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JUBA, Sudan (Reuters) - Sudan's First Vice President Salva Kiir will run for president of south Sudan in elections in April, leaving the post of national president to be contested by a lower-ranking northern member of his party.

Kiir's decision is seen as a signal that southern politicians have prioritised running the semi-autonomous south, which is widely expected to secede when it votes in an independence referendum next year.

Having spent little time in Khartoum, Kiir had always been expected to remain as president in the oil-producing south.

The leader of the Sudan People's Liberation Movement (SPLM), a former southern rebel group, became Sudanese President Omar Hassan al-Bashir's deputy in 2005 when a north-south peace deal ended two decades of civil war.

The fighting claimed 2 million lives, drove 4 million from their homes and destabilised much of east Africa. The growing fragility of the peace deal has led to fears of renewed conflict.

"The SPLM nominee for the position of President of the Republic is Yasir Saeed Arman and the nominee for the President of Southern Sudan is the Chairman of the SPLM Salva Kiir," SPLM Secretary-General Pagan Amum told Reuters on Friday.

Maggie Fick of the U.S.-based anti-genocide group the Enough Project said the nominations would be seen as a signal that the SPLM's priorities are in the south.

"It is difficult not to read it that way," she said.

Since the SPLM formed a coalition government with their one-time northern foes, the National Congress Party, Arman has been the face of his party in Khartoum, heading the SPLM's parliamentary group and acting as a spokesman.
Kiir has shown little interest in the affairs of the north, intervening only when delays in implementing the peace deal reached crisis level, earning him the title of "vice absent" rather than first vice president.

"We want Kiir to continue being the president of the south to take the people of the south to the referendum ... Yasir Arman is a long term SPLM cadre and a capable leader and our best candidate," the SPLM's Amum added.

Although the 2005 north-south peace deal was signed under the slogan of making unity attractive, little has been implemented with good will, fuelling mistrust among southerners of the northern government they had long accused of oppression.

A Muslim who joined the rebels over disillusionment with a succession of military, corrupt and dictatorial Khartoum governments, Arman will run against fellow Muslim Bashir.

Bashir hopes to legitimise his position after the International Criminal Court last year issued a warrant for his arrest for war crimes in Darfur.

The SPLM is thought to have chosen a northerner to run for the presidency as few in the mainly Muslim north would vote for a Christian southerner.

The imposition of Islamic sharia law in 1983 fuelled the rebellion by southerners who follow mostly traditional beliefs or Christianity.

With millions of southerners who fled the war to seek refuge in the north and hundreds of thousands of northerners who have shown support for the SPLM, Arman may be a leading candidate for the presidency.

The elections promise democratic transformation, but with one of the most complex electoral systems in the world and the opposition accusing the ruling NCP of fraud in the registration process, few are optimistic Sudan will see real change.