diff --git a/.trunk/trunk.yaml b/.trunk/trunk.yaml
index f17d1a0..6d91298 100644
--- a/.trunk/trunk.yaml
+++ b/.trunk/trunk.yaml
@@ -11,7 +11,7 @@ runtimes:
   enabled:
     - node@22.16.0
     - python@3.10.8
-    - rust@1.82.0
+    - rust@1.92.0
 
 actions:
   enabled:
@@ -24,16 +24,16 @@ lint:
   enabled:
     - actionlint@1.7.7
     - buildifier@8.2.1
-    - checkov@3.2.474
+    - checkov@3.2.497
     - git-diff-check
-    - markdownlint@0.45.0
+    - markdownlint@0.47.0
     - osv-scanner@2.2.3
-    - prettier@3.6.2
-    - rustfmt@1.65.0
+    - prettier@3.7.4
+    - rustfmt@1.92.0
     - taplo@0.10.0
     - trufflehog@3.90.8
     - yamllint@1.37.1
-    - clippy@1.82.0
+    - clippy@1.92.0
 
 tools:
   runtimes:
diff --git a/Cargo.lock b/Cargo.lock
index 0617369..4ce350e 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -114,9 +114,9 @@ checksum = "b35204fbdc0b3f4446b89fc1ac2cf84a8a68971995d0bf2e925ec7cd960f9cb3"
 
 [[package]]
 name = "cc"
-version = "1.2.49"
+version = "1.2.51"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "90583009037521a116abf44494efecd645ba48b6622457080f080b85544e2215"
+checksum = "7a0aeaff4ff1a90589618835a598e545176939b97874f7abc7851caa0618f203"
 dependencies = [
  "find-msvc-tools",
  "shlex",
@@ -143,9 +143,9 @@ dependencies = [
 
 [[package]]
 name = "clap"
-version = "4.5.53"
+version = "4.5.54"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c9e340e012a1bf4935f5282ed1436d1489548e8f72308207ea5df0e23d2d03f8"
+checksum = "c6e6ff9dcd79cff5cd969a17a545d79e84ab086e444102a591e288a8aa3ce394"
 dependencies = [
  "clap_builder",
  "clap_derive",
@@ -153,9 +153,9 @@ dependencies = [
 
 [[package]]
 name = "clap_builder"
-version = "4.5.53"
+version = "4.5.54"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d76b5d13eaa18c901fd2f7fca939fefe3a0727a953561fefdf3b2922b8569d00"
+checksum = "fa42cf4d2b7a41bc8f663a7cab4031ebafa1bf3875705bfaf8466dc60ab52c00"
 dependencies = [
  "anstream",
  "anstyle",
@@ -293,9 +293,9 @@ checksum = "37909eebbb50d72f9059c3b6d82c0463f2ff062c9e95845c43a6c9c0355411be"
 
 [[package]]
 name = "find-msvc-tools"
-version = "0.1.5"
+version = "0.1.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3a3076410a55c90011c298b04d0cfa770b00fa04e1e3c97d3f6c9de105a03844"
+checksum = "645cbb3a84e60b7531617d5ae4e57f7e27308f6445f5abf653209ea76dec8dff"
 
 [[package]]
 name = "fnv"
@@ -402,9 +402,9 @@ dependencies = [
 
 [[package]]
 name = "h2"
-version = "0.4.12"
+version = "0.4.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f3c0b69cfcb4e1b9f1bf2f53f95f766e4661169728ec61cd3fe5a0166f2d1386"
+checksum = "2f44da3a8150a6703ed5d34e164b875fd14c2cdab9af1252a9a1020bde2bdc54"
 dependencies = [
  "atomic-waker",
  "bytes",
@@ -694,9 +694,9 @@ checksum = "469fb0b9cefa57e3ef31275ee7cacb78f2fdca44e4765491884a2b119d4eb130"
 
 [[package]]
 name = "iri-string"
-version = "0.7.9"
+version = "0.7.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4f867b9d1d896b67beb18518eda36fdb77a32ea590de864f1325b294a6d14397"
+checksum = "c91338f0783edbd6195decb37bae672fd3b165faffb89bf7b9e6942f8b1a731a"
 dependencies = [
  "memchr",
  "serde",
@@ -710,15 +710,15 @@ checksum = "a6cb138bb79a146c1bd460005623e142ef0181e3d0219cb493e02f7d08a35695"
 
 [[package]]
 name = "itoa"
-version = "1.0.15"
+version = "1.0.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4a5f13b858c8d314ee3e8f639011f7ccefe71f97f96e50151fb991f267928e2c"
+checksum = "92ecc6618181def0457392ccd0ee51198e065e016d1d527a7ac1b6dc7c1f09d2"
 
 [[package]]
 name = "jiff"
-version = "0.2.16"
+version = "0.2.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "49cce2b81f2098e7e3efc35bc2e0a6b7abec9d34128283d7a26fa8f32a6dbb35"
+checksum = "e67e8da4c49d6d9909fe03361f9b620f58898859f5c7aded68351e85e71ecf50"
 dependencies = [
  "jiff-static",
  "log",
@@ -729,9 +729,9 @@ dependencies = [
 
 [[package]]
 name = "jiff-static"
-version = "0.2.16"
+version = "0.2.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "980af8b43c3ad5d8d349ace167ec8170839f753a42d233ba19e08afe1850fa69"
+checksum = "e0c84ee7f197eca9a86c6fd6cb771e55eb991632f15f2bc3ca6ec838929e6e78"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -756,9 +756,9 @@ checksum = "bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe"
 
 [[package]]
 name = "libc"
-version = "0.2.178"
+version = "0.2.179"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "37c93d8daa9d8a012fd8ab92f088405fb202ea0b6ab73ee2482ae66af4f42091"
+checksum = "c5a2d376baa530d1238d133232d15e239abad80d05838b4b59354e5268af431f"
 
 [[package]]
 name = "linux-raw-sys"
@@ -1019,9 +1019,9 @@ checksum = "7edddbd0b52d732b21ad9a5fab5c704c14cd949e5e9a1ec5929a24fded1b904c"
 
 [[package]]
 name = "portable-atomic"
-version = "1.11.1"
+version = "1.13.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f84267b20a16ea918e43c6a88433c2d54fa145c92a811b5b047ccbe153674483"
+checksum = "f89776e4d69bb58bc6993e99ffa1d11f228b839984854c7daeb5d37f87cbe950"
 
 [[package]]
 name = "portable-atomic-util"
@@ -1052,18 +1052,18 @@ dependencies = [
 
 [[package]]
 name = "proc-macro2"
-version = "1.0.103"
+version = "1.0.105"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5ee95bc4ef87b8d5ba32e8b7714ccc834865276eab0aed5c9958d00ec45f49e8"
+checksum = "535d180e0ecab6268a3e718bb9fd44db66bbbc256257165fc699dadf70d16fe7"
 dependencies = [
  "unicode-ident",
 ]
 
 [[package]]
 name = "quote"
-version = "1.0.42"
+version = "1.0.43"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a338cc41d27e6cc6dce6cefc13a0729dfbb81c262b1f519331575dd80ef3067f"
+checksum = "dc74d9a594b72ae6656596548f56f667211f8a97b3d4c3d467150794690dc40a"
 dependencies = [
  "proc-macro2",
 ]
@@ -1135,9 +1135,9 @@ checksum = "7a2d987857b319362043e95f5353c0535c1f58eec5336fdfcf626430af7def58"
 
 [[package]]
 name = "reqwest"
-version = "0.12.26"
+version = "0.12.28"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3b4c14b2d9afca6a60277086b0cc6a6ae0b568f6f7916c943a8cdc79f8be240f"
+checksum = "eddd3ca559203180a307f12d114c268abf583f59b03cb906fd0b3ff8646c1147"
 dependencies = [
  "base64",
  "bytes",
@@ -1191,9 +1191,9 @@ dependencies = [
 
 [[package]]
 name = "rustix"
-version = "1.1.2"
+version = "1.1.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "cd15f8a2c5551a84d56efdc1cd049089e409ac19a3072d5037a17fd70719ff3e"
+checksum = "146c9e247ccc180c1f61615433868c99f3de3ae256a30a43b49f67c2d9171f34"
 dependencies = [
  "bitflags",
  "errno",
@@ -1204,9 +1204,9 @@ dependencies = [
 
 [[package]]
 name = "rustls"
-version = "0.23.35"
+version = "0.23.36"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "533f54bc6a7d4f647e46ad909549eda97bf5afc1585190ef692b4286b198bd8f"
+checksum = "c665f33d38cea657d9614f766881e4d510e0eda4239891eea56b4cadcf01801b"
 dependencies = [
  "once_cell",
  "rustls-pki-types",
@@ -1243,9 +1243,9 @@ checksum = "b39cdef0fa800fc44525c84ccb54a029961a8215f9619753635a9c0d2538d46d"
 
 [[package]]
 name = "ryu"
-version = "1.0.20"
+version = "1.0.22"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "28d3b2b1366ec20994f1fd18c3c594f05c5dd4bc44d8bb0c1c632c8d6829481f"
+checksum = "a50f4cf475b65d88e057964e0e9bb1f0aa9bbb2036dc65c64596b42932536984"
 
 [[package]]
 name = "same-file"
@@ -1320,15 +1320,15 @@ dependencies = [
 
 [[package]]
 name = "serde_json"
-version = "1.0.145"
+version = "1.0.149"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "402a6f66d8c709116cf22f558eab210f5a50187f702eb4d7e5ef38d9a7f1c79c"
+checksum = "83fc039473c5595ace860d8c4fafa220ff474b3fc6bfdb4293327f1a37e94d86"
 dependencies = [
  "itoa",
  "memchr",
- "ryu",
  "serde",
  "serde_core",
+ "zmij",
 ]
 
 [[package]]
@@ -1400,9 +1400,9 @@ checksum = "13c2bddecc57b384dee18652358fb23172facb8a2c51ccc10d74c157bdea3292"
 
 [[package]]
 name = "syn"
-version = "2.0.111"
+version = "2.0.113"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "390cc9a294ab71bdb1aa2e99d13be9c753cd2d7bd6560c77118597410c4d2e87"
+checksum = "678faa00651c9eb72dd2020cbdf275d92eccb2400d568e419efdd64838145cb4"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -1452,9 +1452,9 @@ dependencies = [
 
 [[package]]
 name = "tempfile"
-version = "3.23.0"
+version = "3.24.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2d31c77bdf42a745371d260a26ca7163f1e0924b64afa0b688e61b5a9fa02f16"
+checksum = "655da9c7eb6305c55742045d5a8d2037996d61d8de95806335c7c86ce0f82e9c"
 dependencies = [
  "fastrand",
  "getrandom 0.3.4",
@@ -1475,9 +1475,9 @@ dependencies = [
 
 [[package]]
 name = "tokio"
-version = "1.48.0"
+version = "1.49.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ff360e02eab121e0bc37a2d3b4d4dc622e6eda3a8e5253d5435ecf5bd4c68408"
+checksum = "72a2903cd7736441aac9df9d7688bd0ce48edccaadf181c3b90be801e81d3d86"
 dependencies = [
  "bytes",
  "libc",
@@ -1509,9 +1509,9 @@ dependencies = [
 
 [[package]]
 name = "tokio-util"
-version = "0.7.17"
+version = "0.7.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2efa149fe76073d6e8fd97ef4f4eca7b67f599660115591483572e406e165594"
+checksum = "9ae9cec805b01e8fc3fd2fe289f89149a9b66dd16786abd8b19cfa7b48cb0098"
 dependencies = [
  "bytes",
  "futures-core",
@@ -1522,9 +1522,9 @@ dependencies = [
 
 [[package]]
 name = "toml"
-version = "0.9.9+spec-1.0.0"
+version = "0.9.10+spec-1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "eb5238e643fc34a1d5d7e753e1532a91912d74b63b92b3ea51fde8d1b7bc79dd"
+checksum = "0825052159284a1a8b4d6c0c86cbc801f2da5afd2b225fa548c72f2e74002f48"
 dependencies = [
  "indexmap",
  "serde_core",
@@ -1537,27 +1537,27 @@ dependencies = [
 
 [[package]]
 name = "toml_datetime"
-version = "0.7.4+spec-1.0.0"
+version = "0.7.5+spec-1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fe3cea6b2aa3b910092f6abd4053ea464fab5f9c170ba5e9a6aead16ec4af2b6"
+checksum = "92e1cfed4a3038bc5a127e35a2d360f145e1f4b971b551a2ba5fd7aedf7e1347"
 dependencies = [
  "serde_core",
 ]
 
 [[package]]
 name = "toml_parser"
-version = "1.0.5+spec-1.0.0"
+version = "1.0.6+spec-1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4c03bee5ce3696f31250db0bbaff18bc43301ce0e8db2ed1f07cbb2acf89984c"
+checksum = "a3198b4b0a8e11f09dd03e133c0280504d0801269e9afa46362ffde1cbeebf44"
 dependencies = [
  "winnow",
 ]
 
 [[package]]
 name = "toml_writer"
-version = "1.0.5+spec-1.0.0"
+version = "1.0.6+spec-1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a9cd6190959dce0994aa8970cd32ab116d1851ead27e866039acaf2524ce44fa"
+checksum = "ab16f14aed21ee8bfd8ec22513f7287cd4a91aa92e44edfe2c17ddd004e92607"
 
 [[package]]
 name = "tower"
@@ -1606,9 +1606,9 @@ checksum = "8df9b6e13f2d32c91b9bd719c00d1958837bc7dec474d94952798cc8e69eeec3"
 
 [[package]]
 name = "tracing"
-version = "0.1.43"
+version = "0.1.44"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2d15d90a0b5c19378952d479dc858407149d7bb45a14de0142f6c534b16fc647"
+checksum = "63e71662fa4b2a2c3a26f570f037eb95bb1f85397f3cd8076caed2f026a6d100"
 dependencies = [
  "pin-project-lite",
  "tracing-core",
@@ -1616,9 +1616,9 @@ dependencies = [
 
 [[package]]
 name = "tracing-core"
-version = "0.1.35"
+version = "0.1.36"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7a04e24fab5c89c6a36eb8558c9656f30d81de51dfa4d3b45f26b21d61fa0a6c"
+checksum = "db97caf9d906fbde555dd62fa95ddba9eecfd14cb388e4f491a66d74cd5fb79a"
 dependencies = [
  "once_cell",
 ]
@@ -1643,9 +1643,9 @@ checksum = "8ecb6da28b8a351d773b68d5825ac39017e680750f980f3a1a85cd8dd28a47c1"
 
 [[package]]
 name = "url"
-version = "2.5.7"
+version = "2.5.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "08bc136a29a3d1758e07a9cca267be308aeebf5cfd5a10f3f67ab2097683ef5b"
+checksum = "ff67a8a4397373c3ef660812acab3268222035010ab8680ec4215f38ba3d0eed"
 dependencies = [
  "form_urlencoded",
  "idna",
@@ -2128,3 +2128,9 @@ dependencies = [
  "quote",
  "syn",
 ]
+
+[[package]]
+name = "zmij"
+version = "1.0.12"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2fc5a66a20078bf1251bde995aa2fdcc4b800c70b5d92dd2c62abc5c60f679f8"
diff --git a/Cargo.toml b/Cargo.toml
index a5c33a9..9a85193 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -9,7 +9,6 @@ edition = "2021"
 [lib]
 name = "gen"
 path = "src/lib.rs"
-edition = "2021"
 
 [dependencies]
 anyhow = "1.0.100"
diff --git a/README.md b/README.md
index 3de486d..4482ed8 100644
--- a/README.md
+++ b/README.md
@@ -13,6 +13,7 @@ Usage: mq [OPTIONS] [COMMAND]
 Commands:
   generate       Generate pull requests
   enqueue        Enqueue a specific pull request to the merge queue
+  upload-targets Upload impacted targets for a pull request
   test-sim       Simulate a test with flake rate in consideration
   housekeeping   Clean out conflicting PRs and requeue failed PRs
   config         Print current configuration content to json
@@ -34,6 +35,10 @@ requests_per_run value you are specifying to either run in either distributed mo
 distribute the generate load across the specified `run_generate_for` value or burst mode which will
 attempt to create pull requests as quickly as possible given the specified `requests_per_run` value.
 
+Generated PRs will target branches from the `protected_branches` list in round-robin fashion. Each
+PR includes the target branch information in its body, and the tool automatically detects the
+correct target branch when uploading impacted targets or enqueuing PRs via the API.
+
 Burst Mode configuration to create 20 pull requests as quickly as possible
 
 ```toml
@@ -126,6 +131,11 @@ assuming `mq generate` is called every 10 minutes.
 # Default value: "4 hours"
 #close_stale_after = "4 hours"
 
+# List of protected branches that PRs should target
+# PRs will be created targeting these branches in round-robin fashion
+# Default value: ["main"]
+#protected_branches = ["main", "develop", "release"]
+
 [test]
 # Default value: 0.1
 #flake_rate = 0.1
diff --git a/src/cli.rs b/src/cli.rs
index 77cb997..f93e57e 100644
--- a/src/cli.rs
+++ b/src/cli.rs
@@ -60,6 +60,12 @@ pub struct UploadTargets {
     // Path to file that contains github-json block
     #[clap(long = "github-json")]
     pub github_json: String,
+
+    /// Optional: Path to JSON file containing array of targets to upload directly
+    /// If provided, targets will be read from this file instead of extracting from PR body
+    /// File should contain a JSON array: ["target1", "target2", "target3"]
+    #[clap(long = "targets-json")]
+    pub targets_json: Option<String>,
 }
 
 #[derive(Parser, Debug)]
diff --git a/src/config.rs b/src/config.rs
index bb45cd3..cb47b86 100644
--- a/src/config.rs
+++ b/src/config.rs
@@ -98,6 +98,9 @@ pub struct PullRequestConf {
 
     #[config(default = "4 hours")]
     pub close_stale_after: String,
+
+    #[config(default = ["main"])]
+    pub protected_branches: Vec<String>,
 }
 
 #[derive(Config, Serialize, Default)]
diff --git a/src/github.rs b/src/github.rs
index d2a344f..7951263 100644
--- a/src/github.rs
+++ b/src/github.rs
@@ -1,5 +1,6 @@
 use crate::process::try_gh;
 use serde::{Deserialize, Serialize};
+use serde_json::Value;
 
 pub struct GitHub;
 
@@ -15,11 +16,47 @@ impl GitHub {
     pub fn add_label(pr: &str, label: &str, token: &str) -> String {
         try_gh(&["pr", "edit", pr, "--add-label", label], token).expect("Failed to add label to PR")
     }
+
+    pub fn get_pr_base_branch(pr: &str, gh_token: &str) -> String {
+        let result = try_gh(&["pr", "view", pr, "--json", "baseRefName"], gh_token);
+        if result.is_err() {
+            // Log the error and fallback to "main" if we can't get the PR info
+            eprintln!(
+                "Warning: Failed to get base branch for PR {}: {:?}. Falling back to 'main'",
+                pr,
+                result.as_ref().err()
+            );
+            return "main".to_string();
+        }
+        let json_str = result.unwrap();
+        let v: Value = match serde_json::from_str(&json_str) {
+            Ok(val) => val,
+            Err(e) => {
+                eprintln!(
+                    "Warning: Failed to parse PR info JSON for PR {}: {}. Falling back to 'main'",
+                    pr, e
+                );
+                return "main".to_string();
+            }
+        };
+        v["baseRefName"]
+            .as_str()
+            .unwrap_or_else(|| {
+                eprintln!(
+                    "Warning: PR {} JSON does not contain 'baseRefName' field. Falling back to 'main'",
+                    pr
+                );
+                "main"
+            })
+            .to_string()
+    }
 }
 
 #[derive(Serialize, Deserialize, Debug)]
 pub struct GitHubAction {
     repository: String,
+    #[serde(rename = "base_ref")]
+    pub base_ref: Option<String>,
     pub event: Event,
 }
 #[derive(Serialize, Deserialize, Debug)]
@@ -52,4 +89,8 @@ impl GitHubAction {
         let repo_parts: Vec<&str> = self.repository.split('/').collect();
         repo_parts.get(1).expect("Invalid REPOSITORY format")
     }
+
+    pub fn base_branch(&self) -> &str {
+        self.base_ref.as_deref().unwrap_or("main")
+    }
 }
diff --git a/src/main.rs b/src/main.rs
index 366f32f..a442751 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -11,7 +11,7 @@ use gen::config::{Conf, EnqueueTrigger};
 use gen::config_error::handle_config_load_error;
 use gen::edit::edit_files_for_pr;
 use gen::github::GitHub;
-use gen::process::{git, run_cmd, try_gh, try_git};
+use gen::process::{git, run_cmd, try_gh, try_git, try_git_quiet};
 use gen::trunk::{submit_pull_request, upload_targets};
 use rand::Rng;
 use regex::Regex;
@@ -184,16 +184,22 @@ fn enqueue(pr: &str, config: &Conf, cli: &Cli, gh_token: &str) {
                             return;
                         }
                     };
+                    // Get the PR's base branch
+                    let target_branch = GitHub::get_pr_base_branch(pr, gh_token);
+                    println!("Enqueuing PR {} targeting branch: {}", pr, target_branch);
                     match submit_pull_request(
                         &owner,
                         &name,
                         pr_number,
-                        "main", // Default target branch, could be made configurable
-                        None,   // Default priority, could be made configurable
+                        &target_branch,
+                        None, // Default priority, could be made configurable
                         &config.trunk.api,
                         cli,
                     ) {
-                        Ok(_) => println!("Successfully submitted PR {} to Trunk merge queue", pr),
+                        Ok(_) => println!(
+                            "Successfully submitted PR {} to Trunk merge queue (target: {})",
+                            pr, target_branch
+                        ),
                         Err(e) => {
                             eprintln!("Failed to submit PR {} to Trunk merge queue: {}", pr, e);
                             std::process::exit(1);
@@ -264,6 +270,48 @@ fn maybe_add_logical_merge_conflict(last_pr: u32, config: &Conf) -> bool {
     true
 }
 
+fn checkout_branch(branch: &str) -> Result<(), String> {
+    // Check if branch exists locally (quietly - we expect this to fail if branch doesn't exist)
+    let branch_exists_locally =
+        try_git_quiet(&["rev-parse", "--verify", &format!("refs/heads/{}", branch)]).is_ok();
+
+    // Switch to the branch
+    if branch_exists_locally {
+        // Branch exists locally, just checkout
+        if let Err(e) = try_git(&["checkout", branch]) {
+            return Err(format!(
+                "Failed to checkout existing branch '{}': {}",
+                branch, e
+            ));
+        }
+    } else {
+        // Branch doesn't exist locally, fetch from origin to check if it exists there
+        let _ = try_git(&["fetch", "origin", branch]);
+
+        // Check if it exists on origin (quietly - we expect this to fail if branch doesn't exist)
+        let remote_branch = format!("origin/{}", branch);
+        let remote_exists =
+            gen::process::try_git_quiet(&["rev-parse", "--verify", &remote_branch]).is_ok();
+
+        if remote_exists {
+            // Branch exists on origin, create local tracking branch
+            if let Err(e) = try_git(&["checkout", "-b", branch, &remote_branch]) {
+                return Err(format!(
+                    "Failed to create local branch '{}' tracking {}: {}",
+                    branch, remote_branch, e
+                ));
+            }
+        } else {
+            return Err(format!(
+                "Base branch '{}' does not exist locally or on origin.",
+                branch
+            ));
+        }
+    }
+
+    Ok(())
+}
+
 fn get_last_pr(gh_token: &str) -> u32 {
     let result = try_gh(&["pr", "list", "--limit=1", "--json", "number"], gh_token);
     if result.is_err() {
@@ -291,21 +339,45 @@ fn get_last_pr(gh_token: &str) -> u32 {
 }
 
 fn create_pull_request(
-    words: &[String],
+    filenames: &[String],
     last_pr: u32,
     config: &Conf,
     dry_run: bool,
     gh_token: &str,
+    base_branch: &str,
 ) -> Result<String, String> {
     let lc = maybe_add_logical_merge_conflict(last_pr, config);
 
     let current_branch = git(&["branch", "--show-current"]);
 
+    // Checkout the base branch (will fetch from origin if needed)
+    checkout_branch(base_branch)?;
+
+    // Pull latest changes
+    let _ = try_git(&["pull"]);
+
+    // Now edit the files to create changes (after we're on the correct base branch)
+    let next_pr_number = last_pr + 1;
+    let words = edit_files_for_pr(filenames, next_pr_number, config);
+
     let branch_name = format!("change/{}", words.join("-"));
-    git(&["checkout", "-t", "-b", &branch_name]);
+    git(&["checkout", "-b", &branch_name]);
+
+    // Stage all changes (including untracked files)
+    let _ = try_git(&["add", "-A"]);
+
+    // Check if there are any changes to commit
+    let status_output = try_git(&["status", "--porcelain"]);
+    if let Ok(output) = status_output {
+        if output.trim().is_empty() {
+            return Err(format!("No changes to commit for PR. Words: {:?}", words));
+        }
+    }
 
     let commit_msg = format!("Moving words {}", words.join(", "));
-    git(&["commit", "--no-verify", "-am", &commit_msg]);
+    if let Err(e) = try_git(&["commit", "--no-verify", "-m", &commit_msg]) {
+        return Err(format!("Failed to commit changes: {}", e));
+    }
 
     if !dry_run {
         let result = try_git(&["push", "--set-upstream", "origin", "HEAD"]);
@@ -316,7 +388,7 @@ fn create_pull_request(
         }
     }
 
-    let mut title = words.join(", ");
+    let mut title = format!("[{}] {}", base_branch, words.join(", "));
     if lc {
         title = format!("{} (logical-conflict)", title);
     }
@@ -337,8 +409,8 @@ fn create_pull_request(
         config.pullrequest.close_stale_after
     ));
     body.push_str(&format!(
-        "\n\n[pullrequest]\nrequests per hour: {}\n",
-        config.pullrequest.requests_per_hour
+        "\n\n[pullrequest]\nrequests per hour: {}\ntarget branch: {}\n",
+        config.pullrequest.requests_per_hour, base_branch
     ));
 
     let mut first_letters: Vec<_> = words
@@ -354,7 +426,16 @@ fn create_pull_request(
         first_letters.into_iter().collect::<Vec<_>>().join(",")
     ));
 
-    let mut args: Vec<&str> = vec!["pr", "create", "--title", &title, "--body", &body];
+    let mut args: Vec<&str> = vec![
+        "pr",
+        "create",
+        "--title",
+        &title,
+        "--body",
+        &body,
+        "--base",
+        base_branch,
+    ];
 
     for lbl in config.pullrequest.labels.split(',') {
         args.push("--label");
@@ -369,8 +450,11 @@ fn create_pull_request(
 
     let result = try_gh(args.as_slice(), gh_token);
 
-    // no matter what is result - need to reset checkout
+    // no matter what is result - need to reset checkout and clean up
     git(&["checkout", &current_branch]);
+    // Clean up any uncommitted changes and untracked files
+    let _ = try_git(&["reset", "--hard", "HEAD"]);
+    let _ = try_git(&["clean", "-fd"]);
     git(&["pull"]);
 
     if result.is_err() {
@@ -450,23 +534,31 @@ fn generate(config: &Conf, cli: &Cli) -> anyhow::Result<()> {
 
         filenames.sort();
 
-        // Use deterministic dependency count based on PR number
-        let next_pr_number = last_pr + 1;
-        let words = edit_files_for_pr(&filenames, next_pr_number, config);
-
         // Select token for this PR (round-robin)
         let current_token = &github_tokens[token_index % github_tokens.len()];
 
-        let pr_result = create_pull_request(&words, last_pr, config, cli.dry_run, current_token);
+        // Select base branch for this PR (round-robin from protected_branches)
+        let protected_branches = &config.pullrequest.protected_branches;
+        let base_branch = &protected_branches[token_index % protected_branches.len()];
+
+        let pr_result = create_pull_request(
+            &filenames,
+            last_pr,
+            config,
+            cli.dry_run,
+            current_token,
+            base_branch,
+        );
         if pr_result.is_err() {
-            println!("problem created pr for {:?}", words);
+            println!("problem created pr for files: {:?}", filenames);
             continue;
         }
         let duration = start.elapsed();
         let pr = pr_result.unwrap();
         println!(
-            "created pr: {} in {:?} // waiting: {} mins",
+            "created pr: {} (target: {}) in {:?} // waiting: {} mins",
             pr,
+            base_branch,
             duration,
             (pull_request_every as f32 / 60.0)
         );
diff --git a/src/process.rs b/src/process.rs
index a33cefd..668057d 100644
--- a/src/process.rs
+++ b/src/process.rs
@@ -8,6 +8,15 @@ fn exec_with_env(
     cmd: &str,
     args: &[&str],
     env_vars: Option<&[(&str, &str)]>,
+) -> Result<String, String> {
+    exec_with_env_quiet(cmd, args, env_vars, false)
+}
+
+fn exec_with_env_quiet(
+    cmd: &str,
+    args: &[&str],
+    env_vars: Option<&[(&str, &str)]>,
+    quiet: bool,
 ) -> Result<String, String> {
     let mut command = Command::new(cmd);
     command.args(args);
@@ -23,8 +32,10 @@ fn exec_with_env(
         .unwrap_or_else(|_| panic!("Failed to execute {}", cmd));
 
     if !output.status.success() {
-        eprintln!("stderr: {}", String::from_utf8_lossy(&output.stderr));
-        eprintln!("Call to {} {} failed", cmd, args.join(" "));
+        if !quiet {
+            eprintln!("stderr: {}", String::from_utf8_lossy(&output.stderr));
+            eprintln!("Call to {} {} failed", cmd, args.join(" "));
+        }
         return Err(String::from_utf8_lossy(&output.stderr)
             .into_owned()
             .trim()
@@ -53,3 +64,7 @@ pub fn git(args: &[&str]) -> String {
 pub fn try_git(args: &[&str]) -> Result<String, String> {
     exec("git", args)
 }
+
+pub fn try_git_quiet(args: &[&str]) -> Result<String, String> {
+    exec_with_env_quiet("git", args, None, true)
+}
diff --git a/src/trunk.rs b/src/trunk.rs
index 71594fb..a3efa6d 100644
--- a/src/trunk.rs
+++ b/src/trunk.rs
@@ -1,6 +1,6 @@
 use crate::cli::Cli;
 use crate::config::Conf;
-use crate::github::GitHubAction;
+use crate::github::{GitHub, GitHubAction};
 use regex::Regex;
 use reqwest::header::{HeaderMap, CONTENT_TYPE};
 use serde_json::json;
@@ -73,6 +73,7 @@ pub fn upload_targets(config: &Conf, cli: &Cli, github_json_path: &str) {
     let github_json = fs::read_to_string(github_json_path).expect("Failed to read file");
     let ga = GitHubAction::from_json(&github_json);
 
+    // Extract targets from PR body
     if !&ga.event.pull_request.body.is_some() {
         println!("No PR body content found - skipping target upload");
         println!("The PR body is required to extract dependency information using the format: deps=[target1,target2,target3]");
@@ -92,10 +93,21 @@ pub fn upload_targets(config: &Conf, cli: &Cli, github_json_path: &str) {
         return;
     }
 
+    // Get the PR's base branch using GitHub API
+    let github_tokens = cli.get_github_tokens();
+    let gh_token = github_tokens.first().map(|t| t.as_str()).unwrap_or("");
+    let pr_number_str = ga.event.pull_request.number.to_string();
+    let target_branch = if !gh_token.is_empty() {
+        GitHub::get_pr_base_branch(&pr_number_str, gh_token)
+    } else {
+        // Fallback to base_ref from JSON if no token available
+        ga.base_branch().to_string()
+    };
     println!(
-        "Uploading {} impacted targets: {:?}",
+        "Uploading {} impacted targets: {:?} (target branch: {})",
         impacted_targets.len(),
-        impacted_targets
+        impacted_targets,
+        target_branch
     );
 
     let result = post_targets(
@@ -103,7 +115,7 @@ pub fn upload_targets(config: &Conf, cli: &Cli, github_json_path: &str) {
         ga.repo_name(),
         ga.event.pull_request.number,
         &ga.event.pull_request.head.sha,
-        "main",
+        &target_branch,
         impacted_targets,
         &config.trunk.api,
         &cli.trunk_token,
@@ -167,6 +179,7 @@ pub fn post_targets(
         println!("  URL: https://{}:443/v1/setImpactedTargets", api);
         println!("  Repository: {}/{}", repo_owner, repo_name);
         println!("  PR Number: {}", pr_number);
+        println!("  Target Branch: {}", target_branch);
         println!("  Impacted Targets: {:?}", impacted_targets);
 
         match status.as_u16() {