By Lesley Wroughton

JEDDAH, Saudi Arabia (Reuters) - U.S. Secretary of State John Kerry held talks with Saudi Arabia's powerful deputy crown prince, Mohammed bin Salman, into the early hours of Thursday morning on ways to end Yemen's conflict and resume peace talks between the warring sides.

Kerry arrived in Jeddah from Nigeria for discussions with Saudi leaders and other Gulf Arab states and will also update them on U.S. meetings with Russia addressing military cooperation in Syria, a senior U.S. official said ahead of the talks.

Backing by Gulf nations for the Syria plan is vital because they wield influence over Syrian opposition groups involved in Syria's civil war. Russia and Iran support Syrian President Bashar al-Assad.

The talks come as Syrian rebels backed by Turkish special forces, tanks and warplanes entered one of Islamic State's last strongholds on the Turkish-Syrian border, in Turkey's first major U.S.-backed incursion into its southern neighbor.

Earlier, the State Department said Kerry will meet his Russian counterpart, Sergei Lavrov, in Geneva on Friday to try to close a deal on possible military cooperation and intelligence sharing in Syria. It could see Assad's warplanes grounded, while Russian and U.S. militaries coordinate strikes against Islamic State militants.

In Saudi Arabia, talks with Mohammed bin Salman, which began late and lasted three hours, ended at 12:59 a.m. local time, U.S. officials said.

Kerry will meet Saudi King Salman later on Thursday. Afterwards, he joins foreign ministers from Saudi Arabia, the United Arab Emirates, and British Under-Secretary for the Foreign Office Tobias Ellwood, to explore ways to end Yemen's 16-month conflict, which has killed about 6,500 people, half of them civilians.

A Saudi-led air campaign in Yemen in support of the government of President Abdu Rabbu Mansour Hadi against Iran-allied Shi'ite Muslim Houthi rebels has come under increasing scrutiny for causing a large number of civilian casualties.

A senior State Department official declined to elaborate on Kerry's proposals.

"The multilateral meeting on Yemen is designed to share ideas and initiatives for getting the political discussions back on track and trying to get a political solution," the official said. It would also address getting aid delivered.

The U.S. military has coordinated with the Saudi-led air campaign in Yemen, helping ensure Saudi access to precision-guided munitions. The Pentagon has also sent U.S. military lawyers to help train Saudi counterparts in ensuring the legality of coalition strikes.

But there has been growing concern in Washington that the Saudi campaign may have targeted civilian installations including hospitals.

Human rights groups have argued that U.S. forces may also be responsible under the rules of war for civilian casualties because of its support for the Saudi campaign.

Kerry "will raise our concerns about civilian casualties and damage to civilian targets inside Yemen," the U.S. official said, adding that he would press the Saudis to ensure air strikes were "discriminate and precise."

An annual United Nations report on children and armed conflict said the Saudi-led campaign was responsible for 60 percent of child deaths and injuries in Yemen last year. Saudi Arabia has said the report is based on inaccurate information.

(Reporting by Lesley Wroughton; Editing by Dominic Evans and Jonathan Oatis)