
    catch
    {

    }

    return bRet;
}

And usage:

var caPrivKey = GenerateCACertificate("CN=root ca");
var cert = GenerateSelfSignedCertificate("CN=127.0.01", "CN=root ca", caPrivKey);
addCertToStore(cert, StoreName.My, StoreLocation.CurrentUser);

I have not compiled this example code after @wakeupneo comments. @wakeupneo, you might have to slightly edit the code and add proper extensions to each certificate.