Methods for Using Cryptococcus Flavescens Strains for Biological Control of Fusarium Head Blight

A method for identifying the genotype of a Cryptococcus flavescens strain comprising:

• a) performing quantitative PCR (qPCR) on extracted genomic DNA utilizing one or more primer pairs sharing at least 90% sequence identity with the primer pairs of Table 1 (SEQ ID NOs:
• 45-72), wherein sequence identity is determined for each individual forward or reverse primer;
• and
• b) identifying a Cryptococcus flavescens strain as Genotype A or Genotype B, wherein:
• (1) the Cryptococcus flavescens strain is identified as Genotype A when qPCR results in:
• a threshold cycle value of 17-21 when using the btub.1, btub.2, or EF1.2 primer sets;
• a threshold cycle value of 18-20 when using the h22.1, h30.2, or h31.1 primer sets;
• a threshold cycle value of 17-20 when using the h31.2 primer set;
• or a threshold cycle value of 12-15 when using the I2.1 primer set;
• and
• (2) the Cryptococcus flavescens strain is identified as Genotype B when qPCR results in a threshold cycle value of 31-33 when using the btub.1 primer set;
• a threshold cycle value of 32-35 when using the btub.2 primer set;
• a threshold cycle value of 24-26 when using the EF1.2 primer set;
• a threshold cycle value of 22-24 when using the h22.1 or h31.1 primer sets;
• a threshold cycle value of 22-23 when using the h30.2 primer set;
• a threshold cycle value of 34-35 when using the h31.2 primer set;
• or a threshold cycle value of 15-18 when using the I2.1 primer set.

A method for identifying the genotype of a Cryptococcus flavescens strain comprising:

• a) sequencing extracted genomic DNA of a target Cryptococcus flavescens;
• b) comparing the sequence determined in step a) to known homologous sequences of other Cryptococcus flavescens strains;
• and
• c) identifying a Cryptococcus flavescens strain as Genotype A or Genotype B, wherein:
• (1) the Cryptococcus flavescens strain is identified as Genotype A when the sequence of the extracted genomic DNA of the target Cryptococcus flavescens shares:
• 100% sequence identity at the β-tubulin gene to SEQ ID NO:1;
• between 95% and 100% sequence identity at the chitin synthase 1 gene to SEQ ID NOs:
• 2, 3, 4, 5, or 6;
• between 99% and 100% sequence identity at the EF1 gene to SEQ ID NOs:
• 7, 8, 9, 10, or 11;
• between 99% and 100% sequence identity at the hsp70 gene to SEQ ID NOs:
• 12, 13, 14, 15, or 16;
• or between 99% and 100% sequence identity at the cs22 target locus to SEQ ID. NOs:
• 85, 86, 87, 88, or 89;
• and
• (2) the Cryptococcus flavescens strain is identified as Genotype B when the sequence of the extracted genomic DNA of the target Cryptococcus flavescens shares:
• between 99% and 100% sequence identity at the β-tubulin gene to SEQ ID NOs:
• 17, 18, 19, 20, 21, 22 or 23;
• between 97% and 100% sequence identity at the chitin synthase 1 gene to SEQ ID NOs:
• 24, 25, 26, 27, 28, 29 or 30;
• between 99% and 100% sequence identity at the EF1 gene to SEQ ID NOs:
• 31, 32, 33, 34, 35, 36, or 37;
• between 99% and 100% sequence identity at the hsp70 gene to SEQ ID NOs:
• 38, 39, 40, 41, 42, 43 or 44;
• or 100% sequence identity at the cs22 target locus to SEQ ID NO:
• 90.