The firm currently has a flock of 3,000 genetically modified sheep
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The company which created Dolly the sheep clone is to cull hundreds of animals after trials of a new treatment for lung disorders were shelved.
PPL Therapeutics has been in difficulty since its transgenic (genetically modified) sheep programme was put on hold by the firm's German backers.
The company, based at Roslin, near Edinburgh, said it could no longer afford to look after the 3,000-strong flock but it would keep some of the original sheep for future breeding programmes.
In June, the company announced that it would have to lay off between 90 and 140 staff after the project to commercialise recombinant Alpha-1 Antitrypsin (AAT) - a medicine to help lung disorders made from the milk of genetically modified sheep - was halted.
A spokesman confirmed that the firm would be scaling down its operation, but was still assessing how many sheep on its 500-acre site in East Lothian would need to be slaughtered.
In New Zealand, where PPL Therapeutics has a 3,500-strong flock, the company is reportedly planning to slaughter up to 1,000 of the animals.
Dolly death
However the spokesman added that the company would keep some of the original founding sheep for future breeding programmes.
He said: "Unfortunately, placing the AAT programme on hold has also meant that PPL can no longer support all its AAT sheep flock and work is under way to reduce sheep numbers on its farms in both Scotland and New Zealand.
"PPL is evaluating the option of keeping a significant number of its transgenic sheep to maintain the viability of its transgenic technology business.
"The sheep will be euthanased with full concern for animal welfare and in line with the necessary Government regulations."
The firm was behind the creation of Dolly the sheep
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The company developed the world's first transgenic sheep, Tracy, in 1991, before hitting the headlines in 1996 with the creation of Dolly.
In the same year it opened a production facility which included a computer-controlled milking parlour and technology to monitor each sheep electronically.
Dolly - named after country and western singer Dolly Parton because she was cloned from a breast cell - died on St Valentine's Day at the age of six after developing a lung tumour and arthritis.
The company announced major restructuring in the wake of last month's announcement by Bayer. The changes could see up to 90% of the PPL workforce lose their jobs.