VerticiUium wilt disease becomes a major threat to many economically important crops.It is unclear whether and how plant immunity takes place during cotton-Verticillium interaction due to the lack of marker genes.Taking advantage of cotton(Gossypium hirsutum) genome,we discovered pathogenesis-related(PR) gene families,which have been widely used as markers of immune responses in plants.To profile the expression of G.hirsutum PR genes in the process of plant immunity,we treated cotton roots with two immunogenic peptides,flg22 and nlp20 known as pathogen-associated molecular patterns,as well as three VerticiUium dahliae-derived peptides,nlp20~(Vd2),nlp23~(Vd3),and nlp23~(Vd4) which are highly identical to nlp20.Quantitative real-time PCR results revealed that 14 G hirsutum PR gene(GhPR) families were induced or suppressed independently in response to flg22,nlp20,nlp20~(Vd2),nlp23~(Vd3),and nlp23~(Vd4).Most GhPR genes are expressed highest at 3 h post incubation of immunogenic peptides.Compared to flg22 and nlp20,nlp20~(Vd2) is more effective to trigger up-regulated expression of GhPR genes.Notably,both nlp23~(Vd3) and nlp23~(Vd4) are able to induce GhPR gene up-regulation,although they do not induce necrosis on cotton leaves.Thus,our results provide marker genes and new immunogenic peptides for further investigation of cotton-V.dahliae interaction. VerticiUium wilt disease becomes a major threat to many economically important crops. If is unclear whether and how plant immunity takes place during cotton-Verticillium interaction due to the lack of marker genes. Taking advantage of cotton (Gossypium hirsutum) genome, we discovered pathogenesis- related (PR) gene families, which have been widely used as markers of immune responses in plants. To profile the expression of G.hirsutum PR genes in the process of plant immunity, we treated cotton roots with two immunogenic peptides, flg22 and nlp20 known as pathogen-associated molecular patterns, as well as three VerticiUium dahliae-derived peptides, nlp20 ~ (Vd2), nlp23 ~ (Vd3), and nlp23 ~ (Vd4) which are highly identical to nlp20. Quantitative real-time PCR results revealed that 14 G hirsutum PR gene (GhPR) families were induced or suppressed independently in response to flg22, nlp20, nlp20 ~ (Vd2), nlp23 ~ (Vd3), and nlp23 ~ (Vd4) incubation of immunogenic peptides. Co. mpared to flg22 and nlp20, nlp20 ~ (Vd2) is more effective to trigger up-regulated expression of GhPR genes.Notably, both nlp23 ~ (Vd3) and nlp23 ~ (Vd4) are able to induce GhPR gene up-regulation, although they do not induce necrosis on cotton leaves. Thus, our results provide marker genes and new immunogenic peptides for further investigation of cotton-V. DHahliae interaction.