Biochemical and molecular depictions to develop ech42 gene-specific SCAR markers for recognition of chitinolytic Trichoderma inhibiting Macrophomina phaseolina (Maubl.) Ashby.

Trichoderma isolates were inhibited variably in-vitro growth of soil-borne phytopathogen Macrophomina phaseolina (Maubl.) Ashby causes root rot in cotton. The growth inhibition of test-pathogen was found to be higher (90.36%) in T. viride NBAIITv23 followed by T. koningii MTCC796 (85.77%) under dual culture antagonism. The microscopic examination suggested that the antagonists Tv23 and MTCC796 adopted mycoparasitism as a strong mode of action to restrain pathogen growth. However, antagonists T. harzianum NBAIITh1 (77.89%) and T. virens NBAIITvs12 (61.74%) demonstrated strong antibiosis action for growth inhibition of the test pathogen. A significant positive correlation was established between the growth inhibition of M. phaseolina and the release of cell wall degrading enzymes- chitinase (p = 0.001), β-1,3, glucanase (p = 0.01), and protease (p = 0.05) under the influence of pathogen cell wall. The chitinase and β-1,3, glucanase activities were elevated 2.09 and 1.75 folds, respectively, in potent mycoparasitic Tv23 strain influenced by a pathogen cell wall compared to glucose as a carbon source. The three unique DNA-RAPD fragments OPA-07, OPA-16, and OPO-15 amplified by potent mycoparasitic Tv23 strain, were subjected to DNA sequencing and derived functional 864 bp from OPA-16 and have sequence homology to ech42 gene with partial CDs of 262 amino acids (nucleotide accession No. KF723016.1 and protein accession No.AHF57046.1). Novel SCAR markers were developed from a functional sequence of OPA-16 fragments and validated across the genomic DNA of eleven Trichoderma antagonists. The novel SCAR markers evolved from the RAPD-SCAR interface to authenticate chitinolytic Trichoderma associated with mycoparasitic action for eco-friendly biocontrol activity.