Tests showed that she had been shot. Her parents were found shot to death in their home in August, and the girl hadn't been seen since.
Investigators want to talk to a man whose rented house and mobile home in North Carolina were recently searched. Garrison Bowman was last seen in the area the day after the Shorts were killed. A sheriff says authorities know where he can be found in Canada, and will be talking to him.
Court records show that deputies seized nine maps from the mobile home on Saturday -- including one that was marked to show the location of the Shorts' home.
A newspaper (the News and Record of Greensboro) reports that an affidavit said Bowman had threatened to kill a man in Virginia in a dispute over moving the mobile home. The man wasn't identified in the affidavit.
The slain girl's father owned and operated a mobile-home moving
Authorities in North Carolina say DNA tests confirm that the remains that were found in a wooded area last week are those of missing nine-year-old.
The skeletal remains were discovered about 30 miles from where the Short family lived.
Short had been missing since Aug. 15. Investigators said they believed the girl had been abducted.
A skull and bits of bone were discovered Sept. 25 near a home in Stoneville, N.C., about 30 miles south of the Shorts' home.
"The skeletal remains in Rockingham County have been determined to be a positive match with the DNA profile of Short and are hers," Rockingham County Sheriff Sam Page said.
The seven-week investigation and search for the little girl had been emotionally difficult, said Sheriff Frank Cassell of Henry County, Va.
"She's gone now and she's safe now and no evil can befall her," he said.
Tests by a lab in Roanoke, Va., showed Jennifer had been shot, Page said. Neither sheriff would say whether evidence indicated she had been raped or otherwise assaulted.
"I am saddened. I am heartbroken for this little girl and her family," Cassell said. "But at least it's important for them to know she's not out there being abused or hurt."
Cassell said on CBS News' The Early Show in August that police were trying to track down more people who worked with the girl's father. They were also checking out sex offenders in the area.
He confirmed that the home's phone lines had been cut, leading him to believe the crime was planned.
He said they were looking at the crime "from every angle." But he said they still cannot determine whether the target "was the child or the parents — or both."