This may be a precursor to the green stem phenomenon commonly observed at harvest. Bean pod mottle virus is a proven cause of green stem, but is likely just one of several probable causes of plants that do not mature normally in the fall. Seed mottling, resulting from pigments diffusing from the hilum, is another symptom associated with BPMV infected plants. Some seed are entirely black or brown, but bicolored seed are by far more common. Hilum color will determine the color and intensity of seedcoat discoloration.
Mottled seeds are an issue for grain grading, especially for food grade soybeans.
Soybean mosaic virus is another cause of mottled seed, plus non-pathogen causes are often cited as causes. Sources of the virus are perennial legumes, over-wintered bean leaf beetles, and seed, probably in this order of importance. We have detected BPMV in alfalfa, red clover and birdsfoot trefoil. This was a preliminary study, but level of detection was greatest in birdsfoot trefoil. Entomologists in Iowa report bean leaf beetles to feed in forage legumes before entering soybean fields.