Stem rust usually occurs on stems but can also be found on leaves, sheaths, glumes, awns and even seed. Stem rust causes red-brown lesions that develop into pustules that produce numerous black sooty spores. Severe infestations result in weakened plant stems and can result in lodging.
Read more: http://iwheat.org/node/117
Pest photo source
Erick De Wolf et al. KSU