Bioprotective alkaloids produced by Epichloë and closely related asexual Neotyphodium fungal endophytes protect their grass hosts from insect and mammalian herbivory. One class of these compounds, known for antimammalian toxicity, is the indole-diterpenes. The LTM locus of Neotyphodium lolii (Lp19) and Epichloë festuce (Fl1), required for the biosynthesis of the indole-diterpene lolitrem, consists of 10 ltm genes. We have used PCR and Southern analysis to screen a broad taxonomic range of 44 endophyte isolates to determine why indole-diterpenes are present in so few endophyte-grass associations in comparison to that of the other bioprotective alkaloids, which are more widespread among the endophtyes. All 10 ltm genes were present in only three epichloë endophytes. A predominance of the asexual Neotyphodium spp. examined contained 8 of the 10 ltm genes, with only one N. lolii containing the entire LTM locus and the ability to produce lolitrems. Liquid chromatography-tandem mass spectrometry profiles of indole-diterpenes from a subset of endophyte-infected perennial ryegrass showed that endophytes that contained functional genes present in ltm clusters 1 and 2 were capable of producing simple indole-diterpenes such as paspaline, 13-desoxypaxilline, and terpendoles, compounds predicted to be precursors of lolitrem B. Analysis of toxin biosynthesis genes by PCR now enables a diagnostic method to screen endophytes for both beneficial and detrimental alkaloids and can be used as a resource for screening isolates required for forage improvement.Epichloë endophytes systemically colonize cool-season grasses, and comprise sexual Epichloë spp. and their asexual derivatives, the Neoptyphodium spp. Collectively, they produce a range of bioprotective alkaloids, including the ergot alkaloids, pyrrolopyrazine (peramine), aminopyrrolizidines (lolines), and indole-diterpenes (including lolitrems) (5, 63). Most Neotyphodium spp. are of hybrid origin, with two or three Epichloë or Neotyphodium ancestors (11,44,59,66). The alkaloids produced by epichloë endophytes enhance the competitive ability of endophyte-infected grasses by protecting the grass host from insect and mammalian herbivory. Alkaloids such as peramine and the lolines are known for their antiinsect properties (5, 55, 63), while ergovaline and the lolitrems are detrimental to grazing livestock, causing fescue toxicosis and ryegrass staggers, respectively, in pastoral ecosystems (17, 18, 31, 47, 52). Many epichloë endophytes are able to produce multiple classes of alkaloids but, to date, no plant-endophyte combination has been identified that produces lolitrems, lolines, peramine, and ergovaline (5, 10).A number of naturally occurring endophytes have been identified that do not produce the mammalian toxins, ergovaline and lolitrem B, but retain beneficial agronomic properties (26, 27), such as tolerance to abiotic stress (32). Artificially inoculated associations of these endophytes with elite tall fescue (4) and perennial ryegrass cultivars (16) have been commercially e...